Welcome to `nf-scil` ! A **Nextflow** modules and workflows repository for neuroimaging
maintained by the [SCIL team](https://scil-documentation.readthedocs.io/en/latest/). The
@@ -7,6 +12,31 @@ primary focus of the library is to provide pre-built processes and processing se
technologies and made easily available to pipeline's developers through the `nf-core`
framework.
+* [Using modules from nf-scil](README.md#using-modules-from-nf-scil)
+* [Developing in nf-scil](README.md#developing-in-nf-scil)
+ * [Dependencies](README.md#dependencies)
+ * [Developer installation](README.md#developer-installation)
+ * [Loading the project's environment](README.md#loading-the-projects-environment)
+ * [Working with VS Code](README.md#working-with-vs-code)
+ * [Manual configuration of the VS Code project :](README.md#manual-configuration-of-the-vs-code-project-)
+ * [Configuration via the devcontainer :](README.md#configuration-via-the-devcontainer-)
+ * [Contributing to nf-scil](README.md#contributing-to-nf-scil)
+ * [Adding a new module to nf-scil](docs/MODULE.md#adding-a-new-module-to-nf-scil)
+ * [Generate the template](docs/MODULE.md#generate-the-template)
+ * [Edit the template](docs/MODULE.md#edit-the-template)
+ * [Editing the main](docs/MODULE.md#editing-modulesnf-scilcategorytoolmainnf-)
+ * [Editing the metadata](docs/MODULE.md#editing--modulesnf-scilcategorytoolmetayml-)
+ * [Editing the test cases](docs/MODULE.md#editing-testsmodulesnf-scilcategorytoolmainnf-)
+ * [Editing the tests configuration](docs/MODULE.md#editing-testsmodulesnf-scilcategorytoolnextflowconfig-)
+ * [Run the tests to generate the test metadata file](docs/MODULE.md#run-the-tests-to-generate-the-test-metadata-file)
+ * [Last safety test](docs/MODULE.md#last-safety-test)
+ * [Submit your PR](docs/MODULE.md#submit-your-pr)
+ * [Defining processes optional parameters](docs/MODULE.md#defining-processes-optional-parameters)
+ * [Test data infrastructure](docs/MODULE.md#test-data-infrastructure)
+ * [Using the .test_data directory](docs/MODULE.md#using-the-test_data-directory)
+ * [Using Scilpy Fetcher](docs/MODULE.md#using-scilpy-fetcher)
+ * [Running tests](README.md#running-tests)
+
# Using modules from `nf-scil`
To import modules from `nf-scil`, you first need to install [nf-core](https://github.com/nf-core/tools)
diff --git a/docs/deps/gh-md-toc b/docs/deps/gh-md-toc
new file mode 100755
index 000000000..fbe76eeb9
--- /dev/null
+++ b/docs/deps/gh-md-toc
@@ -0,0 +1,415 @@
+#!/usr/bin/env bash
+
+#
+# Steps:
+#
+# 1. Download corresponding html file for some README.md:
+# curl -s $1
+#
+# 2. Discard rows where no substring 'user-content-' (github's markup):
+# awk '/user-content-/ { ...
+#
+# 3.1 Get last number in each row like ' ... sitemap.js.*<\/h/)+2, RLENGTH-5)
+#
+# 5. Find anchor and insert it inside "(...)":
+# substr($0, match($0, "href=\"[^\"]+?\" ")+6, RLENGTH-8)
+#
+
+gh_toc_version="0.9.1"
+
+gh_user_agent="gh-md-toc v$gh_toc_version"
+
+#
+# Download rendered into html README.md by its url.
+#
+#
+gh_toc_load() {
+ local gh_url=$1
+
+ if type curl &>/dev/null; then
+ curl --user-agent "$gh_user_agent" -s "$gh_url"
+ elif type wget &>/dev/null; then
+ wget --user-agent="$gh_user_agent" -qO- "$gh_url"
+ else
+ echo "Please, install 'curl' or 'wget' and try again."
+ exit 1
+ fi
+}
+
+#
+# Converts local md file into html by GitHub
+#
+# -> curl -X POST --data '{"text": "Hello world github/linguist#1 **cool**, and #1!"}' https://api.github.com/markdown
+#
Hello world github/linguist#1 cool, and #1!
'"
+gh_toc_md2html() {
+ local gh_file_md=$1
+ local skip_header=$2
+
+ URL=https://api.github.com/markdown/raw
+
+ if [ ! -z "$GH_TOC_TOKEN" ]; then
+ TOKEN=$GH_TOC_TOKEN
+ else
+ TOKEN_FILE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/token.txt"
+ if [ -f "$TOKEN_FILE" ]; then
+ TOKEN="$(cat $TOKEN_FILE)"
+ fi
+ fi
+ if [ ! -z "${TOKEN}" ]; then
+ AUTHORIZATION="Authorization: token ${TOKEN}"
+ fi
+
+ local gh_tmp_file_md=$gh_file_md
+ if [ "$skip_header" = "yes" ]; then
+ if grep -Fxq "" "$gh_src"; then
+ # cut everything before the toc
+ gh_tmp_file_md=$gh_file_md~~
+ sed '1,//d' $gh_file_md > $gh_tmp_file_md
+ fi
+ fi
+
+ # echo $URL 1>&2
+ OUTPUT=$(curl -s \
+ --user-agent "$gh_user_agent" \
+ --data-binary @"$gh_tmp_file_md" \
+ -H "Content-Type:text/plain" \
+ -H "$AUTHORIZATION" \
+ "$URL")
+
+ rm -f $gh_file_md~~
+
+ if [ "$?" != "0" ]; then
+ echo "XXNetworkErrorXX"
+ fi
+ if [ "$(echo "${OUTPUT}" | awk '/API rate limit exceeded/')" != "" ]; then
+ echo "XXRateLimitXX"
+ else
+ echo "${OUTPUT}"
+ fi
+}
+
+
+#
+# Is passed string url
+#
+gh_is_url() {
+ case $1 in
+ https* | http*)
+ echo "yes";;
+ *)
+ echo "no";;
+ esac
+}
+
+#
+# TOC generator
+#
+gh_toc(){
+ local gh_src=$1
+ local gh_src_copy=$1
+ local gh_ttl_docs=$2
+ local need_replace=$3
+ local no_backup=$4
+ local no_footer=$5
+ local indent=$6
+ local skip_header=$7
+
+ if [ "$gh_src" = "" ]; then
+ echo "Please, enter URL or local path for a README.md"
+ exit 1
+ fi
+
+
+ # Show "TOC" string only if working with one document
+ if [ "$gh_ttl_docs" = "1" ]; then
+
+ echo "Table of Contents"
+ echo "================="
+ echo ""
+ gh_src_copy=""
+
+ fi
+
+ if [ "$(gh_is_url "$gh_src")" == "yes" ]; then
+ gh_toc_load "$gh_src" | gh_toc_grab "$gh_src_copy" "$indent"
+ if [ "${PIPESTATUS[0]}" != "0" ]; then
+ echo "Could not load remote document."
+ echo "Please check your url or network connectivity"
+ exit 1
+ fi
+ if [ "$need_replace" = "yes" ]; then
+ echo
+ echo "!! '$gh_src' is not a local file"
+ echo "!! Can't insert the TOC into it."
+ echo
+ fi
+ else
+ local rawhtml=$(gh_toc_md2html "$gh_src" "$skip_header")
+ if [ "$rawhtml" == "XXNetworkErrorXX" ]; then
+ echo "Parsing local markdown file requires access to github API"
+ echo "Please make sure curl is installed and check your network connectivity"
+ exit 1
+ fi
+ if [ "$rawhtml" == "XXRateLimitXX" ]; then
+ echo "Parsing local markdown file requires access to github API"
+ echo "Error: You exceeded the hourly limit. See: https://developer.github.com/v3/#rate-limiting"
+ TOKEN_FILE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/token.txt"
+ echo "or place GitHub auth token here: ${TOKEN_FILE}"
+ exit 1
+ fi
+ local toc=`echo "$rawhtml" | gh_toc_grab "$gh_src_copy" "$indent"`
+ echo "$toc"
+ if [ "$need_replace" = "yes" ]; then
+ if grep -Fxq "" "$gh_src" && grep -Fxq "" "$gh_src"; then
+ echo "Found markers"
+ else
+ echo "You don't have or in your file...exiting"
+ exit 1
+ fi
+ local ts="<\!--ts-->"
+ local te="<\!--te-->"
+ local dt=`date +'%F_%H%M%S'`
+ local ext=".orig.${dt}"
+ local toc_path="${gh_src}.toc.${dt}"
+ local toc_createdby=""
+ local toc_footer=""
+ # http://fahdshariff.blogspot.ru/2012/12/sed-mutli-line-replacement-between-two.html
+ # clear old TOC
+ sed -i${ext} "/${ts}/,/${te}/{//!d;}" "$gh_src"
+ # create toc file
+ echo "${toc}" > "${toc_path}"
+ if [ "${no_footer}" != "yes" ]; then
+ echo -e "\n${toc_createdby}\n${toc_footer}\n" >> "$toc_path"
+ fi
+
+ # insert toc file
+ if ! sed --version > /dev/null 2>&1; then
+ sed -i "" "/${ts}/r ${toc_path}" "$gh_src"
+ else
+ sed -i "/${ts}/r ${toc_path}" "$gh_src"
+ fi
+ echo
+ if [ "${no_backup}" = "yes" ]; then
+ rm "$toc_path" "$gh_src$ext"
+ fi
+ echo "!! TOC was added into: '$gh_src'"
+ if [ -z "${no_backup}" ]; then
+ echo "!! Origin version of the file: '${gh_src}${ext}'"
+ echo "!! TOC added into a separate file: '${toc_path}'"
+ fi
+ echo
+ fi
+ fi
+}
+
+#
+# Grabber of the TOC from rendered html
+#
+# $1 - a source url of document.
+# It's need if TOC is generated for multiple documents.
+# $2 - number of spaces used to indent.
+#
+gh_toc_grab() {
+
+ href_regex="/href=\"[^\"]+?\"/"
+ common_awk_script='
+ modified_href = ""
+ split(href, chars, "")
+ for (i=1;i <= length(href); i++) {
+ c = chars[i]
+ res = ""
+ if (c == "+") {
+ res = " "
+ } else {
+ if (c == "%") {
+ res = "\\x"
+ } else {
+ res = c ""
+ }
+ }
+ modified_href = modified_href res
+ }
+ print sprintf("%*s", (level-1)*'"$2"', "") "* [" text "](" gh_url modified_href ")"
+ '
+ if [ `uname -s` == "OS/390" ]; then
+ grepcmd="pcregrep -o"
+ echoargs=""
+ awkscript='{
+ level = substr($0, 3, 1)
+ text = substr($0, match($0, /<\/span><\/a>[^<]*<\/h/)+11, RLENGTH-14)
+ href = substr($0, match($0, '$href_regex')+6, RLENGTH-7)
+ '"$common_awk_script"'
+ }'
+ else
+ grepcmd="grep -Eo"
+ echoargs="-e"
+ awkscript='{
+ level = substr($0, 3, 1)
+ text = substr($0, match($0, /<\/span><\/a>.*<\/h/)+11, RLENGTH-14)
+ href = substr($0, match($0, '$href_regex')+6, RLENGTH-7)
+ '"$common_awk_script"'
+ }'
+ fi
+
+ # if closed is on the new line, then move it on the prev line
+ # for example:
+ # was: The command foo1
+ #
+ # became: The command foo1
+ sed -e ':a' -e 'N' -e '$!ba' -e 's/\n<\/h/<\/h/g' |
+
+ # Sometimes a line can start with . Fix that.
+ sed -e ':a' -e 'N' -e '$!ba' -e 's/\n//g' | sed 's/<\/code>//g' |
+
+ # remove g-emoji
+ sed 's/]*[^<]*<\/g-emoji> //g' |
+
+ # now all rows are like:
+ #
-
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
-[![Imports: nf-core](https://img.shields.io/badge/nf--core-nf?label=import&style=flat&labelColor=ef8336&color=24B064)](https://pycqa.github.io/nf-core/)
-[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
-[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-![Code Linting](https://github.com/scilus/nf-scil/workflows/Code%20Linting/badge.svg)
-![Modules Tests](https://github.com/scilus/nf-scil/workflows/Test%20All%20Modules/badge.svg)
-
-Welcome to `nf-scil` ! A **Nextflow** modules and workflows repository for neuroimaging
-maintained by the [SCIL team](https://scil-documentation.readthedocs.io/en/latest/). The
-primary focus of the library is to provide pre-built processes and processing sequences for
-**diffusion Magnetic Resonance Imaging**, optimized for *Nextflow DLS2*, based on open-source
-technologies and made easily available to pipeline's developers through the `nf-core`
-framework.
-
-* [Using modules from nf-scil](README.md#using-modules-from-nf-scil)
-* [Developing in nf-scil](README.md#developing-in-nf-scil)
- * [Dependencies](README.md#dependencies)
- * [Developer installation](README.md#developer-installation)
- * [Loading the project's environment](README.md#loading-the-projects-environment)
- * [Working with VS Code](README.md#working-with-vs-code)
- * [Manual configuration of the VS Code project :](README.md#manual-configuration-of-the-vs-code-project-)
- * [Configuration via the devcontainer :](README.md#configuration-via-the-devcontainer-)
- * [Contributing to nf-scil](README.md#contributing-to-nf-scil)
- * [Adding a new module to nf-scil](docs/MODULE.md#adding-a-new-module-to-nf-scil)
- * [Generate the template](docs/MODULE.md#generate-the-template)
- * [Edit the template](docs/MODULE.md#edit-the-template)
- * [Editing the main](docs/MODULE.md#editing-modulesnf-scilcategorytoolmainnf-)
- * [Editing the metadata](docs/MODULE.md#editing--modulesnf-scilcategorytoolmetayml-)
- * [Editing the test cases](docs/MODULE.md#editing-testsmodulesnf-scilcategorytoolmainnf-)
- * [Editing the tests configuration](docs/MODULE.md#editing-testsmodulesnf-scilcategorytoolnextflowconfig-)
- * [Run the tests to generate the test metadata file](docs/MODULE.md#run-the-tests-to-generate-the-test-metadata-file)
- * [Last safety test](docs/MODULE.md#last-safety-test)
- * [Submit your PR](docs/MODULE.md#submit-your-pr)
- * [Defining processes optional parameters](docs/MODULE.md#defining-processes-optional-parameters)
- * [Test data infrastructure](docs/MODULE.md#test-data-infrastructure)
- * [Using the .test_data directory](docs/MODULE.md#using-the-test_data-directory)
- * [Using Scilpy Fetcher](docs/MODULE.md#using-scilpy-fetcher)
- * [Running tests](README.md#running-tests)
-
-# Using modules from `nf-scil`
-
-To import modules from `nf-scil`, you first need to install [nf-core](https://github.com/nf-core/tools)
-on your system (can be done simply using `pip install nf-core`). Once done, `nf-scil`
-modules are imported using this command :
-
-```bash
-nf-core modules \
- --git-remote https://github.com/scilus/nf-scil.git \
- install /
-```
-
-where you input the `` you want to import from the desired ``. To get
-a list of the available modules, run :
-
-```bash
-nf-core modules \
- --git-remote https://github.com/scilus/nf-scil.git \
- list remote
-```
-
-# Developing in `nf-scil`
-
-## Dependencies
-
-- Python ≥ 3.8, < 3.13
-- Java Runtime ≥ 11, ≤ 17
- - On Ubuntu, install `openjdk-jre-` packages
-- Nextflow ≥ 21.04.3
-
-> [!IMPORTANT]
-> Nextflow might not detect the right `Java virtual machine` by default, more so if
-> multiple versions of the runtime are installed. If so, you need to set the environment
-> variable `JAVA_HOME` to target the right one.
->
-> - Linux : look in `/usr/lib/jvm` for
-> a folder named `java--openjdk-` and use it as `JAVA_HOME`.
->
-> - MacOS : if the `Java jvm` is the preferential one, use `JAVA_HOME=$(/usr/libexec/java_home)`.
-> Else, look into `/Library/Java/JavaVirtualMachines` for the folder with the correct
-> runtime version (named `jdk_1.jdk`) and use the
-> following : `/Library/Java/JavaVirtualMachines/dk_1.jdk/Contents/Home`.
-
-## Developer installation
-
-The project uses *poetry* to manage python dependencies. To install it using pipx,
-run the following commands :
-
-```
-pip install pipx
-pipx ensurepath
-pipx install poetry
-```
-
-> [!NOTE]
-> If the second command above fails, `pipx` cannot be found in the path. Prepend the
- second command with `$(which python) -m` and rerun the whole block.
-
-> [!WARNING]
-> Poetry doesn't like when other python environments are activated around it. Make
- sure to deactivate any before calling `poetry` commands.
-
-Once done, install the project with :
-
-```
-poetry install
-```
-
-## Loading the project's environment
-
-> [!IMPORTANT]
-> Make sure no python environment is activated before running commands !
-
-The project scripts and dependencies can be accessed using :
-
-```
-poetry shell
-```
-
-which will activate the project's python environment in the current shell.
-
-> [!NOTE]
-> You will know the poetry environment is activated by looking at your shell. The
- input line should be prefixed by : `(nf-scil-tools-py)`, with ``
- being the actual Python version used in the environment.
-
-To exit the environment, simply enter the `exit` command in the shell.
-
-> [!IMPORTANT]
-> Do not use traditional deactivation (calling `deactivate`), since it does not relinquish
- the environment gracefully, making it so you won't be able to reactivate it without
- exiting the shell.
-
-## Working with VS Code
-
-### Manual configuration of the VS Code project :
-
-First install the `nf-scil-extensions` package. You can find it easily on the [extension
-marketplace](https://marketplace.visualstudio.com/items?itemName=AlexVCaron.nf-scil-extensions).
-
-### Configuration via the `devcontainer` :
-
-The `devcontainer` definition for the project contains all required dependencies and setup
-steps are automatically executed. Open the cloned repository in *VS Code* and click on the
-arrow box in the lower left corner, to get a prompt to `Reopen in container`. The procedure
-will start a docker build, wait for a few minutes and enjoy your fully configured development
-environment.
-
-- Available in the container :
- - `nf-scil`, `nf-core` all accessible through the terminal, which is configured to load
- the `poetry` environment in shells automatically
- - `git`, `git-lfs`, `github-cli`
- - `curl`, `wget`, `apt-get`
- - `nextflow`, `docker`, `tmux`
-
-- Available in the VS Code IDE through extensions :
- - Docker images and containers management
- - Python and C++ linting, building and debugging tools
- - Github Pull Requests management
- - Github flavored markdown previewing
-
-## Contributing to `nf-scil`
-
-If you want to propose a new `module` to the repository, follow the guidelines in the
-[module creation](./docs/MODULE.md) documentation. we follow standards closely
-aligned with `nf-core`, with some exceptions on process atomicity and how test data is
-handled. Modules that don't abide to them won't be accepted and PR containing them will
-be closed automatically.
-
-## Running tests
-
-Tests are run through `nf-core`, using the command :
-
-```bash
-nf-core modules \
- --git-remote https://github.com/scilus/nf-scil.git \
- test
-```
-
-The tool can be omitted to run tests for all modules in a category.
+
+
+
+
+
+
+
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Imports: nf-core](https://img.shields.io/badge/nf--core-nf?label=import&style=flat&labelColor=ef8336&color=24B064)](https://pycqa.github.io/nf-core/)
+[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
+[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
+![Code Linting](https://github.com/scilus/nf-scil/workflows/Code%20Linting/badge.svg)
+![Modules Tests](https://github.com/scilus/nf-scil/workflows/Test%20All%20Modules/badge.svg)
+
+Welcome to `nf-scil` ! A **Nextflow** modules and workflows repository for neuroimaging
+maintained by the [SCIL team](https://scil-documentation.readthedocs.io/en/latest/). The
+primary focus of the library is to provide pre-built processes and processing sequences for
+**diffusion Magnetic Resonance Imaging**, optimized for _Nextflow DLS2_, based on open-source
+technologies and made easily available to pipeline's developers through the `nf-core`
+framework.
+
+- [Using modules from nf-scil](README.md#using-modules-from-nf-scil)
+- [Developing in nf-scil](README.md#developing-in-nf-scil)
+ - [Dependencies](README.md#dependencies)
+ - [Developer installation](README.md#developer-installation)
+ - [Loading the project's environment](README.md#loading-the-projects-environment)
+ - [Working with VS Code](README.md#working-with-vs-code)
+ - [Manual configuration of the VS Code project :](README.md#manual-configuration-of-the-vs-code-project-)
+ - [Configuration via the devcontainer :](README.md#configuration-via-the-devcontainer-)
+ - [Contributing to nf-scil](README.md#contributing-to-nf-scil)
+ - [Adding a new module to nf-scil](docs/MODULE.md#adding-a-new-module-to-nf-scil)
+ - [Generate the template](docs/MODULE.md#generate-the-template)
+ - [Edit the template](docs/MODULE.md#edit-the-template)
+ - [Editing the main](docs/MODULE.md#editing-modulesnf-scilcategorytoolmainnf-)
+ - [Editing the metadata](docs/MODULE.md#editing--modulesnf-scilcategorytoolmetayml-)
+ - [Editing the test cases](docs/MODULE.md#editing-testsmodulesnf-scilcategorytoolmainnf-)
+ - [Editing the tests configuration](docs/MODULE.md#editing-testsmodulesnf-scilcategorytoolnextflowconfig-)
+ - [Run the tests to generate the test metadata file](docs/MODULE.md#run-the-tests-to-generate-the-test-metadata-file)
+ - [Last safety test](docs/MODULE.md#last-safety-test)
+ - [Submit your PR](docs/MODULE.md#submit-your-pr)
+ - [Defining processes optional parameters](docs/MODULE.md#defining-processes-optional-parameters)
+ - [Test data infrastructure](docs/MODULE.md#test-data-infrastructure)
+ - [Using the .test_data directory](docs/MODULE.md#using-the-test_data-directory)
+ - [Using Scilpy Fetcher](docs/MODULE.md#using-scilpy-fetcher)
+ - [Running tests](README.md#running-tests)
+
+# Using modules from `nf-scil`
+
+To import modules from `nf-scil`, you first need to install [nf-core](https://github.com/nf-core/tools)
+on your system (can be done simply using `pip install nf-core`). Once done, `nf-scil`
+modules are imported using this command :
+
+```bash
+nf-core modules \
+ --git-remote https://github.com/scilus/nf-scil.git \
+ install /
+```
+
+where you input the `` you want to import from the desired ``. To get
+a list of the available modules, run :
+
+```bash
+nf-core modules \
+ --git-remote https://github.com/scilus/nf-scil.git \
+ list remote
+```
+
+# Developing in `nf-scil`
+
+## Dependencies
+
+- Python ≥ 3.8, < 3.13
+- Java Runtime ≥ 11, ≤ 17
+ - On Ubuntu, install `openjdk-jre-` packages
+- Nextflow ≥ 21.04.3
+
+> [!IMPORTANT]
+> Nextflow might not detect the right `Java virtual machine` by default, more so if
+> multiple versions of the runtime are installed. If so, you need to set the environment
+> variable `JAVA_HOME` to target the right one.
+>
+> - Linux : look in `/usr/lib/jvm` for
+> a folder named `java--openjdk-` and use it as `JAVA_HOME`.
+> - MacOS : if the `Java jvm` is the preferential one, use `JAVA_HOME=$(/usr/libexec/java_home)`.
+> Else, look into `/Library/Java/JavaVirtualMachines` for the folder with the correct
+> runtime version (named `jdk_1.jdk`) and use the
+> following : `/Library/Java/JavaVirtualMachines/dk_1.jdk/Contents/Home`.
+
+## Developer installation
+
+The project uses _poetry_ to manage python dependencies. To install it using pipx,
+run the following commands :
+
+```
+pip install pipx
+pipx ensurepath
+pipx install poetry
+```
+
+> [!NOTE]
+> If the second command above fails, `pipx` cannot be found in the path. Prepend the
+> second command with `$(which python) -m` and rerun the whole block.
+
+> [!WARNING]
+> Poetry doesn't like when other python environments are activated around it. Make
+> sure to deactivate any before calling `poetry` commands.
+
+Once done, install the project with :
+
+```
+poetry install
+```
+
+## Loading the project's environment
+
+> [!IMPORTANT]
+> Make sure no python environment is activated before running commands !
+
+The project scripts and dependencies can be accessed using :
+
+```
+poetry shell
+```
+
+which will activate the project's python environment in the current shell.
+
+> [!NOTE]
+> You will know the poetry environment is activated by looking at your shell. The
+> input line should be prefixed by : `(nf-scil-tools-py)`, with ``
+> being the actual Python version used in the environment.
+
+To exit the environment, simply enter the `exit` command in the shell.
+
+> [!IMPORTANT]
+> Do not use traditional deactivation (calling `deactivate`), since it does not relinquish
+> the environment gracefully, making it so you won't be able to reactivate it without
+> exiting the shell.
+
+## Working with VS Code
+
+### Manual configuration of the VS Code project :
+
+First install the `nf-scil-extensions` package. You can find it easily on the [extension
+marketplace](https://marketplace.visualstudio.com/items?itemName=AlexVCaron.nf-scil-extensions).
+
+### Configuration via the `devcontainer` :
+
+The `devcontainer` definition for the project contains all required dependencies and setup
+steps are automatically executed. Open the cloned repository in _VS Code_ and click on the
+arrow box in the lower left corner, to get a prompt to `Reopen in container`. The procedure
+will start a docker build, wait for a few minutes and enjoy your fully configured development
+environment.
+
+- Available in the container :
+
+ - `nf-scil`, `nf-core` all accessible through the terminal, which is configured to load
+ the `poetry` environment in shells automatically
+ - `git`, `git-lfs`, `github-cli`
+ - `curl`, `wget`, `apt-get`
+ - `nextflow`, `docker`, `tmux`
+
+- Available in the VS Code IDE through extensions :
+ - Docker images and containers management
+ - Python and C++ linting, building and debugging tools
+ - Github Pull Requests management
+ - Github flavored markdown previewing
+
+## Contributing to `nf-scil`
+
+If you want to propose a new `module` to the repository, follow the guidelines in the
+[module creation](./docs/MODULE.md) documentation. we follow standards closely
+aligned with `nf-core`, with some exceptions on process atomicity and how test data is
+handled. Modules that don't abide to them won't be accepted and PR containing them will
+be closed automatically.
+
+## Running tests
+
+Tests are run through `nf-core`, using the command :
+
+```bash
+nf-core modules \
+ --git-remote https://github.com/scilus/nf-scil.git \
+ test
+```
+
+The tool can be omitted to run tests for all modules in a category.
diff --git a/docs/MODULE.md b/docs/MODULE.md
index caf6cad24..7f0976da3 100644
--- a/docs/MODULE.md
+++ b/docs/MODULE.md
@@ -30,58 +30,56 @@ nf-core modules create \
You will still have to interact with the **bioconda** prompt, still select `no`.
> [!NOTE]
-> Once used to the conventions, adding `--empty-template` to the command will disable
- auto-generation of comments, examples and TODOs and can be a time-saver.
+> Once used to the conventions, adding `--empty-template` to the command will disable
+> auto-generation of comments, examples and TODOs and can be a time-saver.
## Edit the template
-The template has to be edited in order to work with `nf-scil` and still be importable
-through `nf-core`. Refer to the `betcrop/fslbetcrop` module for an example as it should
+The template has to be edited in order to work with `nf-scil` and still be importable
+through `nf-core`. Refer to the `betcrop/fslbetcrop` module for an example as it should
already follow all guidelines. You will find related files in :
- `modules/nf-scil/betcrop/fslbetcrop`
- `tests/modules/nf-scil/betcrop/fslbetcrop`
-
-
### Editing `./modules/nf-scil///main.nf` :
- Remove the line `conda "YOUR-TOOL-HERE"`.
-- If the process uses the `scilus` container, use the following replacements,
+- If the process uses the `scilus` container, use the following replacements,
else remove the whole section.
- `depot.galaxyproject.org...` ⟹ `scil.usherbrooke.ca/containers/scilus_1.6.0.sif`
+ `depot.galaxyproject.org...` ⟹ `scil.usherbrooke.ca/containers/scilus_1.6.0.sif`
- `biocontainers/YOUR-TOOL-HERE` ⟹ `scilus/scilus:1.6.0`
+ `biocontainers/YOUR-TOOL-HERE` ⟹ `scilus/scilus:1.6.0`
- Add your inputs in the `input:` section :
> [!NOTE]
- > Each line below `input:` defines an input channel for the process. A channel can
- receive one (`val`, `path`, ...) or more (`tuple`) values per item.
+ > Each line below `input:` defines an input channel for the process. A channel can
+ > receive one (`val`, `path`, ...) or more (`tuple`) values per item.
> [!IMPORTANT]
- > When possible, add all optional input parameters (not data !) to `task.ext` instead of
- listing them in the `input:` section (see [this section](#defining-processes-optional-parameters)
- for more information).
+ > When possible, add all optional input parameters (not data !) to `task.ext` instead of
+ > listing them in the `input:` section (see [this section](#defining-processes-optional-parameters)
+ > for more information).
- All inputs are assumed to be `required` by default.
- If an input is scoped to a subject, the line MUST start with `tuple val(meta), `.
- - An input `path` CAN be optional (though it is not officially supported). You simply
- have to pass it an empty list `[]` for Nextflow to consider its value empty, but
+ - An input `path` CAN be optional (though it is not officially supported). You simply
+ have to pass it an empty list `[]` for Nextflow to consider its value empty, but
correct.
> [!IMPORTANT]
- > If you decide an input `path` value is optional, add `/* optional, value = [] */`
- aside the parameter (e.g. f1 is optional, so `path(f1) /* optional, value = [] */`
- or even `tuple val(meta), path(f1) /* optional, value = [] */, path(...` are valid
- syntaxes). This will make input lines long, but they will be detectable. When we
- can define input tuples on multiple lines, we'll deal with this.
+ > If you decide an input `path` value is optional, add `/* optional, value = [] */`
+ > aside the parameter (e.g. f1 is optional, so `path(f1) /* optional, value = [] */`
+ > or even `tuple val(meta), path(f1) /* optional, value = [] */, path(...` are valid
+ > syntaxes). This will make input lines long, but they will be detectable. When we
+ > can define input tuples on multiple lines, we'll deal with this.
- In the script section, before the script definition (in `""" """`), unpack the
+ In the script section, before the script definition (in `""" """`), unpack the
optional argument into a `usable variable`. For a optional input `input1`, add :
def optional_input1 = input1 ? "" : ""
@@ -89,32 +87,32 @@ already follow all guidelines. You will find related files in :
The variable `optional_input1` is the one to use in the script.
> [!NOTE]
- > At its most simple, a variable is `usable` if its conversion to a string is valid
- in the script (e.g. : if a variable can be empty or null, then its conversion to an
- empty string must be valid in the sense of the script for the variable to be considered
- `usable`).
+ > At its most simple, a variable is `usable` if its conversion to a string is valid
+ > in the script (e.g. : if a variable can be empty or null, then its conversion to an
+ > empty string must be valid in the sense of the script for the variable to be considered
+ > `usable`).
- Add all outputs in the `output` section :
- - As for inputs, each line defines an output channel. If an output is scoped to a
+ - As for inputs, each line defines an output channel. If an output is scoped to a
subject, the line MUST start with `tuple val(meta), `.
- File extensions MUST ALWAYS be defined (e.g. `path("*.{nii,nii.gz}")`).
> [!IMPORTANT]
- > Each line MUST use `emit: ` to make its results available inside Nextflow using
- a relevant `name`. Results are accessible using : `PROCESS_NAME.out.`.
-
+ > Each line MUST use `emit: ` to make its results available inside Nextflow using
+ > a relevant `name`. Results are accessible using : `PROCESS_NAME.out.`.
+
> [!NOTE]
> Optional outputs ARE possible, add `, optional: true` after the `emit: ` clause.
- Fill the `script` section :
- - Use the `prefix` variable to name the scoped output files. If needed, modify the
+ - Use the `prefix` variable to name the scoped output files. If needed, modify the
variable definition in the groovy pre-script.
- Define dependencies versions :
-
+
In the versioning section at the bottom of the script :
```bash
@@ -123,37 +121,38 @@ already follow all guidelines. You will find related files in :
END_VERSIONS
```
+
remove the lines in between the `cat` and the `END_VERSIONS` line. In it, add
for each dependency a new line in the format : `: `.
> [!NOTE]
- > You can hard-bake the version as a number here, but if possible extract if from
- the dependency dynamically. Refer to the `betcrop/fslbetcrop` module, in `main.nf`
- for examples on how to extract the version number correctly.
+ > You can hard-bake the version as a number here, but if possible extract if from
+ > the dependency dynamically. Refer to the `betcrop/fslbetcrop` module, in `main.nf`
+ > for examples on how to extract the version number correctly.
- Fill the `stub` section :
Using the same conventions as for the `script` section, define a simple test stub :
- - Call the helps of all scripts used, if possible.
+ - Call the helps of all scripts used, if possible.
- - Call `touch ` to generate empty files for all required outputs.
+ - Call `touch ` to generate empty files for all required outputs.
-### Editing `./modules/nf-scil///meta.yml` :
+### Editing `./modules/nf-scil///meta.yml` :
-Fill the sections you find relevant. There is a lot of metadata in this file, but we
-don't need to specify them all. At least define the `keywords`, describe the process'
+Fill the sections you find relevant. There is a lot of metadata in this file, but we
+don't need to specify them all. At least define the `keywords`, describe the process'
`inputs` and `outputs`, and add a `short documentation` for the tool(s) used in the process.
> [!IMPORTANT]
-> The `tool` documentation does not describe your module, but to the tools you use in
- the module ! If you use scripts from `scilpy`, here you describe scilpy. If using
- `ANTs`, describe ANts. Etcetera.
+> The `tool` documentation does not describe your module, but to the tools you use in
+> the module ! If you use scripts from `scilpy`, here you describe scilpy. If using
+> `ANTs`, describe ANts. Etcetera.
### Editing `./tests/modules/nf-scil///main.nf` :
-The module's test suite is a collection of workflows containing isolated test cases. You
-can add as many more tests as your heart desire (not too much), in addition to the one
+The module's test suite is a collection of workflows containing isolated test cases. You
+can add as many more tests as your heart desire (not too much), in addition to the one
provided.
> [!IMPORTANT]
@@ -161,32 +160,32 @@ provided.
In any case, to get the test workflows working, do the following :
-- Either modify the auto-generated `input` object to add your test data or replace it with
- a *fetcher workflow*. You can do this at the end, when you have defined your test cases.
- Refer to [this section](#test-data-infrastructure) to see which use case fits your tests
+- Either modify the auto-generated `input` object to add your test data or replace it with
+ a _fetcher workflow_. You can do this at the end, when you have defined your test cases.
+ Refer to [this section](#test-data-infrastructure) to see which use case fits your tests
better.
### Editing `./tests/modules/nf-scil///nextflow.config` :
-You don't need to touch anything here, except if you have defined optional parameters
-with `task.ext` and want to alter their values for some test cases. Refer to
-[this section](#defining-processes-optional-parameters) to see how to scope those parameters
+You don't need to touch anything here, except if you have defined optional parameters
+with `task.ext` and want to alter their values for some test cases. Refer to
+[this section](#defining-processes-optional-parameters) to see how to scope those parameters
to specific tests using `selectors`.
## Run the tests to generate the test metadata file
> [!WARNING]
-> Verify you are located at the root of `nf-scil` (not inside modules) before
+> Verify you are located at the root of `nf-scil` (not inside modules) before
> running commands !
-Once the test data has been pushed to the desired location and been made available to the
-test infrastructure using the relevant configurations, the test module has to be pre-tested
-so output files that gets generated are checksum correctly.
+Once the test data has been pushed to the desired location and been made available to the
+test infrastructure using the relevant configurations, the test module has to be pre-tested
+so output files that gets generated are checksum correctly.
> [!IMPORTANT]
-> The test infrastructure uses `pytest-workflow` to run the tests. It is `git-aware`,
-> meaning that only files either `committed` or `staged` will be considered by
-> the tests. To verify that your file will be loaded correctly, check that it is
+> The test infrastructure uses `pytest-workflow` to run the tests. It is `git-aware`,
+> meaning that only files either `committed` or `staged` will be considered by
+> the tests. To verify that your file will be loaded correctly, check that it is
> listed by `git ls-files`.
Run :
@@ -199,26 +198,26 @@ nf-core modules create-test-yml \
```
-All the test case you defined will be run, watch out for errors ! Once everything runs
-smoothly, look at the test metadata file produced : `tests/modules/nf-scil//test.yml`
-and validate that ALL outputs produced by test cases have been caught. Their `md5sum` is
+All the test case you defined will be run, watch out for errors ! Once everything runs
+smoothly, look at the test metadata file produced : `tests/modules/nf-scil//test.yml`
+and validate that ALL outputs produced by test cases have been caught. Their `md5sum` is
critical to ensure future executions of your test produce valid outputs.
## Last safety test
-You're mostly done ! If every tests passes, your module is ready ! Still, you have not tested
-that `nf-core` is able to find and install your module in an actual pipeline. First, to test
-this, your module must be pushed only to your repository, so ensure that. Next, you need to
-either locate yourself in an already existing `DSL2` Nextflow pipeline, or create a `dummy`
+You're mostly done ! If every tests passes, your module is ready ! Still, you have not tested
+that `nf-core` is able to find and install your module in an actual pipeline. First, to test
+this, your module must be pushed only to your repository, so ensure that. Next, you need to
+either locate yourself in an already existing `DSL2` Nextflow pipeline, or create a `dummy`
testing one.
> [!NOTE]
-> To be valid, your `DSL2` Nextflow pipeline must have a `modules/` directory, as well as a
- `writable` or non-existent `.modules.yml` file.
+> To be valid, your `DSL2` Nextflow pipeline must have a `modules/` directory, as well as a
+> `writable` or non-existent `.modules.yml` file.
> [!NOTE]
-> A `dummy` pipeline is simply a directory containing an empty `modules/` directory and a
- `main.nf` file with the following content : `workflow {}`.
+> A `dummy` pipeline is simply a directory containing an empty `modules/` directory and a
+> `main.nf` file with the following content : `workflow {}`.
Run the following command, to try installing the module :
@@ -229,52 +228,52 @@ nf-core module \
install /
```
-You'll get a message at the command line, indicating which `include` line to add to your
-pipeline to use your module. If you do it, add the module to your pipeline, run it and
+You'll get a message at the command line, indicating which `include` line to add to your
+pipeline to use your module. If you do it, add the module to your pipeline, run it and
validate it's working, and you're done !
> [!NOTE]
-> If working with the `dummy`, don't bother running it, we say it's working, so you can
- delete the test and submit the PR !
+> If working with the `dummy`, don't bother running it, we say it's working, so you can
+> delete the test and submit the PR !
## Submit your PR
-Open a PR to the `nf-scil` repository master. We'll test everything, make sure it's
+Open a PR to the `nf-scil` repository master. We'll test everything, make sure it's
working and that code follows standards.
> [!NOTE]
> It's the perfect place to get new tools added to our containers, if need be !
-Once LGTM has been declared, wave to the maintainers and look at your hard work paying off.
+Once LGTM has been declared, wave to the maintainers and look at your hard work paying off.
PR merged !
# Defining processes optional parameters
-Using the DLS2 module framework, we can define passage of optional parameters using a configuration
-proprietary to the `process scope`, the `task.ext` mapping (or dictionary). In `nf-core`, the convention
+Using the DLS2 module framework, we can define passage of optional parameters using a configuration
+proprietary to the `process scope`, the `task.ext` mapping (or dictionary). In `nf-core`, the convention
is to load `task.ext.args` with all optional parameters acceptable by the process.
-This does not work perfectly for our use-cases, and instead, we use the whole `task.ext` as a
+This does not work perfectly for our use-cases, and instead, we use the whole `task.ext` as a
parameters map. To define an optional parameter `param1` through `task.ext`, add the following to
the process script section, before the script definition (in `""" """`) :
```groovy
-def args_for_cmd1 = task.ext.param1 ? " $task.ext.param1"
+def args_for_cmd1 = task.ext.param1 ? " $task.ext.param1"
: ''
```
-Then, use `args_for_cmd1` in the script. Defining the actual value for the parameters is done
-by means of `.config` files, inside the `process` scope. A global affectation of the parameter
+Then, use `args_for_cmd1` in the script. Defining the actual value for the parameters is done
+by means of `.config` files, inside the `process` scope. A global affectation of the parameter
is as simple as :
-```groovy
+```groovy
process {
task.ext.param1 = ""
}
```
-Doing so will affect **ALL** processes. To scope to a specific process, use the
+Doing so will affect **ALL** processes. To scope to a specific process, use the
[process selectors](https://www.nextflow.io/docs/latest/config.html#process-selectors)
(`withName:` or `withLabel:`) :
@@ -286,7 +285,7 @@ process {
}
```
-You can define the selector on multiple levels and use glob matching, making it so that
+You can define the selector on multiple levels and use glob matching, making it so that
it is possible to affect the processes inside a specific workflow as well :
```groovy
@@ -309,20 +308,20 @@ process {
# Test data infrastructure
> [!WARNING]
-> WORK IN PROGRESS, WILL CHANGE SOON-ISH. 2 temporary ways are available now and will be
+> WORK IN PROGRESS, WILL CHANGE SOON-ISH. 2 temporary ways are available now and will be
> deprecated when the **DVC** infrastructure is ready.
## Using the `.test_data` directory
Some test datasets are available under the `.test_data` directory. You can use them as you wish,
-but inspect them before you do, since some dataset have been lean down and could not fit the
-reality of your test cases. **Do not add or modify data in this directory**. Tests packages are
-separated into `heavy` and `light` categories depending on their filesize. Inside, they are divided
+but inspect them before you do, since some dataset have been lean down and could not fit the
+reality of your test cases. **Do not add or modify data in this directory**. Tests packages are
+separated into `heavy` and `light` categories depending on their filesize. Inside, they are divided
into relevant sub-categories (dwi, anat, ...).
-To bind data to test cases using this infrastructure, it first has to be added to `tests/config/test_data.config`
-in order to be visible. The configuration is a nesting of dictionaries, all test data
-files must be added to the `params.test_data` of this structure, using this convention
+To bind data to test cases using this infrastructure, it first has to be added to `tests/config/test_data.config`
+in order to be visible. The configuration is a nesting of dictionaries, all test data
+files must be added to the `params.test_data` of this structure, using this convention
for the `dictionary key` : `params.test_data[][][]`.
Thus, a new binding in `tests/config/test_data.config` should resemble the following
@@ -351,7 +350,7 @@ params {
```
You then use `params.test_data[][][]` in your test cases to
-attach the data to the test case, since the `params.test_data` collection is loaded
+attach the data to the test case, since the `params.test_data` collection is loaded
automatically. To do so, in a test workflow, define an `input` object :
```
@@ -371,7 +370,7 @@ and use it as input to the processes to test.
## Using Scilpy Fetcher
The Scilpy Fetcher is a tool that allows you to download datasets from the Scilpy test data
-depository. To use it, first include the *fetcher workflow* in your test's `main.nf` :
+depository. To use it, first include the _fetcher workflow_ in your test's `main.nf` :
```
include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main'
@@ -400,5 +399,5 @@ input = LOAD_TEST_DATA.out.test_data_directory
> [!NOTE]
> The subworkflow must be called individually in each test workflow, even if they download
-> the same archives, since there is no mechanism to pass data channels to them from the
+> the same archives, since there is no mechanism to pass data channels to them from the
> outside.
diff --git a/docs/SCILPY_DATA.md b/docs/SCILPY_DATA.md
index d2b4dc5d0..0080c2ea3 100644
--- a/docs/SCILPY_DATA.md
+++ b/docs/SCILPY_DATA.md
@@ -3,664 +3,664 @@
Datasets available in Scilpy data.
Entries are indexed by archive name.
- - bids_json.zip
- - result_real_dwi_real_rev_dwi_sbref.json
- - result_real_dwi_real_rev_dwi.json
- - result_complex_dwi_complex_rev_dwi_sbref.json
- - result_real_dwi_epi.json
- - result_complex_dwi_complex_rev_dwi.json
- - result_complex_dwi_epi.json
- - result_real_dwi_real_sbref.json
- - result_complex_dwi_complex_sbref.json
- - plot.zip
- - atlas_brainnetome.nii.gz
- - ad.nii.gz
- - fa.nii.gz
- - map_gm.nii.gz
- - map_wm.nii.gz
- - mask_gm.nii.gz
- - mask_wm.nii.gz
- - atlas_brainnetome.json
- - ihMT.zip
- - B1map.json
- - B1map.nii.gz
- - echo-1_acq-altnp_ihmt.json
- - echo-1_acq-altnp_ihmt.nii.gz
- - echo-1_acq-altpn_ihmt.json
- - echo-1_acq-altpn_ihmt.nii.gz
- - echo-1_acq-mtoff_ihmt.json
- - echo-1_acq-mtoff_ihmt.nii.gz
- - echo-1_acq-neg_ihmt.json
- - echo-1_acq-neg_ihmt.nii.gz
- - echo-1_acq-pos_ihmt.json
- - echo-1_acq-pos_ihmt.nii.gz
- - echo-1_acq-T1w_ihmt.json
- - echo-1_acq-T1w_ihmt.nii.gz
- - echo-2_acq-altnp_ihmt.json
- - echo-2_acq-altnp_ihmt.nii.gz
- - echo-2_acq-altpn_ihmt.json
- - echo-2_acq-altpn_ihmt.nii.gz
- - echo-2_acq-mtoff_ihmt.json
- - echo-2_acq-mtoff_ihmt.nii.gz
- - echo-2_acq-neg_ihmt.json
- - echo-2_acq-neg_ihmt.nii.gz
- - echo-2_acq-pos_ihmt.json
- - echo-2_acq-pos_ihmt.nii.gz
- - echo-2_acq-T1w_ihmt.json
- - echo-2_acq-T1w_ihmt.nii.gz
- - echo-3_acq-altnp_ihmt.json
- - echo-3_acq-altnp_ihmt.nii.gz
- - echo-3_acq-altpn_ihmt.json
- - echo-3_acq-altpn_ihmt.nii.gz
- - echo-3_acq-mtoff_ihmt.json
- - echo-3_acq-mtoff_ihmt.nii.gz
- - echo-3_acq-neg_ihmt.json
- - echo-3_acq-neg_ihmt.nii.gz
- - echo-3_acq-pos_ihmt.json
- - echo-3_acq-pos_ihmt.nii.gz
- - echo-3_acq-T1w_ihmt.json
- - echo-3_acq-T1w_ihmt.nii.gz
- - mask_resample.nii.gz
- - MT.zip
- - mask.nii.gz
- - sub-001_echo-1_acq-mtoff_mtsat.json
- - sub-001_echo-1_acq-mtoff_mtsat.nii.gz
- - sub-001_echo-1_acq-mton_mtsat.json
- - sub-001_echo-1_acq-mton_mtsat.nii.gz
- - sub-001_echo-1_acq-t1w_mtsat.json
- - sub-001_echo-1_acq-t1w_mtsat.nii.gz
- - sub-001_echo-2_acq-mtoff_mtsat.json
- - sub-001_echo-2_acq-mtoff_mtsat.nii.gz
- - sub-001_echo-2_acq-mton_mtsat.json
- - sub-001_echo-2_acq-mton_mtsat.nii.gz
- - sub-001_echo-2_acq-t1w_mtsat.json
- - sub-001_echo-2_acq-t1w_mtsat.nii.gz
- - sub-001_echo-3_acq-mtoff_mtsat.json
- - sub-001_echo-3_acq-mtoff_mtsat.nii.gz
- - sub-001_echo-3_acq-mton_mtsat.json
- - sub-001_echo-3_acq-mton_mtsat.nii.gz
- - sub-001_echo-3_acq-t1w_mtsat.json
- - sub-001_echo-3_acq-t1w_mtsat.nii.gz
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- - sub-001_echo-4_acq-mtoff_mtsat.nii.gz
- - sub-001_echo-4_acq-mton_mtsat.json
- - sub-001_echo-4_acq-mton_mtsat.nii.gz
- - sub-001_echo-4_acq-t1w_mtsat.json
- - sub-001_echo-4_acq-t1w_mtsat.nii.gz
- - sub-001_echo-5_acq-mtoff_mtsat.json
- - sub-001_echo-5_acq-mtoff_mtsat.nii.gz
- - sub-001_echo-5_acq-mton_mtsat.json
- - sub-001_echo-5_acq-mton_mtsat.nii.gz
- - sub-001_echo-5_acq-t1w_mtsat.json
- - sub-001_echo-5_acq-t1w_mtsat.nii.gz
- - sub-001_run-01_B1map.json
- - sub-001_run-01_B1map.nii.gz
- - atlas.zip
- - atlas_freesurfer_v2.nii.gz
- - atlas_freesurfer_v2_LUT.json
- - atlas_freesurfer_v2_labels_list.txt
- - atlas_freesurfer_v2_no_brainstem.nii.gz
- - atlas_freesurfer_v2_single_brainstem.nii.gz
- - atlas_freesurfer_v2_single_brainstem_dil.nii.gz
- - bash.sh
- - brainstem.nii.gz
- - brainstem_173.nii.gz
- - brainstem_174.nii.gz
- - brainstem_175.nii.gz
- - brainstem_bin.nii.gz
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- - 2000.nii.gz
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- - 2002.nii.gz
- - 2003.nii.gz
- - 2005.nii.gz
- - 2006.nii.gz
- - 2007.nii.gz
- - 2008.nii.gz
- - 2009.nii.gz
- - 2010.nii.gz
- - 2011.nii.gz
- - 2012.nii.gz
- - 2013.nii.gz
- - 2014.nii.gz
- - 2015.nii.gz
- - 2016.nii.gz
- - 2017.nii.gz
- - 2018.nii.gz
- - 2019.nii.gz
- - 2020.nii.gz
- - 2021.nii.gz
- - 2022.nii.gz
- - 2023.nii.gz
- - 2024.nii.gz
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- - 2027.nii.gz
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- - 49.nii.gz
- - 50.nii.gz
- - 51.nii.gz
- - 52.nii.gz
- - 53.nii.gz
- - 54.nii.gz
- - 58.nii.gz
- - 60.nii.gz
- - 8.nii.gz
- - 85.nii.gz
- - 8_10.nii.gz
- - left_accumbens_area.nii.gz
- - left_amygdala.nii.gz
- - left_banks_superior_temporal.nii.gz
- - left_caudal_anterior_cingulate.nii.gz
- - left_caudal_middle_fontral.nii.gz
- - left_caudate.nii.gz
- - left_cerebellum_cortex.nii.gz
- - left_corpus_callosum.nii.gz
- - left_cuneus.nii.gz
- - left_entorhinal.nii.gz
- - left_frontal_pole.nii.gz
- - left_fusiform.nii.gz
- - left_hippocampus.nii.gz
- - left_inferior_parietal.nii.gz
- - left_inferior_temporal.nii.gz
- - left_insula.nii.gz
- - left_isthmus_cingulate.nii.gz
- - left_lateral_occipital.nii.gz
- - left_laterral_orbitofrontal.nii.gz
- - left_lingual.nii.gz
- - left_medial_orbitofrontal.nii.gz
- - left_middle_temporal.nii.gz
- - left_pallidum.nii.gz
- - left_paracentral.nii.gz
- - left_parahipocampal.nii.gz
- - left_parsopercularis.nii.gz
- - left_parsorbitalis.nii.gz
- - left_parstriangularis.nii.gz
- - left_pericalcarine.nii.gz
- - left_postcentral.nii.gz
- - left_posteriorcingulate.nii.gz
- - left_precentral.nii.gz
- - left_precuneus.nii.gz
- - left_putamen.nii.gz
- - left_rostral_anterior_cingulate.nii.gz
- - left_rostral_middle_frontal.nii.gz
- - left_superior_frontral.nii.gz
- - left_superior_parietal.nii.gz
- - left_superior_temporal.nii.gz
- - left_supra_marginal.nii.gz
- - left_temporal_pole.nii.gz
- - left_thalamus_proper.nii.gz
- - left_transverse_temporal.nii.gz
- - left_ventraldc.nii.gz
- - midbrain.nii.gz
- - oblongata.nii.gz
- - pons.nii.gz
- - right_accumbens_area.nii.gz
- - right_amygdala.nii.gz
- - right_banks_superior_temporal.nii.gz
- - right_caudal_anterior_cingulate.nii.gz
- - right_caudal_middle_fontral.nii.gz
- - right_caudate.nii.gz
- - right_cerebellum_cortex.nii.gz
- - right_corpus_callosum.nii.gz
- - right_cuneus.nii.gz
- - right_entorhinal.nii.gz
- - right_frontal_pole.nii.gz
- - right_fusiform.nii.gz
- - right_hippocampus.nii.gz
- - right_inferior_parietal.nii.gz
- - right_inferior_temporal.nii.gz
- - right_insula.nii.gz
- - right_isthmus_cingulate.nii.gz
- - right_lateral_occipital.nii.gz
- - right_laterral_orbitofrontal.nii.gz
- - right_lingual.nii.gz
- - right_medial_orbitofrontal.nii.gz
- - right_middle_temporal.nii.gz
- - right_pallidum.nii.gz
- - right_paracentral.nii.gz
- - right_parahipocampal.nii.gz
- - right_parsopercularis.nii.gz
- - right_parsorbitalis.nii.gz
- - right_parstriangularis.nii.gz
- - right_pericalcarine.nii.gz
- - right_postcentral.nii.gz
- - right_posteriorcingulate.nii.gz
- - right_precentral.nii.gz
- - right_precuneus.nii.gz
- - right_putamen.nii.gz
- - right_rostral_anterior_cingulate.nii.gz
- - right_rostral_middle_frontal.nii.gz
- - right_superior_frontral.nii.gz
- - right_superior_parietal.nii.gz
- - right_superior_temporal.nii.gz
- - right_supra_marginal.nii.gz
- - right_temporal_pole.nii.gz
- - right_thalamus_proper.nii.gz
- - right_transverse_temporal.nii.gz
- - right_ventraldc.nii.gz
- - bst.zip
- - todi_mask.nii.gz
- - template_lin.nii.gz
- - rpt_m_warp.trk
- - rpt_m_lin.trk
- - output1InverseWarp.nii.gz
- - output0GenericAffine.mat
- - out_lw_tdi.nii.gz
- - mask.nii.gz
- - lw_todi_sh.nii.gz
- - fodf.nii.gz
- - fa.nii.gz
- - bash.sh
- - template0.nii.gz
- - rpt_m.trk
- - todi_mask.nii.gz
- - priors.nii.gz
- - endpoints_mask.nii.gz
- - efod.nii.gz
- - bundles.zip
- - transformation_rigid.txt
- - sagittal_glass.png
- - sagittal_3d.png
- - coronal_glass.png
- - coronal_3d.png
- - clusters.pkl
- - bundle_all_1mm_ic.trk
- - bundle_all_1mm.trk
- - bundle_all_1mm.nii.gz
- - bundle_0_similarity.json
- - bundle_0_reco.tck
- - bundle_0_measures.json
- - bundle_0_binary.json
- - bash.sh
- - axial_glass.png
- - axial_3d.png
- - affine.txt
- - results.json
- - logfile.txt
- - bundle_6.trk
- - bundle_5.trk
- - bundle_4.trk
- - bundle_3.trk
- - bundle_2.trk
- - bundle_1.trk
- - bundle_0.trk
- - default_config_sim.json
- - bundle_all_1mm.nii.gz
- - bundle_6.trk
- - bundle_5.trk
- - bundle_4.trk
- - bundle_3.trk
- - bundle_2.trk
- - bundle_1.trk
- - bundle_0.trk
- - bundle_6.trk
- - bundle_5.trk
- - bundle_4.trk
- - bundle_3.trk
- - bundle_2.trk
- - bundle_1.trk
- - bundle_0.trk
- - bundle_6.trk
- - bundle_5.trk
- - bundle_4.trk
- - bundle_3.trk
- - bundle_2.trk
- - bundle_1.trk
- - bundle_0.trk
- - commit_amico.zip
- - cmd
- - tracking.trk
- - dwi.bvec
- - dwi.bval
- - wm_frf.txt
- - gm_frf.txt
- - csf_frf.txt
- - peaks.nii.gz
- - mask.nii.gz
- - md.nii.gz
- - fa.nii.gz
- - dwi.nii.gz
- - ad.nii.gz
- - connectivity.zip
- - vol.npy
- - success.txt
- - sim.npy
- - sc_thr.npy
- - sc_reo_fake.npy
- - sc_normalize.npy
- - sc_norm_vol.npy
- - sc_norm.png
- - sc_norm.npy
- - sc_masked.npy
- - sc_lower_threshold.npy
- - sc_add_10.npy
- - sc.npy
- - reorder.txt
- - pval.npy
- - mask.npy
- - len.npy
- - labels_list.txt
- - gtm.json
- - fodf.nii.gz
- - endpoints_atlas.nii.gz
- - decompose_afd_rd.h5
- - decompose.h5
- - bundle_all_1mm.trk
- - bash.sh
- - affine.txt
- - afd_max.npy
- - afd_max.nii.gz
- - 9_9.trk
- - 5_6.trk
- - 4_8.trk
- - 3_7.trk
- - 2_7.trk
- - 1_7.trk
- - 1_10.trk
- - 9_9.nii.gz
- - 5_6.nii.gz
- - 4_8.nii.gz
- - 3_7.nii.gz
- - 2_7.nii.gz
- - 1_7.nii.gz
- - 1_10.nii.gz
- - filtering.zip
- - voting_voxels.nii.gz
- - voting_streamlines.trk
- - sc.bdo
- - mosaic.png
- - mask.nii.gz
- - centroids.trk
- - bundle_all_1mm_inliers.trk
- - bundle_all_1mm.trk
- - bundle_all_1mm.nii.gz
- - bundle_4_filtered_no_loops.trk
- - bundle_4_filtered.trk
- - bundle_4_filtered.nii.gz
- - bundle_4.trk
- - bash.sh
- - cluster_9.trk
- - cluster_8.trk
- - cluster_7.trk
- - cluster_6.trk
- - cluster_5.trk
- - cluster_4.trk
- - cluster_3.trk
- - cluster_2.trk
- - cluster_19.trk
- - cluster_18.trk
- - cluster_17.trk
- - cluster_16.trk
- - cluster_15.trk
- - cluster_14.trk
- - cluster_13.trk
- - cluster_12.trk
- - cluster_11.trk
- - cluster_10.trk
- - cluster_1.trk
- - cluster_0.trk
- - others.zip
- - t1_reshape.nii.gz
- - t1_resample.nii.gz
- - t1_crop_denoised.nii.gz
- - t1_crop.nii.gz
- - t1.nii.gz
- - rgb_.nii.gz
- - rgb.nii.gz
- - fibercup_bundles_color.trk
- - fibercup_bundles.trk
- - fibercup_bundle_0_color.trk
- - fibercup_bundle_0.trk
- - fa_resample.nii.gz
- - fa.nii.gz
- - encoding.b
- - empty.trk
- - density.nii.gz
- - bash.sh
- - atlas_freesurfer_v2_LUT.json
- - atlas_freesurfer_v2.nii.gz
- - IFGWM_sub.trk
- - IFGWM.trk
- - processing.zip
- - fodf_descoteaux07_sub_full.nii.gz
- - fodf_descoteaux07_sub.nii.gz
- - fd.nii.gz
- - fodf_bingham.nii.gz
- - dwi_noise_mask.nii.gz
- - 1000.b
- - 1000.bval
- - 1000.bvec
- - 1000_flip.b
- - 3000.bval
- - 3000.bvec
- - ad.nii.gz
- - ad_ransanc.nii.gz
- - afd_max.nii.gz
- - afd_sum.nii.gz
- - afd_test.nii.gz
- - afd_tot.nii.gz
- - b0_mean.nii.gz
- - b0_mean_n4.nii.gz
- - bias_field_b0.nii.gz
- - diff.nii.gz
- - dki_ad.nii.gz
- - dki_fa.nii.gz
- - dki_md.nii.gz
- - dki_rd.nii.gz
- - dwi.bval
- - dwi.bvec
- - dwi.nii.gz
- - dwi_crop.nii.gz
- - dwi_crop_1000.nii.gz
- - dwi_crop_3000.nii.gz
- - dwi_crop_n4.nii.gz
- - fa.nii.gz
- - fa_low.nii.gz
- - fa_thr.nii.gz
- - fodf.nii.gz
- - fodf_descoteaux07.nii.gz
- - frf.txt
- - md.nii.gz
- - mfrf.txt
- - mni_masked_2x2x2.nii.gz
- - nfrf.txt
- - nufo.nii.gz
- - peaks.nii.gz
- - rd.nii.gz
- - rd_test.nii.gz
- - seed.nii.gz
- - sh.nii.gz
- - sh_1000.nii.gz
- - sh_3000.nii.gz
- - tracking.trk
- - cc.nii.gz
- - dwi_graph.png
- - dwi_SNR.json
- - small_roi_gm_mask.nii.gz
- - axial.png
- - coronal.png
- - sagittal.png
- - surface_vtk_fib.zip
- - rhpialt.vtk
- - log.txt
- - lhpialt_smooth.vtk
- - lhpialt_lin.vtk
- - lhpialt.vtk
- - lh.pialt_xform
- - gyri_fanning_c.trk
- - gyri_fanning.trk
- - gyri_fanning.tck
- - gyri_fanning.fib
- - fa_flip.nii.gz
- - fa.nii.gz
- - bash.sh
- - affine.txt
- - tracking.zip
- - interface.nii.gz
- - bash.sh
- - fa.nii.gz
- - fodf.nii.gz
- - local.trk
- - local_split_0.trk
- - local_split_1.trk
- - local_split_2.trk
- - map_csf.nii.gz
- - map_exclude.nii.gz
- - map_exclude_corr.nii.gz
- - map_gm.nii.gz
- - map_include.nii.gz
- - map_include_corr.nii.gz
- - map_wm.nii.gz
- - peaks.nii.gz
- - pft.trk
- - seeding_mask.nii.gz
- - union.trk
- - union_shuffle.trk
- - union_shuffle_sub.trk
- - union_shuffle_sub_smooth.trk
- - tractograms.zip
- - bundle_4_cut_endpoints.tck
- - bundle_4_cut_center.tck
- - bundle_4_endpoints_5points.nii.gz
- - bundle_4_center.nii.gz
- - bundle_4_head_tail.nii.gz
- - bundle_4_head_tail_offset.nii.gz
- - bundle_4.tck
- - bundle_4_endpoints_1point.nii.gz
- - bundle_4_wm.nii.gz
- - bundle_4_endpoints_1point.nii.gz
- - bundle_4_cut_endpoints.tck
- - bundle_4_center.nii.gz
- - bundle_4_head_tail.nii.gz
- - bundle_4_head_tail_offset.nii.gz
- - bundle_4.tck
- - bundle_4_wm.nii.gz
- - bundle_4_cut_center.tck
- - bundle_4_endpoints_5points.nii.gz
- - tractometry.zip
- - tail.nii.gz
- - mni_masked.nii.gz
- - metric_label.json
- - length_stats_2.json
- - length_stats_1.json
- - length_stats.xlsx
- - label.npz
- - head.nii.gz
- - distance.npz
- - bash.sh
- - IFGWM_uni_c_10.trk
- - IFGWM_uni_c.trk
- - IFGWM_uni.trk
- - IFGWM_labels_map.nii.gz
- - IFGWM_color.trk
- - IFGWM.trk
- - IFGWM.nii.gz
- - IFGWM_mni_masked.png
- - stats.zip
- - participants.tsv
- - meanstd_all.json
- - sub-2120_rd.npy
- - sub-2120_nufo.npy
- - sub-2120_md.npy
- - sub-2120_fa.npy
- - sub-2120_afd_total.npy
- - sub-2120_afd_fixel.npy
- - sub-2120_ad.npy
- - sub-1230_rd.npy
- - sub-1230_nufo.npy
- - sub-1230_md.npy
- - sub-1230_fa.npy
- - sub-1230_afd_total.npy
- - sub-1230_afd_fixel.npy
- - sub-1230_ad.npy
- - sub-1108_rd.npy
- - sub-1108_nufo.npy
- - sub-1108_md.npy
- - sub-1108_fa.npy
- - sub-1108_afd_total.npy
- - sub-1108_afd_fixel.npy
- - sub-1108_ad.npy
- - sub-1005_rd.npy
- - sub-1005_nufo.npy
- - sub-1005_md.npy
- - sub-1005_fa.npy
- - sub-1005_afd_total.npy
- - sub-1005_afd_fixel.npy
- - sub-1005_ad.npy
- - list_id.txt
- - anatomical_filtering.zip
- - tractogram_filter_ana.trk
- - wmparc_filter_ana.nii.gz
- - btensor_testdata.zip
- - wm_frf.txt
- - spherical.bvecs
- - spherical.bvals
- - planar.bvecs
- - planar.bvals
- - md.nii.gz
- - linear.bvecs
- - linear.bvals
- - gm_frf.txt
- - fa.nii.gz
- - dwi_spherical.nii.gz
- - dwi_planar.nii.gz
- - dwi_linear.nii.gz
- - csf_frf.txt
- - fodf_filtering.zip
- - fodf_descoteaux07_sub_twice.nii.gz
- - fodf_descoteaux07_sub_sym.nii.gz
- - fodf_descoteaux07_sub_full.nii.gz
- - fodf_descoteaux07_sub.nii.gz
+- bids_json.zip
+ - result_real_dwi_real_rev_dwi_sbref.json
+ - result_real_dwi_real_rev_dwi.json
+ - result_complex_dwi_complex_rev_dwi_sbref.json
+ - result_real_dwi_epi.json
+ - result_complex_dwi_complex_rev_dwi.json
+ - result_complex_dwi_epi.json
+ - result_real_dwi_real_sbref.json
+ - result_complex_dwi_complex_sbref.json
+- plot.zip
+ - atlas_brainnetome.nii.gz
+ - ad.nii.gz
+ - fa.nii.gz
+ - map_gm.nii.gz
+ - map_wm.nii.gz
+ - mask_gm.nii.gz
+ - mask_wm.nii.gz
+ - atlas_brainnetome.json
+- ihMT.zip
+ - B1map.json
+ - B1map.nii.gz
+ - echo-1_acq-altnp_ihmt.json
+ - echo-1_acq-altnp_ihmt.nii.gz
+ - echo-1_acq-altpn_ihmt.json
+ - echo-1_acq-altpn_ihmt.nii.gz
+ - echo-1_acq-mtoff_ihmt.json
+ - echo-1_acq-mtoff_ihmt.nii.gz
+ - echo-1_acq-neg_ihmt.json
+ - echo-1_acq-neg_ihmt.nii.gz
+ - echo-1_acq-pos_ihmt.json
+ - echo-1_acq-pos_ihmt.nii.gz
+ - echo-1_acq-T1w_ihmt.json
+ - echo-1_acq-T1w_ihmt.nii.gz
+ - echo-2_acq-altnp_ihmt.json
+ - echo-2_acq-altnp_ihmt.nii.gz
+ - echo-2_acq-altpn_ihmt.json
+ - echo-2_acq-altpn_ihmt.nii.gz
+ - echo-2_acq-mtoff_ihmt.json
+ - echo-2_acq-mtoff_ihmt.nii.gz
+ - echo-2_acq-neg_ihmt.json
+ - echo-2_acq-neg_ihmt.nii.gz
+ - echo-2_acq-pos_ihmt.json
+ - echo-2_acq-pos_ihmt.nii.gz
+ - echo-2_acq-T1w_ihmt.json
+ - echo-2_acq-T1w_ihmt.nii.gz
+ - echo-3_acq-altnp_ihmt.json
+ - echo-3_acq-altnp_ihmt.nii.gz
+ - echo-3_acq-altpn_ihmt.json
+ - echo-3_acq-altpn_ihmt.nii.gz
+ - echo-3_acq-mtoff_ihmt.json
+ - echo-3_acq-mtoff_ihmt.nii.gz
+ - echo-3_acq-neg_ihmt.json
+ - echo-3_acq-neg_ihmt.nii.gz
+ - echo-3_acq-pos_ihmt.json
+ - echo-3_acq-pos_ihmt.nii.gz
+ - echo-3_acq-T1w_ihmt.json
+ - echo-3_acq-T1w_ihmt.nii.gz
+ - mask_resample.nii.gz
+- MT.zip
+ - mask.nii.gz
+ - sub-001_echo-1_acq-mtoff_mtsat.json
+ - sub-001_echo-1_acq-mtoff_mtsat.nii.gz
+ - sub-001_echo-1_acq-mton_mtsat.json
+ - sub-001_echo-1_acq-mton_mtsat.nii.gz
+ - sub-001_echo-1_acq-t1w_mtsat.json
+ - sub-001_echo-1_acq-t1w_mtsat.nii.gz
+ - sub-001_echo-2_acq-mtoff_mtsat.json
+ - sub-001_echo-2_acq-mtoff_mtsat.nii.gz
+ - sub-001_echo-2_acq-mton_mtsat.json
+ - sub-001_echo-2_acq-mton_mtsat.nii.gz
+ - sub-001_echo-2_acq-t1w_mtsat.json
+ - sub-001_echo-2_acq-t1w_mtsat.nii.gz
+ - sub-001_echo-3_acq-mtoff_mtsat.json
+ - sub-001_echo-3_acq-mtoff_mtsat.nii.gz
+ - sub-001_echo-3_acq-mton_mtsat.json
+ - sub-001_echo-3_acq-mton_mtsat.nii.gz
+ - sub-001_echo-3_acq-t1w_mtsat.json
+ - sub-001_echo-3_acq-t1w_mtsat.nii.gz
+ - sub-001_echo-4_acq-mtoff_mtsat.json
+ - sub-001_echo-4_acq-mtoff_mtsat.nii.gz
+ - sub-001_echo-4_acq-mton_mtsat.json
+ - sub-001_echo-4_acq-mton_mtsat.nii.gz
+ - sub-001_echo-4_acq-t1w_mtsat.json
+ - sub-001_echo-4_acq-t1w_mtsat.nii.gz
+ - sub-001_echo-5_acq-mtoff_mtsat.json
+ - sub-001_echo-5_acq-mtoff_mtsat.nii.gz
+ - sub-001_echo-5_acq-mton_mtsat.json
+ - sub-001_echo-5_acq-mton_mtsat.nii.gz
+ - sub-001_echo-5_acq-t1w_mtsat.json
+ - sub-001_echo-5_acq-t1w_mtsat.nii.gz
+ - sub-001_run-01_B1map.json
+ - sub-001_run-01_B1map.nii.gz
+- atlas.zip
+ - atlas_freesurfer_v2.nii.gz
+ - atlas_freesurfer_v2_LUT.json
+ - atlas_freesurfer_v2_labels_list.txt
+ - atlas_freesurfer_v2_no_brainstem.nii.gz
+ - atlas_freesurfer_v2_single_brainstem.nii.gz
+ - atlas_freesurfer_v2_single_brainstem_dil.nii.gz
+ - bash.sh
+ - brainstem.nii.gz
+ - brainstem_173.nii.gz
+ - brainstem_174.nii.gz
+ - brainstem_175.nii.gz
+ - brainstem_bin.nii.gz
+ - 10.nii.gz
+ - 1000.nii.gz
+ - 1001.nii.gz
+ - 1002.nii.gz
+ - 1003.nii.gz
+ - 1005.nii.gz
+ - 1006.nii.gz
+ - 1008.nii.gz
+ - 1009.nii.gz
+ - 1010.nii.gz
+ - 1011.nii.gz
+ - 1012.nii.gz
+ - 1013.nii.gz
+ - 1014.nii.gz
+ - 1015.nii.gz
+ - 1016.nii.gz
+ - 1017.nii.gz
+ - 1018.nii.gz
+ - 1019.nii.gz
+ - 1020.nii.gz
+ - 1021.nii.gz
+ - 1022.nii.gz
+ - 1023.nii.gz
+ - 1024.nii.gz
+ - 1025.nii.gz
+ - 1026.nii.gz
+ - 1027.nii.gz
+ - 1028.nii.gz
+ - 1029.nii.gz
+ - 1030.nii.gz
+ - 1031.nii.gz
+ - 1032.nii.gz
+ - 1033.nii.gz
+ - 1034.nii.gz
+ - 1035.nii.gz
+ - 11.nii.gz
+ - 12.nii.gz
+ - 13.nii.gz
+ - 17.nii.gz
+ - 173.nii.gz
+ - 174.nii.gz
+ - 175.nii.gz
+ - 18.nii.gz
+ - 2000.nii.gz
+ - 2001.nii.gz
+ - 2002.nii.gz
+ - 2003.nii.gz
+ - 2005.nii.gz
+ - 2006.nii.gz
+ - 2007.nii.gz
+ - 2008.nii.gz
+ - 2009.nii.gz
+ - 2010.nii.gz
+ - 2011.nii.gz
+ - 2012.nii.gz
+ - 2013.nii.gz
+ - 2014.nii.gz
+ - 2015.nii.gz
+ - 2016.nii.gz
+ - 2017.nii.gz
+ - 2018.nii.gz
+ - 2019.nii.gz
+ - 2020.nii.gz
+ - 2021.nii.gz
+ - 2022.nii.gz
+ - 2023.nii.gz
+ - 2024.nii.gz
+ - 2025.nii.gz
+ - 2026.nii.gz
+ - 2027.nii.gz
+ - 2028.nii.gz
+ - 2029.nii.gz
+ - 2030.nii.gz
+ - 2031.nii.gz
+ - 2032.nii.gz
+ - 2033.nii.gz
+ - 2034.nii.gz
+ - 2035.nii.gz
+ - 26.nii.gz
+ - 28.nii.gz
+ - 47.nii.gz
+ - 49.nii.gz
+ - 50.nii.gz
+ - 51.nii.gz
+ - 52.nii.gz
+ - 53.nii.gz
+ - 54.nii.gz
+ - 58.nii.gz
+ - 60.nii.gz
+ - 8.nii.gz
+ - 85.nii.gz
+ - 8_10.nii.gz
+ - left_accumbens_area.nii.gz
+ - left_amygdala.nii.gz
+ - left_banks_superior_temporal.nii.gz
+ - left_caudal_anterior_cingulate.nii.gz
+ - left_caudal_middle_fontral.nii.gz
+ - left_caudate.nii.gz
+ - left_cerebellum_cortex.nii.gz
+ - left_corpus_callosum.nii.gz
+ - left_cuneus.nii.gz
+ - left_entorhinal.nii.gz
+ - left_frontal_pole.nii.gz
+ - left_fusiform.nii.gz
+ - left_hippocampus.nii.gz
+ - left_inferior_parietal.nii.gz
+ - left_inferior_temporal.nii.gz
+ - left_insula.nii.gz
+ - left_isthmus_cingulate.nii.gz
+ - left_lateral_occipital.nii.gz
+ - left_laterral_orbitofrontal.nii.gz
+ - left_lingual.nii.gz
+ - left_medial_orbitofrontal.nii.gz
+ - left_middle_temporal.nii.gz
+ - left_pallidum.nii.gz
+ - left_paracentral.nii.gz
+ - left_parahipocampal.nii.gz
+ - left_parsopercularis.nii.gz
+ - left_parsorbitalis.nii.gz
+ - left_parstriangularis.nii.gz
+ - left_pericalcarine.nii.gz
+ - left_postcentral.nii.gz
+ - left_posteriorcingulate.nii.gz
+ - left_precentral.nii.gz
+ - left_precuneus.nii.gz
+ - left_putamen.nii.gz
+ - left_rostral_anterior_cingulate.nii.gz
+ - left_rostral_middle_frontal.nii.gz
+ - left_superior_frontral.nii.gz
+ - left_superior_parietal.nii.gz
+ - left_superior_temporal.nii.gz
+ - left_supra_marginal.nii.gz
+ - left_temporal_pole.nii.gz
+ - left_thalamus_proper.nii.gz
+ - left_transverse_temporal.nii.gz
+ - left_ventraldc.nii.gz
+ - midbrain.nii.gz
+ - oblongata.nii.gz
+ - pons.nii.gz
+ - right_accumbens_area.nii.gz
+ - right_amygdala.nii.gz
+ - right_banks_superior_temporal.nii.gz
+ - right_caudal_anterior_cingulate.nii.gz
+ - right_caudal_middle_fontral.nii.gz
+ - right_caudate.nii.gz
+ - right_cerebellum_cortex.nii.gz
+ - right_corpus_callosum.nii.gz
+ - right_cuneus.nii.gz
+ - right_entorhinal.nii.gz
+ - right_frontal_pole.nii.gz
+ - right_fusiform.nii.gz
+ - right_hippocampus.nii.gz
+ - right_inferior_parietal.nii.gz
+ - right_inferior_temporal.nii.gz
+ - right_insula.nii.gz
+ - right_isthmus_cingulate.nii.gz
+ - right_lateral_occipital.nii.gz
+ - right_laterral_orbitofrontal.nii.gz
+ - right_lingual.nii.gz
+ - right_medial_orbitofrontal.nii.gz
+ - right_middle_temporal.nii.gz
+ - right_pallidum.nii.gz
+ - right_paracentral.nii.gz
+ - right_parahipocampal.nii.gz
+ - right_parsopercularis.nii.gz
+ - right_parsorbitalis.nii.gz
+ - right_parstriangularis.nii.gz
+ - right_pericalcarine.nii.gz
+ - right_postcentral.nii.gz
+ - right_posteriorcingulate.nii.gz
+ - right_precentral.nii.gz
+ - right_precuneus.nii.gz
+ - right_putamen.nii.gz
+ - right_rostral_anterior_cingulate.nii.gz
+ - right_rostral_middle_frontal.nii.gz
+ - right_superior_frontral.nii.gz
+ - right_superior_parietal.nii.gz
+ - right_superior_temporal.nii.gz
+ - right_supra_marginal.nii.gz
+ - right_temporal_pole.nii.gz
+ - right_thalamus_proper.nii.gz
+ - right_transverse_temporal.nii.gz
+ - right_ventraldc.nii.gz
+- bst.zip
+ - todi_mask.nii.gz
+ - template_lin.nii.gz
+ - rpt_m_warp.trk
+ - rpt_m_lin.trk
+ - output1InverseWarp.nii.gz
+ - output0GenericAffine.mat
+ - out_lw_tdi.nii.gz
+ - mask.nii.gz
+ - lw_todi_sh.nii.gz
+ - fodf.nii.gz
+ - fa.nii.gz
+ - bash.sh
+ - template0.nii.gz
+ - rpt_m.trk
+ - todi_mask.nii.gz
+ - priors.nii.gz
+ - endpoints_mask.nii.gz
+ - efod.nii.gz
+- bundles.zip
+ - transformation_rigid.txt
+ - sagittal_glass.png
+ - sagittal_3d.png
+ - coronal_glass.png
+ - coronal_3d.png
+ - clusters.pkl
+ - bundle_all_1mm_ic.trk
+ - bundle_all_1mm.trk
+ - bundle_all_1mm.nii.gz
+ - bundle_0_similarity.json
+ - bundle_0_reco.tck
+ - bundle_0_measures.json
+ - bundle_0_binary.json
+ - bash.sh
+ - axial_glass.png
+ - axial_3d.png
+ - affine.txt
+ - results.json
+ - logfile.txt
+ - bundle_6.trk
+ - bundle_5.trk
+ - bundle_4.trk
+ - bundle_3.trk
+ - bundle_2.trk
+ - bundle_1.trk
+ - bundle_0.trk
+ - default_config_sim.json
+ - bundle_all_1mm.nii.gz
+ - bundle_6.trk
+ - bundle_5.trk
+ - bundle_4.trk
+ - bundle_3.trk
+ - bundle_2.trk
+ - bundle_1.trk
+ - bundle_0.trk
+ - bundle_6.trk
+ - bundle_5.trk
+ - bundle_4.trk
+ - bundle_3.trk
+ - bundle_2.trk
+ - bundle_1.trk
+ - bundle_0.trk
+ - bundle_6.trk
+ - bundle_5.trk
+ - bundle_4.trk
+ - bundle_3.trk
+ - bundle_2.trk
+ - bundle_1.trk
+ - bundle_0.trk
+- commit_amico.zip
+ - cmd
+ - tracking.trk
+ - dwi.bvec
+ - dwi.bval
+ - wm_frf.txt
+ - gm_frf.txt
+ - csf_frf.txt
+ - peaks.nii.gz
+ - mask.nii.gz
+ - md.nii.gz
+ - fa.nii.gz
+ - dwi.nii.gz
+ - ad.nii.gz
+- connectivity.zip
+ - vol.npy
+ - success.txt
+ - sim.npy
+ - sc_thr.npy
+ - sc_reo_fake.npy
+ - sc_normalize.npy
+ - sc_norm_vol.npy
+ - sc_norm.png
+ - sc_norm.npy
+ - sc_masked.npy
+ - sc_lower_threshold.npy
+ - sc_add_10.npy
+ - sc.npy
+ - reorder.txt
+ - pval.npy
+ - mask.npy
+ - len.npy
+ - labels_list.txt
+ - gtm.json
+ - fodf.nii.gz
+ - endpoints_atlas.nii.gz
+ - decompose_afd_rd.h5
+ - decompose.h5
+ - bundle_all_1mm.trk
+ - bash.sh
+ - affine.txt
+ - afd_max.npy
+ - afd_max.nii.gz
+ - 9_9.trk
+ - 5_6.trk
+ - 4_8.trk
+ - 3_7.trk
+ - 2_7.trk
+ - 1_7.trk
+ - 1_10.trk
+ - 9_9.nii.gz
+ - 5_6.nii.gz
+ - 4_8.nii.gz
+ - 3_7.nii.gz
+ - 2_7.nii.gz
+ - 1_7.nii.gz
+ - 1_10.nii.gz
+- filtering.zip
+ - voting_voxels.nii.gz
+ - voting_streamlines.trk
+ - sc.bdo
+ - mosaic.png
+ - mask.nii.gz
+ - centroids.trk
+ - bundle_all_1mm_inliers.trk
+ - bundle_all_1mm.trk
+ - bundle_all_1mm.nii.gz
+ - bundle_4_filtered_no_loops.trk
+ - bundle_4_filtered.trk
+ - bundle_4_filtered.nii.gz
+ - bundle_4.trk
+ - bash.sh
+ - cluster_9.trk
+ - cluster_8.trk
+ - cluster_7.trk
+ - cluster_6.trk
+ - cluster_5.trk
+ - cluster_4.trk
+ - cluster_3.trk
+ - cluster_2.trk
+ - cluster_19.trk
+ - cluster_18.trk
+ - cluster_17.trk
+ - cluster_16.trk
+ - cluster_15.trk
+ - cluster_14.trk
+ - cluster_13.trk
+ - cluster_12.trk
+ - cluster_11.trk
+ - cluster_10.trk
+ - cluster_1.trk
+ - cluster_0.trk
+- others.zip
+ - t1_reshape.nii.gz
+ - t1_resample.nii.gz
+ - t1_crop_denoised.nii.gz
+ - t1_crop.nii.gz
+ - t1.nii.gz
+ - rgb\_.nii.gz
+ - rgb.nii.gz
+ - fibercup_bundles_color.trk
+ - fibercup_bundles.trk
+ - fibercup_bundle_0_color.trk
+ - fibercup_bundle_0.trk
+ - fa_resample.nii.gz
+ - fa.nii.gz
+ - encoding.b
+ - empty.trk
+ - density.nii.gz
+ - bash.sh
+ - atlas_freesurfer_v2_LUT.json
+ - atlas_freesurfer_v2.nii.gz
+ - IFGWM_sub.trk
+ - IFGWM.trk
+- processing.zip
+ - fodf_descoteaux07_sub_full.nii.gz
+ - fodf_descoteaux07_sub.nii.gz
+ - fd.nii.gz
+ - fodf_bingham.nii.gz
+ - dwi_noise_mask.nii.gz
+ - 1000.b
+ - 1000.bval
+ - 1000.bvec
+ - 1000_flip.b
+ - 3000.bval
+ - 3000.bvec
+ - ad.nii.gz
+ - ad_ransanc.nii.gz
+ - afd_max.nii.gz
+ - afd_sum.nii.gz
+ - afd_test.nii.gz
+ - afd_tot.nii.gz
+ - b0_mean.nii.gz
+ - b0_mean_n4.nii.gz
+ - bias_field_b0.nii.gz
+ - diff.nii.gz
+ - dki_ad.nii.gz
+ - dki_fa.nii.gz
+ - dki_md.nii.gz
+ - dki_rd.nii.gz
+ - dwi.bval
+ - dwi.bvec
+ - dwi.nii.gz
+ - dwi_crop.nii.gz
+ - dwi_crop_1000.nii.gz
+ - dwi_crop_3000.nii.gz
+ - dwi_crop_n4.nii.gz
+ - fa.nii.gz
+ - fa_low.nii.gz
+ - fa_thr.nii.gz
+ - fodf.nii.gz
+ - fodf_descoteaux07.nii.gz
+ - frf.txt
+ - md.nii.gz
+ - mfrf.txt
+ - mni_masked_2x2x2.nii.gz
+ - nfrf.txt
+ - nufo.nii.gz
+ - peaks.nii.gz
+ - rd.nii.gz
+ - rd_test.nii.gz
+ - seed.nii.gz
+ - sh.nii.gz
+ - sh_1000.nii.gz
+ - sh_3000.nii.gz
+ - tracking.trk
+ - cc.nii.gz
+ - dwi_graph.png
+ - dwi_SNR.json
+ - small_roi_gm_mask.nii.gz
+ - axial.png
+ - coronal.png
+ - sagittal.png
+- surface_vtk_fib.zip
+ - rhpialt.vtk
+ - log.txt
+ - lhpialt_smooth.vtk
+ - lhpialt_lin.vtk
+ - lhpialt.vtk
+ - lh.pialt_xform
+ - gyri_fanning_c.trk
+ - gyri_fanning.trk
+ - gyri_fanning.tck
+ - gyri_fanning.fib
+ - fa_flip.nii.gz
+ - fa.nii.gz
+ - bash.sh
+ - affine.txt
+- tracking.zip
+ - interface.nii.gz
+ - bash.sh
+ - fa.nii.gz
+ - fodf.nii.gz
+ - local.trk
+ - local_split_0.trk
+ - local_split_1.trk
+ - local_split_2.trk
+ - map_csf.nii.gz
+ - map_exclude.nii.gz
+ - map_exclude_corr.nii.gz
+ - map_gm.nii.gz
+ - map_include.nii.gz
+ - map_include_corr.nii.gz
+ - map_wm.nii.gz
+ - peaks.nii.gz
+ - pft.trk
+ - seeding_mask.nii.gz
+ - union.trk
+ - union_shuffle.trk
+ - union_shuffle_sub.trk
+ - union_shuffle_sub_smooth.trk
+- tractograms.zip
+ - bundle_4_cut_endpoints.tck
+ - bundle_4_cut_center.tck
+ - bundle_4_endpoints_5points.nii.gz
+ - bundle_4_center.nii.gz
+ - bundle_4_head_tail.nii.gz
+ - bundle_4_head_tail_offset.nii.gz
+ - bundle_4.tck
+ - bundle_4_endpoints_1point.nii.gz
+ - bundle_4_wm.nii.gz
+ - bundle_4_endpoints_1point.nii.gz
+ - bundle_4_cut_endpoints.tck
+ - bundle_4_center.nii.gz
+ - bundle_4_head_tail.nii.gz
+ - bundle_4_head_tail_offset.nii.gz
+ - bundle_4.tck
+ - bundle_4_wm.nii.gz
+ - bundle_4_cut_center.tck
+ - bundle_4_endpoints_5points.nii.gz
+- tractometry.zip
+ - tail.nii.gz
+ - mni_masked.nii.gz
+ - metric_label.json
+ - length_stats_2.json
+ - length_stats_1.json
+ - length_stats.xlsx
+ - label.npz
+ - head.nii.gz
+ - distance.npz
+ - bash.sh
+ - IFGWM_uni_c_10.trk
+ - IFGWM_uni_c.trk
+ - IFGWM_uni.trk
+ - IFGWM_labels_map.nii.gz
+ - IFGWM_color.trk
+ - IFGWM.trk
+ - IFGWM.nii.gz
+ - IFGWM_mni_masked.png
+- stats.zip
+ - participants.tsv
+ - meanstd_all.json
+ - sub-2120_rd.npy
+ - sub-2120_nufo.npy
+ - sub-2120_md.npy
+ - sub-2120_fa.npy
+ - sub-2120_afd_total.npy
+ - sub-2120_afd_fixel.npy
+ - sub-2120_ad.npy
+ - sub-1230_rd.npy
+ - sub-1230_nufo.npy
+ - sub-1230_md.npy
+ - sub-1230_fa.npy
+ - sub-1230_afd_total.npy
+ - sub-1230_afd_fixel.npy
+ - sub-1230_ad.npy
+ - sub-1108_rd.npy
+ - sub-1108_nufo.npy
+ - sub-1108_md.npy
+ - sub-1108_fa.npy
+ - sub-1108_afd_total.npy
+ - sub-1108_afd_fixel.npy
+ - sub-1108_ad.npy
+ - sub-1005_rd.npy
+ - sub-1005_nufo.npy
+ - sub-1005_md.npy
+ - sub-1005_fa.npy
+ - sub-1005_afd_total.npy
+ - sub-1005_afd_fixel.npy
+ - sub-1005_ad.npy
+ - list_id.txt
+- anatomical_filtering.zip
+ - tractogram_filter_ana.trk
+ - wmparc_filter_ana.nii.gz
+- btensor_testdata.zip
+ - wm_frf.txt
+ - spherical.bvecs
+ - spherical.bvals
+ - planar.bvecs
+ - planar.bvals
+ - md.nii.gz
+ - linear.bvecs
+ - linear.bvals
+ - gm_frf.txt
+ - fa.nii.gz
+ - dwi_spherical.nii.gz
+ - dwi_planar.nii.gz
+ - dwi_linear.nii.gz
+ - csf_frf.txt
+- fodf_filtering.zip
+ - fodf_descoteaux07_sub_twice.nii.gz
+ - fodf_descoteaux07_sub_sym.nii.gz
+ - fodf_descoteaux07_sub_full.nii.gz
+ - fodf_descoteaux07_sub.nii.gz
diff --git a/docs/pull_request_template.md b/docs/pull_request_template.md
index becc2918d..6b7e8ff4e 100644
--- a/docs/pull_request_template.md
+++ b/docs/pull_request_template.md
@@ -6,13 +6,13 @@
- Create the tool:
- [ ] Edit `./modules/nf-scil///main.nf`
- - [ ] Edit `./modules/nf-scil///meta.yml`
+ - [ ] Edit `./modules/nf-scil///meta.yml`
- Generate the tests:
- [ ] Edit `./tests/modules/nf-scil///main.nf`
- [ ] Edit `./tests/modules/nf-scil///nextflow.config`
- [ ] Add test data locally for tests with the fork repository
- - [ ] Generate the test infrastructure and *md5sum* for all outputs
- - [ ] Test the module in a **REAL** DSL2 pipeline or a *dummy* one
+ - [ ] Generate the test infrastructure and _md5sum_ for all outputs
+ - [ ] Test the module in a **REAL** DSL2 pipeline or a _dummy_ one
- Ensure the syntax is correct :
- [ ] Check indentation abides with the rest of the library (don't hesitate to correct others !)
- [ ] Lint everything. Ensure your variables have good names.
diff --git a/modules/nf-scil/betcrop/fslbetcrop/meta.yml b/modules/nf-scil/betcrop/fslbetcrop/meta.yml
index ffe9c5ed8..a047812ba 100644
--- a/modules/nf-scil/betcrop/fslbetcrop/meta.yml
+++ b/modules/nf-scil/betcrop/fslbetcrop/meta.yml
@@ -58,7 +58,7 @@ output:
- bbox:
type: file
- description: DWI BoundingBox used for cropping.
+ description: DWI BoundingBox used for cropping.
pattern: "*dwi_boundingBox.pkl"
- versions:
diff --git a/modules/nf-scil/denoising/mppca/meta.yml b/modules/nf-scil/denoising/mppca/meta.yml
index 753824015..ea3dc9b87 100644
--- a/modules/nf-scil/denoising/mppca/meta.yml
+++ b/modules/nf-scil/denoising/mppca/meta.yml
@@ -1,7 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "denoising_mppca"
-description: denoise a dataset with the Marchenko-Pastur principal component analysis
+description: denoise a dataset with the Marchenko-Pastur principal component analysis
keywords:
- nifti
- denoising
diff --git a/modules/nf-scil/preproc/gibbs/meta.yml b/modules/nf-scil/preproc/gibbs/meta.yml
index 494efb967..fab72e822 100644
--- a/modules/nf-scil/preproc/gibbs/meta.yml
+++ b/modules/nf-scil/preproc/gibbs/meta.yml
@@ -18,7 +18,7 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
-
+
- dwi:
type: file
description: Nifti image file to correct
diff --git a/modules/nf-scil/preproc/n4/meta.yml b/modules/nf-scil/preproc/n4/meta.yml
index 055dae56c..59b140cd2 100644
--- a/modules/nf-scil/preproc/n4/meta.yml
+++ b/modules/nf-scil/preproc/n4/meta.yml
@@ -17,7 +17,7 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
-
+
- dwi:
type: file
description: Nifti image file to correct
@@ -31,7 +31,7 @@ input:
- b0_mask:
type: file
description: Nifti image file mask
- pattern: "*.{nii,nii.gz}"
+ pattern: "*.{nii,nii.gz}"
output:
- meta:
diff --git a/modules/nf-scil/reconst/dtimetrics/meta.yml b/modules/nf-scil/reconst/dtimetrics/meta.yml
index 7e623e4f6..1bc1bc21f 100644
--- a/modules/nf-scil/reconst/dtimetrics/meta.yml
+++ b/modules/nf-scil/reconst/dtimetrics/meta.yml
@@ -19,7 +19,7 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
-
+
- dwi:
type: file
description: Nifti DWI volume used to extract DTI metrics.
@@ -134,16 +134,16 @@ output:
- nonphysical:
type: file
- description: Output filename for the voxels with physically implausible
- signals where the mean of b=0 images is below one or more
- diffusion-weighted images.
+ description: Output filename for the voxels with physically implausible
+ signals where the mean of b=0 images is below one or more
+ diffusion-weighted images.
pattern: "*__nonphysical.{nii,nii.gz}"
- pulsation_std_dwi:
type: file
- description: Standard deviation map across all diffusion-weighted images
- and across b=0 images if more than one is available.Shows
- pulsation and misalignment artifacts.
+ description: Standard deviation map across all diffusion-weighted images
+ and across b=0 images if more than one is available.Shows
+ pulsation and misalignment artifacts.
pattern: "*__pulsation_std_dwi.{nii,nii.gz}"
- residual:
diff --git a/modules/nf-scil/reconst/frf/meta.yml b/modules/nf-scil/reconst/frf/meta.yml
index a1f875495..b0210067f 100644
--- a/modules/nf-scil/reconst/frf/meta.yml
+++ b/modules/nf-scil/reconst/frf/meta.yml
@@ -21,7 +21,7 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
-
+
- dwi:
type: file
description: Nifti image of DWI.
diff --git a/modules/nf-scil/reconst/meanfrf/meta.yml b/modules/nf-scil/reconst/meanfrf/meta.yml
index 5e64e4ac5..a37a30d5c 100644
--- a/modules/nf-scil/reconst/meanfrf/meta.yml
+++ b/modules/nf-scil/reconst/meanfrf/meta.yml
@@ -2,7 +2,7 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "reconst_meanfrf"
description: Compute the mean Fiber Response Function from a set of individually
- computed Response Functions.
+ computed Response Functions.
keywords:
- FRF
@@ -12,14 +12,12 @@ tools:
homepage: "https://github.com/scilus/scilpy.git"
input:
-
- frf_list:
type: Path
description: List of individual Fiber Response Function (FRF) path.
pattern: "*.txt"
output:
-
- meanfrf:
type: file
description: Averaged Fiber Response Function (FRF).
diff --git a/modules/nf-scil/reconst/noddi/meta.yml b/modules/nf-scil/reconst/noddi/meta.yml
index d2813ec84..105372982 100644
--- a/modules/nf-scil/reconst/noddi/meta.yml
+++ b/modules/nf-scil/reconst/noddi/meta.yml
@@ -92,4 +92,4 @@ output:
pattern: "versions.yml"
authors:
- - "@Manonedde"
\ No newline at end of file
+ - "@Manonedde"
diff --git a/modules/nf-scil/segmentation/fastseg/meta.yml b/modules/nf-scil/segmentation/fastseg/meta.yml
index b3c689982..440c8fd7f 100644
--- a/modules/nf-scil/segmentation/fastseg/meta.yml
+++ b/modules/nf-scil/segmentation/fastseg/meta.yml
@@ -35,7 +35,7 @@ output:
- wm_mask:
type: file
- description: Nifti WM mask volume.
+ description: Nifti WM mask volume.
pattern: "*.{nii,nii.gz}"
- gm_mask:
diff --git a/modules/nf-scil/segmentation/freesurferseg/meta.yml b/modules/nf-scil/segmentation/freesurferseg/meta.yml
index d59aad005..cb1663a7f 100644
--- a/modules/nf-scil/segmentation/freesurferseg/meta.yml
+++ b/modules/nf-scil/segmentation/freesurferseg/meta.yml
@@ -19,10 +19,10 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
-
+
- aparc_aseg:
type: file
- description: FreeSurfer cortical and subcortical parcellation output file.
+ description: FreeSurfer cortical and subcortical parcellation output file.
pattern: "*.mgz"
- wmparc:
@@ -44,12 +44,12 @@ output:
- gm_mask:
type: file
- description: Nifti GM mask file.
+ description: Nifti GM mask file.
pattern: "*.{nii,nii.gz}"
- csf_mask:
type: file
- description: Nifti CSF mask file.
+ description: Nifti CSF mask file.
pattern: "*.{nii,nii.gz}"
- versions:
diff --git a/modules/nf-scil/testdata/scilpy/meta.yml b/modules/nf-scil/testdata/scilpy/meta.yml
index 1d877ec82..f5e7edd05 100644
--- a/modules/nf-scil/testdata/scilpy/meta.yml
+++ b/modules/nf-scil/testdata/scilpy/meta.yml
@@ -22,14 +22,14 @@ input:
- test_data_path:
type: file
description: Directory where to store the test data
- pattern: "*"
+ pattern: "*"
output:
- test_data_path:
type: file
description: Directory where to store the test data
- pattern: "*"
-
+ pattern: "*"
+
- versions:
type: file
description: File containing software versions
diff --git a/modules/nf-scil/tracking/pfttracking/meta.yml b/modules/nf-scil/tracking/pfttracking/meta.yml
index c891c1835..d2b8c5167 100644
--- a/modules/nf-scil/tracking/pfttracking/meta.yml
+++ b/modules/nf-scil/tracking/pfttracking/meta.yml
@@ -2,9 +2,9 @@
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: "tracking_pfttracking"
description: Compute include and exclude maps, and the seeding mask
- from partial volume estimation (PVE) maps.
- Generates a tractogram using anatomically-constrained particle
- filter tracking, Particle Filtering Tractography (PFT).
+ from partial volume estimation (PVE) maps.
+ Generates a tractogram using anatomically-constrained particle
+ filter tracking, Particle Filtering Tractography (PFT).
keywords:
- PFT
- tractography
diff --git a/modules/nf-scil/utils/extractb0/meta.yml b/modules/nf-scil/utils/extractb0/meta.yml
index bd2141e15..4073264ef 100644
--- a/modules/nf-scil/utils/extractb0/meta.yml
+++ b/modules/nf-scil/utils/extractb0/meta.yml
@@ -18,7 +18,7 @@ input:
description: |
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
-
+
- dwi:
type: file
description: Nifti DWI volume to perform BET + crop.
diff --git a/nf-scil-extensions/.vscode/launch.json b/nf-scil-extensions/.vscode/launch.json
index 0e191b592..ace09d79f 100644
--- a/nf-scil-extensions/.vscode/launch.json
+++ b/nf-scil-extensions/.vscode/launch.json
@@ -3,15 +3,13 @@
// Hover to view descriptions of existing attributes.
// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
{
- "version": "0.2.0",
+ "version": "0.2.0",
"configurations": [
{
"name": "Extension",
"type": "extensionHost",
"request": "launch",
- "args": [
- "--extensionDevelopmentPath=${workspaceFolder}"
- ]
+ "args": ["--extensionDevelopmentPath=${workspaceFolder}"]
}
]
-}
\ No newline at end of file
+}
diff --git a/nf-scil-extensions/package.json b/nf-scil-extensions/package.json
index 4d250188b..3b190d55c 100644
--- a/nf-scil-extensions/package.json
+++ b/nf-scil-extensions/package.json
@@ -1,51 +1,51 @@
{
- "name": "nf-scil-extensions",
- "displayName": "nf-scil-extensions",
- "description": "Extension pack for VS Code development of nf-scil",
- "repository": {
- "type": "git",
- "url": "https://github.com/scilus/nf-scil.git"
- },
- "icon": "icon.avif",
- "version": "0.0.2",
- "publisher": "AlexVCaron",
- "engines": {
- "vscode": "^1.84.0"
- },
- "categories": [
- "Extension Packs"
- ],
- "extensionPack": [
- "bierner.github-markdown-preview",
- "bierner.markdown-checkbox",
- "bierner.markdown-emoji",
- "bierner.markdown-footnotes",
- "bierner.markdown-mermaid",
- "bierner.markdown-preview-github-styles",
- "bierner.markdown-yaml-preamble",
- "github.vscode-github-actions",
- "GitHub.vscode-pull-request-github",
- "mhutchie.git-graph",
- "ms-azuretools.vscode-docker",
- "ms-python.isort",
- "ms-python.python",
- "ms-python.vscode-pylance",
- "ms-vscode-remote.remote-containers",
- "ms-vscode-remote.remote-ssh",
- "ms-vscode-remote.remote-ssh-edit",
- "ms-vscode-remote.remote-wsl",
- "ms-vscode-remote.vscode-remote-extensionpack",
- "ms-vscode.cmake-tools",
- "ms-vscode.cpptools",
- "ms-vscode.cpptools-extension-pack",
- "ms-vscode.cpptools-themes",
- "ms-vscode.makefile-tools",
- "ms-vscode.remote-explorer",
- "ms-vscode.remote-server",
- "ms-vsliveshare.vsliveshare",
- "nf-core.nf-core-extensionpack",
- "twxs.cmake",
- "yahyabatulu.vscode-markdown-alert",
- "yzhang.markdown-all-in-one"
- ]
+ "name": "nf-scil-extensions",
+ "displayName": "nf-scil-extensions",
+ "description": "Extension pack for VS Code development of nf-scil",
+ "repository": {
+ "type": "git",
+ "url": "https://github.com/scilus/nf-scil.git"
+ },
+ "icon": "icon.avif",
+ "version": "0.0.2",
+ "publisher": "AlexVCaron",
+ "engines": {
+ "vscode": "^1.84.0"
+ },
+ "categories": [
+ "Extension Packs"
+ ],
+ "extensionPack": [
+ "bierner.github-markdown-preview",
+ "bierner.markdown-checkbox",
+ "bierner.markdown-emoji",
+ "bierner.markdown-footnotes",
+ "bierner.markdown-mermaid",
+ "bierner.markdown-preview-github-styles",
+ "bierner.markdown-yaml-preamble",
+ "github.vscode-github-actions",
+ "GitHub.vscode-pull-request-github",
+ "mhutchie.git-graph",
+ "ms-azuretools.vscode-docker",
+ "ms-python.isort",
+ "ms-python.python",
+ "ms-python.vscode-pylance",
+ "ms-vscode-remote.remote-containers",
+ "ms-vscode-remote.remote-ssh",
+ "ms-vscode-remote.remote-ssh-edit",
+ "ms-vscode-remote.remote-wsl",
+ "ms-vscode-remote.vscode-remote-extensionpack",
+ "ms-vscode.cmake-tools",
+ "ms-vscode.cpptools",
+ "ms-vscode.cpptools-extension-pack",
+ "ms-vscode.cpptools-themes",
+ "ms-vscode.makefile-tools",
+ "ms-vscode.remote-explorer",
+ "ms-vscode.remote-server",
+ "ms-vsliveshare.vsliveshare",
+ "nf-core.nf-core-extensionpack",
+ "twxs.cmake",
+ "yahyabatulu.vscode-markdown-alert",
+ "yzhang.markdown-all-in-one"
+ ]
}
diff --git a/nf-scil-extensions/vsc-extension-quickstart.md b/nf-scil-extensions/vsc-extension-quickstart.md
index 2086acfec..1b1f14a4f 100644
--- a/nf-scil-extensions/vsc-extension-quickstart.md
+++ b/nf-scil-extensions/vsc-extension-quickstart.md
@@ -2,20 +2,20 @@
## What's in the folder
-* This folder contains all of the files necessary for your extension pack.
-* `package.json` - this is the manifest file that defines the list of extensions of the extension pack.
+- This folder contains all of the files necessary for your extension pack.
+- `package.json` - this is the manifest file that defines the list of extensions of the extension pack.
## Get up and running straight away
-* Press `F5` to open a new window with your extension loaded.
-* Open `Extensions Viewlet` and check your extensions are installed.
+- Press `F5` to open a new window with your extension loaded.
+- Open `Extensions Viewlet` and check your extensions are installed.
## Make changes
-* You can relaunch the extension from the debug toolbar after making changes to the files listed above.
-* You can also reload (`Ctrl+R` or `Cmd+R` on Mac) the VS Code window with your extension to load your changes.
+- You can relaunch the extension from the debug toolbar after making changes to the files listed above.
+- You can also reload (`Ctrl+R` or `Cmd+R` on Mac) the VS Code window with your extension to load your changes.
## Install your extension
-* To start using your extension with Visual Studio Code copy it into the `/.vscode/extensions` folder and restart Code.
-* To share your extension with the world, read on https://code.visualstudio.com/docs about publishing an extension.
+- To start using your extension with Visual Studio Code copy it into the `/.vscode/extensions` folder and restart Code.
+- To share your extension with the world, read on https://code.visualstudio.com/docs about publishing an extension.
diff --git a/tests/modules/nf-scil/tracking/localtracking/test.yml b/tests/modules/nf-scil/tracking/localtracking/test.yml
index 612414541..f3c40f62a 100644
--- a/tests/modules/nf-scil/tracking/localtracking/test.yml
+++ b/tests/modules/nf-scil/tracking/localtracking/test.yml
@@ -8,7 +8,7 @@
md5sum: e4e926fce399749c2cd68c92eccf04be
- path: output/wm/test__local_tracking.trk
contains:
- - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead '
+ - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
- path: output/wm/test__local_tracking_config.json
md5sum: c250bbac61d4f4a377d29dc0be4efada
- path: output/wm/test__local_tracking_mask.nii.gz
@@ -25,7 +25,7 @@
md5sum: 49c19bc6c0f47af32dea7af992b40490
- path: output/fa/test__local_tracking.trk
contains:
- - '# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead '
+ - "# TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead "
- path: output/fa/test__local_tracking_config.json
md5sum: 2e37c9f077b7d1422c54b39be37590db
- path: output/fa/test__local_tracking_mask.nii.gz
From 7a72b39a006786157f0147ff9818b08e68bbc3c8 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Mon, 8 Jan 2024 21:38:56 +0000
Subject: [PATCH 17/41] add other ignores for prettier
---
.prettierignore | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/.prettierignore b/.prettierignore
index 701ff1e7b..bf54d8208 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -8,3 +8,8 @@ nf_core/module-template/tests/tags.yml
nf_core/subworkflow-template/tests/tags.yml
.github
.devcontainer
+.vscode
+venv
+.venv
+.test_data
+.pytest_cache
From 45495b3c4dd3d6fdcec42b6d880658836b31a46e Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Mon, 8 Jan 2024 22:00:17 +0000
Subject: [PATCH 18/41] fix editorconfig
---
.devcontainer/Dockerfile | 22 ++++----
.github/ISSUE_TEMPLATE/bug_report.md | 6 +--
.gitignore | 2 +-
docs/generate_scil_data_md.py | 4 +-
modules/nf-scil/betcrop/fslbetcrop/main.nf | 2 +-
modules/nf-scil/denoising/mppca/main.nf | 2 +-
modules/nf-scil/denoising/nlmeans/main.nf | 2 +-
modules/nf-scil/reconst/fodf/main.nf | 4 +-
modules/nf-scil/reconst/frf/main.nf | 3 +-
modules/nf-scil/reconst/noddi/main.nf | 2 +-
.../segmentation/freesurferseg/main.nf | 50 ++++++++++---------
.../nf-scil/tracking/localtracking/main.nf | 2 +-
modules/nf-scil/tracking/pfttracking/main.nf | 2 +-
13 files changed, 53 insertions(+), 50 deletions(-)
diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index ab225177f..c2dad6abe 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,11 +1,11 @@
-FROM scilus/scilus:1.6.0
-
-RUN apt update && apt install -y \
- git \
- python3-venv \
- wget \
- && rm -rf /var/lib/apt/lists/*
-
-RUN python3 -m pip install pipx && \
- python3 -m pipx ensurepath && \
- pipx install poetry
+FROM scilus/scilus:1.6.0
+
+RUN apt update && apt install -y \
+ git \
+ python3-venv \
+ wget \
+ && rm -rf /var/lib/apt/lists/*
+
+RUN python3 -m pip install pipx && \
+ python3 -m pipx ensurepath && \
+ pipx install poetry
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index c887f4986..8ed9b5239 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -8,9 +8,9 @@ assignees: AlexVCaron
---
**System (complete the following information, else the issue will be closed):**
- - OS: [e.g. Ubuntu, CentOS, other Linux distributions, MacOS, WSL, Windows, ...]
- - Python version [e.g. 3.10, PyPa 3.7, CPython 3.9, ...]
- - `nf-scil` version [e.g. 1.0.0, 1.2.post3, 0.1.dev0, main, feat/awesome_module, ...]
+ - OS: [e.g. Ubuntu, CentOS, other Linux distributions, MacOS, WSL, Windows, ...]
+ - Python version [e.g. 3.10, PyPa 3.7, CPython 3.9, ...]
+ - `nf-scil` version [e.g. 1.0.0, 1.2.post3, 0.1.dev0, main, feat/awesome_module, ...]
**Describe the bug**
A clear and concise description of what the bug is.
diff --git a/.gitignore b/.gitignore
index 9c575d5ed..f56ee8e99 100644
--- a/.gitignore
+++ b/.gitignore
@@ -6,4 +6,4 @@
*.vsix
.DS_Store
-*.code-workspace
\ No newline at end of file
+*.code-workspace
diff --git a/docs/generate_scil_data_md.py b/docs/generate_scil_data_md.py
index ae006cd4a..567215512 100644
--- a/docs/generate_scil_data_md.py
+++ b/docs/generate_scil_data_md.py
@@ -21,7 +21,7 @@ def _unpack_archive(_upload_root, _archive, _test_dict, _fetcher):
_fetcher(_test_dict, _archive)
return os.path.join(_upload_root, ".".join(_archive.split(".")[:-1]))
-
+
def main():
@@ -69,4 +69,4 @@ def main():
if __name__ == '__main__':
- main()
\ No newline at end of file
+ main()
diff --git a/modules/nf-scil/betcrop/fslbetcrop/main.nf b/modules/nf-scil/betcrop/fslbetcrop/main.nf
index ba25ac9ae..f1acaee0c 100644
--- a/modules/nf-scil/betcrop/fslbetcrop/main.nf
+++ b/modules/nf-scil/betcrop/fslbetcrop/main.nf
@@ -54,7 +54,7 @@ process BETCROP_FSLBETCROP {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
-
+
"""
scil_extract_b0.py -h
bet -h
diff --git a/modules/nf-scil/denoising/mppca/main.nf b/modules/nf-scil/denoising/mppca/main.nf
index c2ff182a5..15b6b1252 100644
--- a/modules/nf-scil/denoising/mppca/main.nf
+++ b/modules/nf-scil/denoising/mppca/main.nf
@@ -20,7 +20,7 @@ process DENOISING_MPPCA {
script:
def prefix = task.ext.prefix ?: "${meta.id}"
def extent = task.ext.extent ? "-extent " + task.ext.extent : ""
-
+
"""
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
export OMP_NUM_THREADS=1
diff --git a/modules/nf-scil/denoising/nlmeans/main.nf b/modules/nf-scil/denoising/nlmeans/main.nf
index c913d6290..097ba09b6 100644
--- a/modules/nf-scil/denoising/nlmeans/main.nf
+++ b/modules/nf-scil/denoising/nlmeans/main.nf
@@ -37,7 +37,7 @@ process DENOISING_NLMEANS {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
-
+
"""
scil_run_nlmeans.py -h
diff --git a/modules/nf-scil/reconst/fodf/main.nf b/modules/nf-scil/reconst/fodf/main.nf
index 0bff1bd66..52f1e42a3 100644
--- a/modules/nf-scil/reconst/fodf/main.nf
+++ b/modules/nf-scil/reconst/fodf/main.nf
@@ -52,11 +52,11 @@ process RECONST_FODF {
scil_extract_dwi_shell.py $dwi $bval $bvec $fodf_shells \
dwi_fodf_shells.nii.gz bval_fodf_shells bvec_fodf_shells \
$dwi_shell_tolerance -f
-
+
scil_compute_ssst_fodf.py dwi_fodf_shells.nii.gz bval_fodf_shells bvec_fodf_shells $frf ${prefix}__fodf.nii.gz \
$sh_order $sh_basis --force_b0_threshold \
$set_mask $processes
-
+
scil_compute_fodf_max_in_ventricles.py ${prefix}__fodf.nii.gz $fa $md \
--max_value_output ventricles_fodf_max_value.txt $sh_basis \
$fa_threshold $md_threshold -f
diff --git a/modules/nf-scil/reconst/frf/main.nf b/modules/nf-scil/reconst/frf/main.nf
index 7e3856952..e2743767b 100644
--- a/modules/nf-scil/reconst/frf/main.nf
+++ b/modules/nf-scil/reconst/frf/main.nf
@@ -15,7 +15,6 @@ process RECONST_FRF {
tuple val(meta), path("*__frf.txt") , emit: frf
path "versions.yml" , emit: versions
-
when:
task.ext.when == null || task.ext.when
@@ -49,7 +48,7 @@ process RECONST_FRF {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
-
+
"""
scil_compute_ssst_frf.py -h
scil_set_response_function.py -h
diff --git a/modules/nf-scil/reconst/noddi/main.nf b/modules/nf-scil/reconst/noddi/main.nf
index 45fbbfa03..f7fe963b8 100644
--- a/modules/nf-scil/reconst/noddi/main.nf
+++ b/modules/nf-scil/reconst/noddi/main.nf
@@ -37,7 +37,7 @@ process RECONST_NODDI {
"""
scil_compute_NODDI.py $dwi $bval $bvec $para_diff $iso_diff $lambda1 \
$lambda2 $nb_threads $b_thr $set_mask $set_kernels
-
+
if [ ! -z "$kernels" ]; then
mv results/FIT_dir.nii.gz ${prefix}__FIT_dir.nii.gz
diff --git a/modules/nf-scil/segmentation/freesurferseg/main.nf b/modules/nf-scil/segmentation/freesurferseg/main.nf
index f7bb15678..2cee624fa 100644
--- a/modules/nf-scil/segmentation/freesurferseg/main.nf
+++ b/modules/nf-scil/segmentation/freesurferseg/main.nf
@@ -39,36 +39,40 @@ process SEGMENTATION_FREESURFERSEG {
scil_split_volume_by_labels.py aparc+aseg_int16.nii.gz --scilpy_lut freesurfer_subcortical --out_dir aparc+aseg_subcortical
scil_image_math.py union wmparc_desikan/*\
- wmparc_subcortical/right-cerebellum-cortex.nii.gz\
- wmparc_subcortical/left-cerebellum-cortex.nii.gz\
- mask_cortex_m.nii.gz -f
+ wmparc_subcortical/right-cerebellum-cortex.nii.gz\
+ wmparc_subcortical/left-cerebellum-cortex.nii.gz\
+ mask_cortex_m.nii.gz -f
+
scil_image_math.py union wmparc_subcortical/corpus-callosum-*\
- aparc+aseg_subcortical/*white-matter*\
- wmparc_subcortical/brain-stem.nii.gz\
- aparc+aseg_subcortical/*ventraldc*\
- mask_wm_m.nii.gz -f
+ aparc+aseg_subcortical/*white-matter*\
+ wmparc_subcortical/brain-stem.nii.gz\
+ aparc+aseg_subcortical/*ventraldc*\
+ mask_wm_m.nii.gz -f
+
scil_image_math.py union wmparc_subcortical/*thalamus*\
- wmparc_subcortical/*putamen*\
- wmparc_subcortical/*pallidum*\
- wmparc_subcortical/*hippocampus*\
- wmparc_subcortical/*caudate*\
- wmparc_subcortical/*amygdala*\
- wmparc_subcortical/*accumbens*\
- wmparc_subcortical/*plexus*\
- mask_nuclei_m.nii.gz -f
+ wmparc_subcortical/*putamen*\
+ wmparc_subcortical/*pallidum*\
+ wmparc_subcortical/*hippocampus*\
+ wmparc_subcortical/*caudate*\
+ wmparc_subcortical/*amygdala*\
+ wmparc_subcortical/*accumbens*\
+ wmparc_subcortical/*plexus*\
+ mask_nuclei_m.nii.gz -f
+
scil_image_math.py union wmparc_subcortical/*-lateral-ventricle.nii.gz\
- wmparc_subcortical/*-inferior-lateral-ventricle.nii.gz\
- wmparc_subcortical/cerebrospinal-fluid.nii.gz\
- wmparc_subcortical/*th-ventricle.nii.gz\
- mask_csf_1_m.nii.gz -f
+ wmparc_subcortical/*-inferior-lateral-ventricle.nii.gz\
+ wmparc_subcortical/cerebrospinal-fluid.nii.gz\
+ wmparc_subcortical/*th-ventricle.nii.gz\
+ mask_csf_1_m.nii.gz -f
+
scil_image_math.py lower_threshold mask_wm_m.nii.gz 0.1\
- ${prefix}__mask_wm_bin.nii.gz -f
+ ${prefix}__mask_wm_bin.nii.gz -f
scil_image_math.py lower_threshold mask_cortex_m.nii.gz 0.1\
- ${prefix}__mask_gm.nii.gz -f
+ ${prefix}__mask_gm.nii.gz -f
scil_image_math.py lower_threshold mask_nuclei_m.nii.gz 0.1\
- ${prefix}__mask_nuclei_bin.nii.gz -f
+ ${prefix}__mask_nuclei_bin.nii.gz -f
scil_image_math.py lower_threshold mask_csf_1_m.nii.gz 0.1\
- ${prefix}__mask_csf.nii.gz -f
+ ${prefix}__mask_csf.nii.gz -f
scil_image_math.py addition ${prefix}__mask_wm_bin.nii.gz\
${prefix}__mask_nuclei_bin.nii.gz\
${prefix}__mask_wm.nii.gz --data_type int16
diff --git a/modules/nf-scil/tracking/localtracking/main.nf b/modules/nf-scil/tracking/localtracking/main.nf
index 69cbc0efd..ac4ab1bb4 100644
--- a/modules/nf-scil/tracking/localtracking/main.nf
+++ b/modules/nf-scil/tracking/localtracking/main.nf
@@ -59,7 +59,7 @@ process TRACKING_LOCALTRACKING {
elif [ "${local_seeding_mask}" == "fa" ]; then
mrcalc $fa $local_fa_seeding_mask_threshold -ge ${prefix}__local_seeding_mask.nii.gz\
- -datatype uint8
+ -datatype uint8
fi
scil_compute_local_tracking.py $fodf ${prefix}__local_seeding_mask.nii.gz ${prefix}__local_tracking_mask.nii.gz tmp.trk\
diff --git a/modules/nf-scil/tracking/pfttracking/main.nf b/modules/nf-scil/tracking/pfttracking/main.nf
index 3e9eb59e0..563b8354f 100644
--- a/modules/nf-scil/tracking/pfttracking/main.nf
+++ b/modules/nf-scil/tracking/pfttracking/main.nf
@@ -108,7 +108,7 @@ process TRACKING_PFTTRACKING {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
-
+
"""
scil_compute_pft.py -h
scil_compute_maps_for_particle_filter_tracking.py -h
From 1917a4f18745c64d7537cd792bbc50f973639da8 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Mon, 8 Jan 2024 22:06:08 +0000
Subject: [PATCH 19/41] fix indent for editorconfig
---
.editorconfig | 3 +
docs/deps/gh-md-toc | 68 ++++++++++----------
modules/nf-scil/tracking/pfttracking/main.nf | 2 +-
modules/nf-scil/utils/extractb0/main.nf | 2 +-
4 files changed, 39 insertions(+), 36 deletions(-)
diff --git a/.editorconfig b/.editorconfig
index 014c2383b..f640980e2 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -10,3 +10,6 @@ indent_style = space
[*.{md,yml,yaml,html,css,scss,js,cff}]
indent_size = 2
+
+[LICENSE]
+indent_size = 1
diff --git a/docs/deps/gh-md-toc b/docs/deps/gh-md-toc
index fbe76eeb9..241eb7ed4 100755
--- a/docs/deps/gh-md-toc
+++ b/docs/deps/gh-md-toc
@@ -70,9 +70,9 @@ gh_toc_md2html() {
local gh_tmp_file_md=$gh_file_md
if [ "$skip_header" = "yes" ]; then
if grep -Fxq "" "$gh_src"; then
- # cut everything before the toc
- gh_tmp_file_md=$gh_file_md~~
- sed '1,//d' $gh_file_md > $gh_tmp_file_md
+ # cut everything before the toc
+ gh_tmp_file_md=$gh_file_md~~
+ sed '1,//d' $gh_file_md > $gh_tmp_file_md
fi
fi
@@ -154,16 +154,16 @@ gh_toc(){
else
local rawhtml=$(gh_toc_md2html "$gh_src" "$skip_header")
if [ "$rawhtml" == "XXNetworkErrorXX" ]; then
- echo "Parsing local markdown file requires access to github API"
- echo "Please make sure curl is installed and check your network connectivity"
- exit 1
+ echo "Parsing local markdown file requires access to github API"
+ echo "Please make sure curl is installed and check your network connectivity"
+ exit 1
fi
if [ "$rawhtml" == "XXRateLimitXX" ]; then
- echo "Parsing local markdown file requires access to github API"
- echo "Error: You exceeded the hourly limit. See: https://developer.github.com/v3/#rate-limiting"
- TOKEN_FILE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/token.txt"
- echo "or place GitHub auth token here: ${TOKEN_FILE}"
- exit 1
+ echo "Parsing local markdown file requires access to github API"
+ echo "Error: You exceeded the hourly limit. See: https://developer.github.com/v3/#rate-limiting"
+ TOKEN_FILE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/token.txt"
+ echo "or place GitHub auth token here: ${TOKEN_FILE}"
+ exit 1
fi
local toc=`echo "$rawhtml" | gh_toc_grab "$gh_src_copy" "$indent"`
echo "$toc"
@@ -221,21 +221,21 @@ gh_toc_grab() {
href_regex="/href=\"[^\"]+?\"/"
common_awk_script='
- modified_href = ""
- split(href, chars, "")
- for (i=1;i <= length(href); i++) {
- c = chars[i]
- res = ""
- if (c == "+") {
- res = " "
- } else {
- if (c == "%") {
- res = "\\x"
- } else {
- res = c ""
- }
- }
- modified_href = modified_href res
+ modified_href = ""
+ split(href, chars, "")
+ for (i=1;i <= length(href); i++) {
+ c = chars[i]
+ res = ""
+ if (c == "+") {
+ res = " "
+ } else {
+ if (c == "%") {
+ res = "\\x"
+ } else {
+ res = c ""
+ }
+ }
+ modified_href = modified_href res
}
print sprintf("%*s", (level-1)*'"$2"', "") "* [" text "](" gh_url modified_href ")"
'
@@ -243,19 +243,19 @@ gh_toc_grab() {
grepcmd="pcregrep -o"
echoargs=""
awkscript='{
- level = substr($0, 3, 1)
- text = substr($0, match($0, /<\/span><\/a>[^<]*<\/h/)+11, RLENGTH-14)
- href = substr($0, match($0, '$href_regex')+6, RLENGTH-7)
- '"$common_awk_script"'
+ level = substr($0, 3, 1)
+ text = substr($0, match($0, /<\/span><\/a>[^<]*<\/h/)+11, RLENGTH-14)
+ href = substr($0, match($0, '$href_regex')+6, RLENGTH-7)
+ '"$common_awk_script"'
}'
else
grepcmd="grep -Eo"
echoargs="-e"
awkscript='{
- level = substr($0, 3, 1)
- text = substr($0, match($0, /<\/span><\/a>.*<\/h/)+11, RLENGTH-14)
- href = substr($0, match($0, '$href_regex')+6, RLENGTH-7)
- '"$common_awk_script"'
+ level = substr($0, 3, 1)
+ text = substr($0, match($0, /<\/span><\/a>.*<\/h/)+11, RLENGTH-14)
+ href = substr($0, match($0, '$href_regex')+6, RLENGTH-7)
+ '"$common_awk_script"'
}'
fi
diff --git a/modules/nf-scil/tracking/pfttracking/main.nf b/modules/nf-scil/tracking/pfttracking/main.nf
index 563b8354f..a2e44248c 100644
--- a/modules/nf-scil/tracking/pfttracking/main.nf
+++ b/modules/nf-scil/tracking/pfttracking/main.nf
@@ -66,7 +66,7 @@ process TRACKING_PFTTRACKING {
elif [ "${pft_seeding_mask}" == "fa" ]; then
mrcalc $fa $pft_fa_threshold -ge ${prefix}__pft_seeding_mask.nii.gz\
- -datatype uint8
+ -datatype uint8
fi
scil_compute_pft.py $fodf ${prefix}__pft_seeding_mask.nii.gz \
diff --git a/modules/nf-scil/utils/extractb0/main.nf b/modules/nf-scil/utils/extractb0/main.nf
index 1e199069a..51a2b44af 100644
--- a/modules/nf-scil/utils/extractb0/main.nf
+++ b/modules/nf-scil/utils/extractb0/main.nf
@@ -40,7 +40,7 @@ process UTILS_EXTRACTB0 {
stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
-
+
"""
scil_extract_b0.py - h
From 2460df5f328eaa0c8585417e12fadb7a54406827 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Mon, 8 Jan 2024 22:09:05 +0000
Subject: [PATCH 20/41] add schema for metadata
---
modules/nf-scil/meta-schema.json | 186 +++++++++++++++++++++++++++++++
1 file changed, 186 insertions(+)
create mode 100644 modules/nf-scil/meta-schema.json
diff --git a/modules/nf-scil/meta-schema.json b/modules/nf-scil/meta-schema.json
new file mode 100644
index 000000000..0b855d76d
--- /dev/null
+++ b/modules/nf-scil/meta-schema.json
@@ -0,0 +1,186 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "title": "Meta yaml",
+ "description": "Validate the meta yaml file for an nf-core module",
+ "type": "object",
+ "properties": {
+ "name": {
+ "type": "string",
+ "description": "Name of the module"
+ },
+ "description": {
+ "type": "string",
+ "description": "Description of the module"
+ },
+ "keywords": {
+ "type": "array",
+ "description": "Keywords for the module",
+ "items": {
+ "type": "string"
+ },
+ "minItems": 3
+ },
+ "authors": {
+ "type": "array",
+ "description": "Authors of the module",
+ "items": {
+ "type": "string"
+ }
+ },
+ "maintainers": {
+ "type": "array",
+ "description": "Maintainers of the module",
+ "items": {
+ "type": "string"
+ }
+ },
+ "input": {
+ "type": "array",
+ "description": "Input channels for the module",
+ "items": {
+ "type": "object",
+ "patternProperties": {
+ ".*": {
+ "type": "object",
+ "properties": {
+ "type": {
+ "type": "string",
+ "description": "Type of the input channel",
+ "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
+ },
+ "description": {
+ "type": "string",
+ "description": "Description of the input channel"
+ },
+ "pattern": {
+ "type": "string",
+ "description": "Pattern of the input channel, given in Java glob syntax"
+ },
+ "default": {
+ "type": ["string", "number", "boolean", "array", "object"],
+ "description": "Default value for the input channel"
+ },
+ "enum": {
+ "type": "array",
+ "description": "List of allowed values for the input channel",
+ "items": {
+ "type": ["string", "number", "boolean", "array", "object"]
+ },
+ "uniqueItems": true
+ }
+ },
+ "required": ["type", "description"]
+ }
+ }
+ }
+ },
+ "output": {
+ "type": "array",
+ "description": "Output channels for the module",
+ "items": {
+ "type": "object",
+ "patternProperties": {
+ ".*": {
+ "type": "object",
+ "properties": {
+ "type": {
+ "type": "string",
+ "description": "Type of the output channel",
+ "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
+ },
+ "description": {
+ "type": "string",
+ "description": "Description of the output channel"
+ },
+ "pattern": {
+ "type": "string",
+ "description": "Pattern of the input channel, given in Java glob syntax"
+ },
+ "enum": {
+ "type": "array",
+ "description": "List of allowed values for the output channel",
+ "items": {
+ "type": ["string", "number", "boolean", "array", "object"]
+ },
+ "uniqueItems": true
+ }
+ },
+ "required": ["type", "description"]
+ }
+ }
+ }
+ },
+ "tools": {
+ "type": "array",
+ "description": "Tools used by the module",
+ "items": {
+ "type": "object",
+ "patternProperties": {
+ ".*": {
+ "type": "object",
+ "properties": {
+ "description": {
+ "type": "string",
+ "description": "Description of the output channel"
+ },
+ "homepage": {
+ "type": "string",
+ "description": "Homepage of the tool",
+ "pattern": "^(http|https)://.*$"
+ },
+ "documentation": {
+ "type": "string",
+ "description": "Documentation of the tool",
+ "pattern": "^(http|https|ftp)://.*$"
+ },
+ "tool_dev_url": {
+ "type": "string",
+ "description": "URL of the development version of the tool's documentation",
+ "pattern": "^(http|https)://.*$"
+ },
+ "doi": {
+ "description": "DOI of the tool",
+ "anyOf": [
+ {
+ "type": "string",
+ "pattern": "^10\\.\\d{4,9}\\/[^,]+$"
+ },
+ {
+ "type": "string",
+ "enum": ["no DOI available"]
+ }
+ ]
+ },
+ "licence": {
+ "type": "array",
+ "items": {
+ "type": "string"
+ },
+ "description": "Licence of the tool",
+ "minItems": 1,
+ "uniqueItems": true,
+ "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
+ }
+ },
+ "required": ["description"],
+ "anyOf": [
+ {
+ "required": ["homepage"]
+ },
+ {
+ "required": ["documentation"]
+ },
+ {
+ "required": ["tool_dev_url"]
+ },
+ {
+ "required": ["doi"]
+ }
+ ]
+ }
+ }
+ }
+ }
+ },
+ "required": ["name", "description", "keywords", "authors", "output", "tools"]
+}
From a6fbb79033d00a0415520595a41970f622bb31fc Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 04:22:02 +0000
Subject: [PATCH 21/41] fix
---
modules/nf-scil/meta-schema.json | 186 -------------------------------
1 file changed, 186 deletions(-)
delete mode 100644 modules/nf-scil/meta-schema.json
diff --git a/modules/nf-scil/meta-schema.json b/modules/nf-scil/meta-schema.json
deleted file mode 100644
index 0b855d76d..000000000
--- a/modules/nf-scil/meta-schema.json
+++ /dev/null
@@ -1,186 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-07/schema",
- "title": "Meta yaml",
- "description": "Validate the meta yaml file for an nf-core module",
- "type": "object",
- "properties": {
- "name": {
- "type": "string",
- "description": "Name of the module"
- },
- "description": {
- "type": "string",
- "description": "Description of the module"
- },
- "keywords": {
- "type": "array",
- "description": "Keywords for the module",
- "items": {
- "type": "string"
- },
- "minItems": 3
- },
- "authors": {
- "type": "array",
- "description": "Authors of the module",
- "items": {
- "type": "string"
- }
- },
- "maintainers": {
- "type": "array",
- "description": "Maintainers of the module",
- "items": {
- "type": "string"
- }
- },
- "input": {
- "type": "array",
- "description": "Input channels for the module",
- "items": {
- "type": "object",
- "patternProperties": {
- ".*": {
- "type": "object",
- "properties": {
- "type": {
- "type": "string",
- "description": "Type of the input channel",
- "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
- },
- "description": {
- "type": "string",
- "description": "Description of the input channel"
- },
- "pattern": {
- "type": "string",
- "description": "Pattern of the input channel, given in Java glob syntax"
- },
- "default": {
- "type": ["string", "number", "boolean", "array", "object"],
- "description": "Default value for the input channel"
- },
- "enum": {
- "type": "array",
- "description": "List of allowed values for the input channel",
- "items": {
- "type": ["string", "number", "boolean", "array", "object"]
- },
- "uniqueItems": true
- }
- },
- "required": ["type", "description"]
- }
- }
- }
- },
- "output": {
- "type": "array",
- "description": "Output channels for the module",
- "items": {
- "type": "object",
- "patternProperties": {
- ".*": {
- "type": "object",
- "properties": {
- "type": {
- "type": "string",
- "description": "Type of the output channel",
- "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
- },
- "description": {
- "type": "string",
- "description": "Description of the output channel"
- },
- "pattern": {
- "type": "string",
- "description": "Pattern of the input channel, given in Java glob syntax"
- },
- "enum": {
- "type": "array",
- "description": "List of allowed values for the output channel",
- "items": {
- "type": ["string", "number", "boolean", "array", "object"]
- },
- "uniqueItems": true
- }
- },
- "required": ["type", "description"]
- }
- }
- }
- },
- "tools": {
- "type": "array",
- "description": "Tools used by the module",
- "items": {
- "type": "object",
- "patternProperties": {
- ".*": {
- "type": "object",
- "properties": {
- "description": {
- "type": "string",
- "description": "Description of the output channel"
- },
- "homepage": {
- "type": "string",
- "description": "Homepage of the tool",
- "pattern": "^(http|https)://.*$"
- },
- "documentation": {
- "type": "string",
- "description": "Documentation of the tool",
- "pattern": "^(http|https|ftp)://.*$"
- },
- "tool_dev_url": {
- "type": "string",
- "description": "URL of the development version of the tool's documentation",
- "pattern": "^(http|https)://.*$"
- },
- "doi": {
- "description": "DOI of the tool",
- "anyOf": [
- {
- "type": "string",
- "pattern": "^10\\.\\d{4,9}\\/[^,]+$"
- },
- {
- "type": "string",
- "enum": ["no DOI available"]
- }
- ]
- },
- "licence": {
- "type": "array",
- "items": {
- "type": "string"
- },
- "description": "Licence of the tool",
- "minItems": 1,
- "uniqueItems": true,
- "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
- }
- },
- "required": ["description"],
- "anyOf": [
- {
- "required": ["homepage"]
- },
- {
- "required": ["documentation"]
- },
- {
- "required": ["tool_dev_url"]
- },
- {
- "required": ["doi"]
- }
- ]
- }
- }
- }
- }
- },
- "required": ["name", "description", "keywords", "authors", "output", "tools"]
-}
From 118c1ff6935df2a91ec6f743522f99bfffb3787d Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 04:34:52 +0000
Subject: [PATCH 22/41] fix linting
---
modules/nf-scil/reconst/frf/meta.yml | 6 +++---
modules/nf-scil/reconst/meanfrf/meta.yml | 5 ++++-
modules/nf-scil/reconst/noddi/meta.yml | 3 ++-
modules/nf-scil/tracking/localtracking/meta.yml | 1 +
modules/nf-scil/tracking/pfttracking/meta.yml | 5 +++--
5 files changed, 13 insertions(+), 7 deletions(-)
diff --git a/modules/nf-scil/reconst/frf/meta.yml b/modules/nf-scil/reconst/frf/meta.yml
index b0210067f..076590487 100644
--- a/modules/nf-scil/reconst/frf/meta.yml
+++ b/modules/nf-scil/reconst/frf/meta.yml
@@ -3,9 +3,9 @@
name: "reconst_frf"
description: Compute a single Fiber Response Function from a DWI.
keywords:
- - DWI
- - FRF
-
+ - Fiber Orientation Distribution Function
+ - Diffusion MRI
+ - Fiber Response Function
tools:
- "DIPY":
description: "DIPY is the paragon 3D/4D+ imaging library in Python."
diff --git a/modules/nf-scil/reconst/meanfrf/meta.yml b/modules/nf-scil/reconst/meanfrf/meta.yml
index a37a30d5c..9d553c8e1 100644
--- a/modules/nf-scil/reconst/meanfrf/meta.yml
+++ b/modules/nf-scil/reconst/meanfrf/meta.yml
@@ -4,7 +4,10 @@ name: "reconst_meanfrf"
description: Compute the mean Fiber Response Function from a set of individually
computed Response Functions.
keywords:
- - FRF
+ - Fiber Orientation Distribution Function
+ - Diffusion MRI
+ - Fiber Response Function
+ - Average
tools:
- "Scilpy":
diff --git a/modules/nf-scil/reconst/noddi/meta.yml b/modules/nf-scil/reconst/noddi/meta.yml
index 105372982..ba05e99aa 100644
--- a/modules/nf-scil/reconst/noddi/meta.yml
+++ b/modules/nf-scil/reconst/noddi/meta.yml
@@ -3,8 +3,9 @@
name: "reconst_noddi"
description: Run NODDI modelling pipeline using AMICO from DWI data.
keywords:
- - DWI
+ - Diffusion MRI
- NODDI
+ - Microstructure modeling
tools:
- "Scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
diff --git a/modules/nf-scil/tracking/localtracking/meta.yml b/modules/nf-scil/tracking/localtracking/meta.yml
index 3fb33a2b8..7d9fbea5a 100644
--- a/modules/nf-scil/tracking/localtracking/meta.yml
+++ b/modules/nf-scil/tracking/localtracking/meta.yml
@@ -4,6 +4,7 @@ description: process local tracking
keywords:
- Tractography
- Local tracking
+ - Diffusion MRI
tools:
- "Scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
diff --git a/modules/nf-scil/tracking/pfttracking/meta.yml b/modules/nf-scil/tracking/pfttracking/meta.yml
index d2b8c5167..0e15e72e5 100644
--- a/modules/nf-scil/tracking/pfttracking/meta.yml
+++ b/modules/nf-scil/tracking/pfttracking/meta.yml
@@ -6,8 +6,9 @@ description: Compute include and exclude maps, and the seeding mask
Generates a tractogram using anatomically-constrained particle
filter tracking, Particle Filtering Tractography (PFT).
keywords:
- - PFT
- - tractography
+ - Diffusion MRI
+ - Tractography
+ - Particle Filtering Tractography
tools:
- "DIPY":
From a25331c756754f5312fe9b2d3e44b502090d24b7 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 04:38:25 +0000
Subject: [PATCH 23/41] fix linting
---
modules/nf-scil/reconst/meanfrf/meta.yml | 2 +-
modules/nf-scil/reconst/noddi/meta.yml | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/nf-scil/reconst/meanfrf/meta.yml b/modules/nf-scil/reconst/meanfrf/meta.yml
index 9d553c8e1..f1d40db9b 100644
--- a/modules/nf-scil/reconst/meanfrf/meta.yml
+++ b/modules/nf-scil/reconst/meanfrf/meta.yml
@@ -16,7 +16,7 @@ tools:
input:
- frf_list:
- type: Path
+ type: list
description: List of individual Fiber Response Function (FRF) path.
pattern: "*.txt"
diff --git a/modules/nf-scil/reconst/noddi/meta.yml b/modules/nf-scil/reconst/noddi/meta.yml
index ba05e99aa..cb6cae235 100644
--- a/modules/nf-scil/reconst/noddi/meta.yml
+++ b/modules/nf-scil/reconst/noddi/meta.yml
@@ -46,7 +46,7 @@ input:
pattern: "*mask.{nii,nii.gz}"
- kernels:
- type: folder
+ type: directory
description: Folder containg kernels.
pattern: "kernels"
@@ -83,7 +83,7 @@ output:
pattern: "*__FIT_OD.{nii,nii.gz}"
- kernels:
- type: folder
+ type: directory
description: Folder containg kernels.
pattern: "kernels"
From ccdee41fd41d582dd20ed9c165deb15cb0fccdab Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 04:49:30 +0000
Subject: [PATCH 24/41] reinstate publishdir
---
tests/modules/nf-scil/betcrop/fslbetcrop/nextflow.config | 2 +-
.../nf-scil/reconst/diffusivitypriors/nextflow.config | 1 +
tests/modules/nf-scil/reconst/dtimetrics/nextflow.config | 7 ++++---
tests/modules/nf-scil/reconst/fodf/nextflow.config | 4 ++--
tests/modules/nf-scil/reconst/frf/nextflow.config | 5 ++---
tests/modules/nf-scil/reconst/meanfrf/nextflow.config | 3 ++-
tests/modules/nf-scil/reconst/noddi/nextflow.config | 3 ++-
.../nf-scil/segmentation/freesurferseg/nextflow.config | 8 ++------
.../nf-scil/tracking/localtracking/nextflow.config | 5 +++--
.../modules/nf-scil/tracking/pfttracking/nextflow.config | 3 ++-
10 files changed, 21 insertions(+), 20 deletions(-)
diff --git a/tests/modules/nf-scil/betcrop/fslbetcrop/nextflow.config b/tests/modules/nf-scil/betcrop/fslbetcrop/nextflow.config
index a862d22b7..32f7bc96f 100644
--- a/tests/modules/nf-scil/betcrop/fslbetcrop/nextflow.config
+++ b/tests/modules/nf-scil/betcrop/fslbetcrop/nextflow.config
@@ -2,7 +2,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
- withNAME: "BETCROP_FSLBETCROP" {
+ withName: "BETCROP_FSLBETCROP" {
ext.bet_dwi_f = 0.16
ext.b0_thr = 10
}
diff --git a/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config b/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config
index f832d4387..fa8c4a0a7 100644
--- a/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config
+++ b/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config
@@ -1,4 +1,5 @@
process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "RECONST_DIFFUSIVITYPRIORS" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
diff --git a/tests/modules/nf-scil/reconst/dtimetrics/nextflow.config b/tests/modules/nf-scil/reconst/dtimetrics/nextflow.config
index 9b36be53c..a7f3eaf86 100644
--- a/tests/modules/nf-scil/reconst/dtimetrics/nextflow.config
+++ b/tests/modules/nf-scil/reconst/dtimetrics/nextflow.config
@@ -1,7 +1,7 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+
withName: "RECONST_DTIMETRICS" {
ext.ad = true
ext.evecs = true
@@ -18,7 +18,8 @@ process {
ext.pulsation = true
ext.residual = true
}
- withName: "test_reconst_dtimetrics_with_b0mask:RECONST_DTIMETRICS" {
+
+ withName: "test_reconst_dtimetrics_with_b0mask:RECONST_DTIMETRICS" {
ext.ad = false
ext.evecs = false
ext.evals = false
@@ -34,4 +35,4 @@ process {
ext.pulsation = false
ext.residual = false
}
-}
\ No newline at end of file
+}
diff --git a/tests/modules/nf-scil/reconst/fodf/nextflow.config b/tests/modules/nf-scil/reconst/fodf/nextflow.config
index 847409318..c4de284c7 100644
--- a/tests/modules/nf-scil/reconst/fodf/nextflow.config
+++ b/tests/modules/nf-scil/reconst/fodf/nextflow.config
@@ -1,4 +1,5 @@
process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "RECONST_FODF" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
@@ -28,5 +29,4 @@ process {
ext.afd_sum = false
ext.nufo = false
}
-
-}
\ No newline at end of file
+}
diff --git a/tests/modules/nf-scil/reconst/frf/nextflow.config b/tests/modules/nf-scil/reconst/frf/nextflow.config
index bf1c9999b..6265affd9 100644
--- a/tests/modules/nf-scil/reconst/frf/nextflow.config
+++ b/tests/modules/nf-scil/reconst/frf/nextflow.config
@@ -1,7 +1,6 @@
process {
-
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+
withName: "RECONST_FRF" {
ext.fa = 0.7
ext.fa_min = 0.5
@@ -27,4 +26,4 @@ process {
ext.set_frf = true
ext.manual_frf = "15,4,4"
}
-}
\ No newline at end of file
+}
diff --git a/tests/modules/nf-scil/reconst/meanfrf/nextflow.config b/tests/modules/nf-scil/reconst/meanfrf/nextflow.config
index 662808e43..398430ccd 100644
--- a/tests/modules/nf-scil/reconst/meanfrf/nextflow.config
+++ b/tests/modules/nf-scil/reconst/meanfrf/nextflow.config
@@ -1,6 +1,7 @@
process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "RECONST_MEANFRF" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}
-}
\ No newline at end of file
+}
diff --git a/tests/modules/nf-scil/reconst/noddi/nextflow.config b/tests/modules/nf-scil/reconst/noddi/nextflow.config
index b44a2a9b5..0b09884d9 100644
--- a/tests/modules/nf-scil/reconst/noddi/nextflow.config
+++ b/tests/modules/nf-scil/reconst/noddi/nextflow.config
@@ -1,4 +1,5 @@
process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "RECONST_NODDI" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
@@ -9,4 +10,4 @@ process {
ext.b_thr = 40
ext.nb_threads = 1
}
-}
\ No newline at end of file
+}
diff --git a/tests/modules/nf-scil/segmentation/freesurferseg/nextflow.config b/tests/modules/nf-scil/segmentation/freesurferseg/nextflow.config
index 200d377f1..0293c16f9 100644
--- a/tests/modules/nf-scil/segmentation/freesurferseg/nextflow.config
+++ b/tests/modules/nf-scil/segmentation/freesurferseg/nextflow.config
@@ -1,7 +1,3 @@
process {
-
- withName: "SEGMENTATION_FREESURFERSEG" {
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
- }
-
-}
\ No newline at end of file
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+}
diff --git a/tests/modules/nf-scil/tracking/localtracking/nextflow.config b/tests/modules/nf-scil/tracking/localtracking/nextflow.config
index 122004637..868467212 100644
--- a/tests/modules/nf-scil/tracking/localtracking/nextflow.config
+++ b/tests/modules/nf-scil/tracking/localtracking/nextflow.config
@@ -1,4 +1,5 @@
process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "WM_TRACKING" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
@@ -38,5 +39,5 @@ process {
ext.local_max_len = 200
ext.basis = "descoteaux07"
}
-
-}
\ No newline at end of file
+
+}
diff --git a/tests/modules/nf-scil/tracking/pfttracking/nextflow.config b/tests/modules/nf-scil/tracking/pfttracking/nextflow.config
index 180db7b97..9f21b4e01 100644
--- a/tests/modules/nf-scil/tracking/pfttracking/nextflow.config
+++ b/tests/modules/nf-scil/tracking/pfttracking/nextflow.config
@@ -1,4 +1,5 @@
process {
+ publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "WM_TRACKING" {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
@@ -63,4 +64,4 @@ process {
ext.pft_front = 1
ext.basis = "descoteaux07"
}
-}
\ No newline at end of file
+}
From 777e7fa1c3c27ef6cd7ad024f78458eb2cb9330d Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 04:52:36 +0000
Subject: [PATCH 25/41] fix linting
---
modules/nf-scil/reconst/diffusivitypriors/meta.yml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/nf-scil/reconst/diffusivitypriors/meta.yml b/modules/nf-scil/reconst/diffusivitypriors/meta.yml
index 4f6f41e8c..cc3e8b596 100644
--- a/modules/nf-scil/reconst/diffusivitypriors/meta.yml
+++ b/modules/nf-scil/reconst/diffusivitypriors/meta.yml
@@ -34,7 +34,7 @@ input:
pattern: "*.{nii,nii.gz}"
- priors:
- type: folder
+ type: directory
description: Folder containg text files for iso and para diffusivity values.
pattern: "priors"
@@ -66,7 +66,7 @@ output:
pattern: "*.txt"
- priors:
- type: folder
+ type: directory
description: Folder containg text files for iso and para diffusivity values.
pattern: "priors"
From d0e779156257376212b52e0fe580d31419b51972 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 05:14:47 +0000
Subject: [PATCH 26/41] add protocol to sif images
---
docs/MODULE.md | 2 +-
modules/nf-scil/preproc/gibbs/main.nf | 2 +-
modules/nf-scil/preproc/n4/main.nf | 2 +-
modules/nf-scil/testdata/scilpy/main.nf | 4 ++--
modules/nf-scil/tracking/localtracking/main.nf | 2 +-
tests/modules/nf-scil/denoising/mppca/test.yml | 2 --
6 files changed, 6 insertions(+), 8 deletions(-)
diff --git a/docs/MODULE.md b/docs/MODULE.md
index 7f0976da3..2f4240e95 100644
--- a/docs/MODULE.md
+++ b/docs/MODULE.md
@@ -49,7 +49,7 @@ already follow all guidelines. You will find related files in :
- If the process uses the `scilus` container, use the following replacements,
else remove the whole section.
- `depot.galaxyproject.org...` ⟹ `scil.usherbrooke.ca/containers/scilus_1.6.0.sif`
+ `depot.galaxyproject.org...` ⟹ `https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif`
`biocontainers/YOUR-TOOL-HERE` ⟹ `scilus/scilus:1.6.0`
diff --git a/modules/nf-scil/preproc/gibbs/main.nf b/modules/nf-scil/preproc/gibbs/main.nf
index 4008cf4b0..849f9f429 100644
--- a/modules/nf-scil/preproc/gibbs/main.nf
+++ b/modules/nf-scil/preproc/gibbs/main.nf
@@ -3,7 +3,7 @@ process PREPROC_GIBBS {
label 'process_single'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+ 'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
'scilus/scilus:1.6.0' }"
input:
diff --git a/modules/nf-scil/preproc/n4/main.nf b/modules/nf-scil/preproc/n4/main.nf
index 9bc435953..e568d58cd 100644
--- a/modules/nf-scil/preproc/n4/main.nf
+++ b/modules/nf-scil/preproc/n4/main.nf
@@ -3,7 +3,7 @@ process PREPROC_N4 {
label 'process_single'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+ 'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
'scilus/scilus:1.6.0' }"
input:
diff --git a/modules/nf-scil/testdata/scilpy/main.nf b/modules/nf-scil/testdata/scilpy/main.nf
index ea0a78096..880d1589d 100644
--- a/modules/nf-scil/testdata/scilpy/main.nf
+++ b/modules/nf-scil/testdata/scilpy/main.nf
@@ -4,7 +4,7 @@ process TESTDATA_SCILPY {
label 'process_single'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+ 'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
'scilus/scilus:1.6.0' }"
input:
@@ -44,4 +44,4 @@ process TESTDATA_SCILPY {
scilpy: 1.6.0
END_VERSIONS
"""
-}
\ No newline at end of file
+}
diff --git a/modules/nf-scil/tracking/localtracking/main.nf b/modules/nf-scil/tracking/localtracking/main.nf
index ac4ab1bb4..2bebb988f 100644
--- a/modules/nf-scil/tracking/localtracking/main.nf
+++ b/modules/nf-scil/tracking/localtracking/main.nf
@@ -3,7 +3,7 @@ process TRACKING_LOCALTRACKING {
label 'process_single'
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+ 'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
'scilus/scilus:1.6.0' }"
input:
diff --git a/tests/modules/nf-scil/denoising/mppca/test.yml b/tests/modules/nf-scil/denoising/mppca/test.yml
index e9b313aa8..b0a4918fa 100644
--- a/tests/modules/nf-scil/denoising/mppca/test.yml
+++ b/tests/modules/nf-scil/denoising/mppca/test.yml
@@ -4,8 +4,6 @@
- denoising/mppca
- denoising
files:
- - path: output/denoising/test__pre_dwi_denoised.nii.gz
- md5sum: ece4b6fe910ae6502edd52b526609638
- path: output/denoising/test_dwi_denoised.nii.gz
md5sum: 0cfa480f702173a047f076bbba9fe25e
- path: output/denoising/versions.yml
From 0acf7af48ad6943e02d5a24a6d26df8c8e6d8bca Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Tue, 9 Jan 2024 05:26:22 +0000
Subject: [PATCH 27/41] priors is a directory, no matter what
---
modules/nf-scil/reconst/diffusivitypriors/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/nf-scil/reconst/diffusivitypriors/main.nf b/modules/nf-scil/reconst/diffusivitypriors/main.nf
index c71a3cba5..a6d440c42 100644
--- a/modules/nf-scil/reconst/diffusivitypriors/main.nf
+++ b/modules/nf-scil/reconst/diffusivitypriors/main.nf
@@ -31,7 +31,7 @@ process RECONST_DIFFUSIVITYPRIORS {
def roi_radius = task.ext.roi_radius ? "--roi_radius " + task.ext.roi_radius : ""
"""
- if [ ! -z "$priors" ]
+ if [ -d "$priors" ]
then
cat $priors/*__para_diff.txt > all_para_diff.txt
awk '{ total += \$1; count++ } END { print total/count }' all_para_diff.txt > mean_para_diff.txt
From 5f1c3008b4b234fd883e5c18af876fe4540912fa Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Wed, 10 Jan 2024 22:00:17 +0000
Subject: [PATCH 28/41] bind /tmp to volume to prevent out-of-space
---
.devcontainer/devcontainer.json | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 0f627bb5e..fab32d98e 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -59,5 +59,6 @@
}
},
"init": true,
- "privileged": true
+ "privileged": true,
+ "runArgs": ["--mount", "type=volume,target=/tmp/"]
}
From 450d86124fd73e14d03805212ae9f76f7c2d4b52 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 00:59:07 +0000
Subject: [PATCH 29/41] fix noddi, n4, fslbetcrop
---
modules/nf-scil/reconst/noddi/main.nf | 2 +-
.../nf-scil/betcrop/fslbetcrop/test.yml | 2 +-
.../nf-scil/preproc/n4/nextflow.config | 8 +-
tests/modules/nf-scil/preproc/n4/test.yml | 2 +-
tests/modules/nf-scil/reconst/noddi/main.nf | 10 +-
.../nf-scil/reconst/noddi/nextflow.config | 1 -
tests/modules/nf-scil/reconst/noddi/test.yml | 584 +++++++++---------
7 files changed, 306 insertions(+), 303 deletions(-)
diff --git a/modules/nf-scil/reconst/noddi/main.nf b/modules/nf-scil/reconst/noddi/main.nf
index f7fe963b8..66ec20fa9 100644
--- a/modules/nf-scil/reconst/noddi/main.nf
+++ b/modules/nf-scil/reconst/noddi/main.nf
@@ -39,7 +39,7 @@ process RECONST_NODDI {
$lambda2 $nb_threads $b_thr $set_mask $set_kernels
- if [ ! -z "$kernels" ]; then
+ if [ -d "$kernels" ]; then
mv results/FIT_dir.nii.gz ${prefix}__FIT_dir.nii.gz
mv results/FIT_ICVF.nii.gz ${prefix}__FIT_ICVF.nii.gz
mv results/FIT_ISOVF.nii.gz ${prefix}__FIT_ISOVF.nii.gz
diff --git a/tests/modules/nf-scil/betcrop/fslbetcrop/test.yml b/tests/modules/nf-scil/betcrop/fslbetcrop/test.yml
index 4ad11b8cf..ada9e7cb5 100644
--- a/tests/modules/nf-scil/betcrop/fslbetcrop/test.yml
+++ b/tests/modules/nf-scil/betcrop/fslbetcrop/test.yml
@@ -7,7 +7,7 @@
- path: output/betcrop/test__dwi_bet_cropped.nii.gz
md5sum: e597e3030800fbf9de681c1a5e539c9d
- path: output/betcrop/test__dwi_bet_cropped_mask.nii.gz
- md5sum: 2fc5bd8704c86fe94b79c1d651e94032
+ md5sum: d511acb62d15958b5a8f2116cdb3ce3a
- path: output/betcrop/test__dwi_boundingBox.pkl
md5sum: 89012d5b4f0f1bee03658b193911e0a1
- path: output/betcrop/versions.yml
diff --git a/tests/modules/nf-scil/preproc/n4/nextflow.config b/tests/modules/nf-scil/preproc/n4/nextflow.config
index 50f50a7a3..0ec7cb244 100644
--- a/tests/modules/nf-scil/preproc/n4/nextflow.config
+++ b/tests/modules/nf-scil/preproc/n4/nextflow.config
@@ -1,5 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
+
+ withName: "PREPROC_N4" {
+ ext.bspline_knot_per_voxel = 0.25
+ ext.shrink_factor = 4
+ }
+}
diff --git a/tests/modules/nf-scil/preproc/n4/test.yml b/tests/modules/nf-scil/preproc/n4/test.yml
index 408e7237b..1cc5d9159 100644
--- a/tests/modules/nf-scil/preproc/n4/test.yml
+++ b/tests/modules/nf-scil/preproc/n4/test.yml
@@ -5,5 +5,5 @@
- preproc/n4
files:
- path: output/preproc/test__dwi_n4.nii.gz
- md5sum: d7a741dcf1a1f9176619790e9d708940
+ md5sum: 1068c745054b73e4cd836100d34c54a7
- path: output/preproc/versions.yml
diff --git a/tests/modules/nf-scil/reconst/noddi/main.nf b/tests/modules/nf-scil/reconst/noddi/main.nf
index 8d9a6d086..dc573cbc7 100644
--- a/tests/modules/nf-scil/reconst/noddi/main.nf
+++ b/tests/modules/nf-scil/reconst/noddi/main.nf
@@ -4,9 +4,9 @@ nextflow.enable.dsl = 2
include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main.nf'
-include {
- RECONST_NODDI as COMPUTE_KERNELS;
- RECONST_NODDI as COMPUTE_METRICS} from '../../../../../modules/nf-scil/reconst/noddi/main.nf'
+include {
+ RECONST_NODDI as RECONST_NODDI_KERNELS;
+ RECONST_NODDI as RECONST_NODDI_METRICS} from '../../../../../modules/nf-scil/reconst/noddi/main.nf'
workflow test_reconst_noddi_save_kernels {
@@ -24,7 +24,7 @@ workflow test_reconst_noddi_save_kernels {
[]
]}
- COMPUTE_KERNELS ( input_noddi )
+ RECONST_NODDI_KERNELS ( input_noddi )
}
workflow test_reconst_noddi_save_kernels_no_mask {
@@ -42,5 +42,5 @@ workflow test_reconst_noddi_save_kernels_no_mask {
[], []
]}
- COMPUTE_KERNELS ( input_noddi )
+ RECONST_NODDI_KERNELS ( input_noddi )
}
diff --git a/tests/modules/nf-scil/reconst/noddi/nextflow.config b/tests/modules/nf-scil/reconst/noddi/nextflow.config
index 0b09884d9..e18972fe9 100644
--- a/tests/modules/nf-scil/reconst/noddi/nextflow.config
+++ b/tests/modules/nf-scil/reconst/noddi/nextflow.config
@@ -2,7 +2,6 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "RECONST_NODDI" {
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.para_diff = 1.7e-3
ext.iso_diff = 3e-3
ext.lambda1 = 0.5
diff --git a/tests/modules/nf-scil/reconst/noddi/test.yml b/tests/modules/nf-scil/reconst/noddi/test.yml
index 6e9338c54..e5e336e7c 100644
--- a/tests/modules/nf-scil/reconst/noddi/test.yml
+++ b/tests/modules/nf-scil/reconst/noddi/test.yml
@@ -4,297 +4,297 @@
- reconst/noddi
- reconst
files:
- - path: output/compute/kernels/A_001.npy
+ - path: output/reconst/kernels/A_001.npy
md5sum: 7685778d192b6e900af06af03de1c40a
- - path: output/compute/kernels/A_002.npy
+ - path: output/reconst/kernels/A_002.npy
md5sum: dcc12f440bef6378ff60c0819dee2908
- - path: output/compute/kernels/A_003.npy
+ - path: output/reconst/kernels/A_003.npy
md5sum: ed1167026a33c054d763281e1557a4e3
- - path: output/compute/kernels/A_004.npy
+ - path: output/reconst/kernels/A_004.npy
md5sum: 54c0d829a6aa1e4e64494557cc5eb9e6
- - path: output/compute/kernels/A_005.npy
+ - path: output/reconst/kernels/A_005.npy
md5sum: 3a8b3795e38d8b3bd0e4bcb7e68fd1b1
- - path: output/compute/kernels/A_006.npy
+ - path: output/reconst/kernels/A_006.npy
md5sum: a4d016455774b4fa0e2fed7d332b20da
- - path: output/compute/kernels/A_007.npy
+ - path: output/reconst/kernels/A_007.npy
md5sum: 4c0e816675bdad94211a915f68378af1
- - path: output/compute/kernels/A_008.npy
+ - path: output/reconst/kernels/A_008.npy
md5sum: 7cf5b62efc28be3e853ef51851a49790
- - path: output/compute/kernels/A_009.npy
+ - path: output/reconst/kernels/A_009.npy
md5sum: bd46f9cfebc7c819a890c367ab6cb1da
- - path: output/compute/kernels/A_010.npy
+ - path: output/reconst/kernels/A_010.npy
md5sum: 609c7b5227168255d8cb7f1bee7333c2
- - path: output/compute/kernels/A_011.npy
+ - path: output/reconst/kernels/A_011.npy
md5sum: 63bb74c9f92484bf928468994efb8f78
- - path: output/compute/kernels/A_012.npy
+ - path: output/reconst/kernels/A_012.npy
md5sum: 9a5a92dabd50ab72bf03442a61656499
- - path: output/compute/kernels/A_013.npy
+ - path: output/reconst/kernels/A_013.npy
md5sum: 0039dedb0f99de263117075648c1ba0c
- - path: output/compute/kernels/A_014.npy
+ - path: output/reconst/kernels/A_014.npy
md5sum: 8ef7c0316b06ab56b1bb239124bce91b
- - path: output/compute/kernels/A_015.npy
+ - path: output/reconst/kernels/A_015.npy
md5sum: 3b1f91a5ba7c52a1d9c7d4c5d7c170e1
- - path: output/compute/kernels/A_016.npy
+ - path: output/reconst/kernels/A_016.npy
md5sum: 5d1b88ffe98c426eeb761b0c2ea17e52
- - path: output/compute/kernels/A_017.npy
+ - path: output/reconst/kernels/A_017.npy
md5sum: abd1b83fa7d8ad6d5f248c11f9056ba3
- - path: output/compute/kernels/A_018.npy
+ - path: output/reconst/kernels/A_018.npy
md5sum: d251399b3c9cd9204a4870504da4d281
- - path: output/compute/kernels/A_019.npy
+ - path: output/reconst/kernels/A_019.npy
md5sum: 849ab4311ec7b01b684fc2b40c1b2778
- - path: output/compute/kernels/A_020.npy
+ - path: output/reconst/kernels/A_020.npy
md5sum: 3f4c04129b1e7985bf0771ddfba8c015
- - path: output/compute/kernels/A_021.npy
+ - path: output/reconst/kernels/A_021.npy
md5sum: 1994666f9141d28b907b8718e7e6f777
- - path: output/compute/kernels/A_022.npy
+ - path: output/reconst/kernels/A_022.npy
md5sum: 4aaa5e9a86fb8fb01da26e41e2b06b1c
- - path: output/compute/kernels/A_023.npy
+ - path: output/reconst/kernels/A_023.npy
md5sum: 17e198034e513baeac9ff73ea15ee25a
- - path: output/compute/kernels/A_024.npy
+ - path: output/reconst/kernels/A_024.npy
md5sum: 3490a078a05053501c4aeac7f0b4f552
- - path: output/compute/kernels/A_025.npy
+ - path: output/reconst/kernels/A_025.npy
md5sum: 4b5e35e1fb093421c673fba6d6c9b6df
- - path: output/compute/kernels/A_026.npy
+ - path: output/reconst/kernels/A_026.npy
md5sum: 9f50a6cf0ae4fece488696e057a275d6
- - path: output/compute/kernels/A_027.npy
+ - path: output/reconst/kernels/A_027.npy
md5sum: fa1be584c09c3618734c96d702df53a8
- - path: output/compute/kernels/A_028.npy
+ - path: output/reconst/kernels/A_028.npy
md5sum: 48dd2b0ed0cd5eb36602b5318e8e7a3a
- - path: output/compute/kernels/A_029.npy
+ - path: output/reconst/kernels/A_029.npy
md5sum: b3eb55ae0f277a19dc8f1d84a8dd895a
- - path: output/compute/kernels/A_030.npy
+ - path: output/reconst/kernels/A_030.npy
md5sum: d57c41283368a9b66b487f9db2d05fc2
- - path: output/compute/kernels/A_031.npy
+ - path: output/reconst/kernels/A_031.npy
md5sum: 3cf5adb3ad92b1d67993722d9eab380b
- - path: output/compute/kernels/A_032.npy
+ - path: output/reconst/kernels/A_032.npy
md5sum: 779aa382425bedf4b966ed43a2609801
- - path: output/compute/kernels/A_033.npy
+ - path: output/reconst/kernels/A_033.npy
md5sum: 4d4248fb123b63af721b3e097ff9903f
- - path: output/compute/kernels/A_034.npy
+ - path: output/reconst/kernels/A_034.npy
md5sum: a0f02c3980cd5a125f262d7e68a9a23c
- - path: output/compute/kernels/A_035.npy
+ - path: output/reconst/kernels/A_035.npy
md5sum: 8d919c8600bbb6f586b6c334fec84f9f
- - path: output/compute/kernels/A_036.npy
+ - path: output/reconst/kernels/A_036.npy
md5sum: d6edbee74e08a8c20b015ed4ae18b2ab
- - path: output/compute/kernels/A_037.npy
+ - path: output/reconst/kernels/A_037.npy
md5sum: f6f6d482a7ca42369f4c62e6f8eef552
- - path: output/compute/kernels/A_038.npy
+ - path: output/reconst/kernels/A_038.npy
md5sum: 9dff1ac269b381a75f5c25bf051bf1c5
- - path: output/compute/kernels/A_039.npy
+ - path: output/reconst/kernels/A_039.npy
md5sum: 8892bea5472f1b40c5868a536294f134
- - path: output/compute/kernels/A_040.npy
+ - path: output/reconst/kernels/A_040.npy
md5sum: 99adce8e31e9288ea1550b8029f2bae0
- - path: output/compute/kernels/A_041.npy
+ - path: output/reconst/kernels/A_041.npy
md5sum: 1b3fecb234dfc9e4554ac7df11017595
- - path: output/compute/kernels/A_042.npy
+ - path: output/reconst/kernels/A_042.npy
md5sum: 1bc1a2afe6f03b031d7667566a084cb1
- - path: output/compute/kernels/A_043.npy
+ - path: output/reconst/kernels/A_043.npy
md5sum: 3743e4a06a8c52b21e46d20bbb68c89c
- - path: output/compute/kernels/A_044.npy
+ - path: output/reconst/kernels/A_044.npy
md5sum: 022bc4586ed94d71e03096de6fdf2443
- - path: output/compute/kernels/A_045.npy
+ - path: output/reconst/kernels/A_045.npy
md5sum: cd15743a7139f981fa65905ebb4c669f
- - path: output/compute/kernels/A_046.npy
+ - path: output/reconst/kernels/A_046.npy
md5sum: 89d46a8684dcbed0b84892f536745aeb
- - path: output/compute/kernels/A_047.npy
+ - path: output/reconst/kernels/A_047.npy
md5sum: 607d4cf2568437a32e130640033b2eb6
- - path: output/compute/kernels/A_048.npy
+ - path: output/reconst/kernels/A_048.npy
md5sum: 080089c3ee74f6a670ba2f4629739523
- - path: output/compute/kernels/A_049.npy
+ - path: output/reconst/kernels/A_049.npy
md5sum: ab43ede1e8e72e93985dbafe52fcae41
- - path: output/compute/kernels/A_050.npy
+ - path: output/reconst/kernels/A_050.npy
md5sum: 89e79074000af7660861fe8596abf2dc
- - path: output/compute/kernels/A_051.npy
+ - path: output/reconst/kernels/A_051.npy
md5sum: dd8a8961ff769c358961b589c9fd605c
- - path: output/compute/kernels/A_052.npy
+ - path: output/reconst/kernels/A_052.npy
md5sum: c5f520b60797e0dc88aefaa705442a82
- - path: output/compute/kernels/A_053.npy
+ - path: output/reconst/kernels/A_053.npy
md5sum: 7355cc61e1edf1576f8d695285b56d88
- - path: output/compute/kernels/A_054.npy
+ - path: output/reconst/kernels/A_054.npy
md5sum: dc5d18d1f95b9b1251c6f1007231dd41
- - path: output/compute/kernels/A_055.npy
+ - path: output/reconst/kernels/A_055.npy
md5sum: 51815fd6d8717d7bf729bbd8f0215bbf
- - path: output/compute/kernels/A_056.npy
+ - path: output/reconst/kernels/A_056.npy
md5sum: ede3f55419c4e8a41de56ea2fa357c2f
- - path: output/compute/kernels/A_057.npy
+ - path: output/reconst/kernels/A_057.npy
md5sum: 0be644cc5e4e962f38d7a60d6894cf08
- - path: output/compute/kernels/A_058.npy
+ - path: output/reconst/kernels/A_058.npy
md5sum: a60bfda5b16ceb96f6e3a4a26ff8913f
- - path: output/compute/kernels/A_059.npy
+ - path: output/reconst/kernels/A_059.npy
md5sum: 71b34384955060e2cb2cb4cf3329842b
- - path: output/compute/kernels/A_060.npy
+ - path: output/reconst/kernels/A_060.npy
md5sum: 90a2a4f915947c7d2ee99969ba394f16
- - path: output/compute/kernels/A_061.npy
+ - path: output/reconst/kernels/A_061.npy
md5sum: 29127b6428928197cd999fba5cc15962
- - path: output/compute/kernels/A_062.npy
+ - path: output/reconst/kernels/A_062.npy
md5sum: c4cb3322d1f57543f3a4c24bdd6542d0
- - path: output/compute/kernels/A_063.npy
+ - path: output/reconst/kernels/A_063.npy
md5sum: f2a434d9087486822d9467aa9a2949c6
- - path: output/compute/kernels/A_064.npy
+ - path: output/reconst/kernels/A_064.npy
md5sum: 14629aaf9c0381e548ffa2859f02c7f2
- - path: output/compute/kernels/A_065.npy
+ - path: output/reconst/kernels/A_065.npy
md5sum: 82964736555dd0e33d107b8d1ba04b99
- - path: output/compute/kernels/A_066.npy
+ - path: output/reconst/kernels/A_066.npy
md5sum: aa282cb662a2581296f8c6432bec5def
- - path: output/compute/kernels/A_067.npy
+ - path: output/reconst/kernels/A_067.npy
md5sum: a8273af0f3f0f78ec36a9256b8e8838b
- - path: output/compute/kernels/A_068.npy
+ - path: output/reconst/kernels/A_068.npy
md5sum: 0243467ee9f75aafda13e586d3292236
- - path: output/compute/kernels/A_069.npy
+ - path: output/reconst/kernels/A_069.npy
md5sum: 70b6e1cf69afa7861cdc71209bff19e3
- - path: output/compute/kernels/A_070.npy
+ - path: output/reconst/kernels/A_070.npy
md5sum: ee159bf58499762488db9a3e80038e09
- - path: output/compute/kernels/A_071.npy
+ - path: output/reconst/kernels/A_071.npy
md5sum: c255bfec1bebe547bce036b3d276b158
- - path: output/compute/kernels/A_072.npy
+ - path: output/reconst/kernels/A_072.npy
md5sum: 5a7785fdd6906e33bbad4a4610e39dc0
- - path: output/compute/kernels/A_073.npy
+ - path: output/reconst/kernels/A_073.npy
md5sum: 83d41cc79f305d9a097a91f18250319d
- - path: output/compute/kernels/A_074.npy
+ - path: output/reconst/kernels/A_074.npy
md5sum: 4b30b4210b3e5c4e026a58892308a4e3
- - path: output/compute/kernels/A_075.npy
+ - path: output/reconst/kernels/A_075.npy
md5sum: f6f83ea9451b3f96a7bbe015cc9c8c21
- - path: output/compute/kernels/A_076.npy
+ - path: output/reconst/kernels/A_076.npy
md5sum: 40e72cd83f75039825e15d9ce4ed05e4
- - path: output/compute/kernels/A_077.npy
+ - path: output/reconst/kernels/A_077.npy
md5sum: c961a829523e020ef5e0ebf1a733c19b
- - path: output/compute/kernels/A_078.npy
+ - path: output/reconst/kernels/A_078.npy
md5sum: c24066930825c7756342742df6331c82
- - path: output/compute/kernels/A_079.npy
+ - path: output/reconst/kernels/A_079.npy
md5sum: 07ddc1e8a148442e83e6aca66e13acd5
- - path: output/compute/kernels/A_080.npy
+ - path: output/reconst/kernels/A_080.npy
md5sum: 709ac9b7c8301153f0317b96cda75552
- - path: output/compute/kernels/A_081.npy
+ - path: output/reconst/kernels/A_081.npy
md5sum: 8bede120aa60737b83b61d8d0aac582a
- - path: output/compute/kernels/A_082.npy
+ - path: output/reconst/kernels/A_082.npy
md5sum: 3945f973add1a6db95fe58e329ec91e7
- - path: output/compute/kernels/A_083.npy
+ - path: output/reconst/kernels/A_083.npy
md5sum: 4c201bac152c7e9130830d8915886683
- - path: output/compute/kernels/A_084.npy
+ - path: output/reconst/kernels/A_084.npy
md5sum: 233696d75a8e674a0820b0f4123b621b
- - path: output/compute/kernels/A_085.npy
+ - path: output/reconst/kernels/A_085.npy
md5sum: 783ed22541c2470a64236cfb9745a787
- - path: output/compute/kernels/A_086.npy
+ - path: output/reconst/kernels/A_086.npy
md5sum: c4df82fe0257e943bff9bbfe97c8bd01
- - path: output/compute/kernels/A_087.npy
+ - path: output/reconst/kernels/A_087.npy
md5sum: 69ffd05ba012ae164e882e2f0720492b
- - path: output/compute/kernels/A_088.npy
+ - path: output/reconst/kernels/A_088.npy
md5sum: 0b41b02520099e6945a34fdbcc5ee7a8
- - path: output/compute/kernels/A_089.npy
+ - path: output/reconst/kernels/A_089.npy
md5sum: 0eea673e2d6ecfa072bc8e72c878cdcd
- - path: output/compute/kernels/A_090.npy
+ - path: output/reconst/kernels/A_090.npy
md5sum: be79cf920ab80d7f6ebd04ec878eb6f6
- - path: output/compute/kernels/A_091.npy
+ - path: output/reconst/kernels/A_091.npy
md5sum: a33b58f20a68bdc59f262c714c0f5616
- - path: output/compute/kernels/A_092.npy
+ - path: output/reconst/kernels/A_092.npy
md5sum: d0f3e9e8b8ce77c4c91a95f6bf91dadf
- - path: output/compute/kernels/A_093.npy
+ - path: output/reconst/kernels/A_093.npy
md5sum: 8af839b27f6b1b3e0c712c73b9ca95d5
- - path: output/compute/kernels/A_094.npy
+ - path: output/reconst/kernels/A_094.npy
md5sum: 33045a5adb24c5a4c04e28f1495e4af2
- - path: output/compute/kernels/A_095.npy
+ - path: output/reconst/kernels/A_095.npy
md5sum: 747034be17ce34ac1837a7ef4a785675
- - path: output/compute/kernels/A_096.npy
+ - path: output/reconst/kernels/A_096.npy
md5sum: 93d719b74fb1fb304784aece5b6c5ab4
- - path: output/compute/kernels/A_097.npy
+ - path: output/reconst/kernels/A_097.npy
md5sum: 013fa7ae6870925e17fb73ee78809502
- - path: output/compute/kernels/A_098.npy
+ - path: output/reconst/kernels/A_098.npy
md5sum: 096edd9c291d4f9d85152b50e86a3112
- - path: output/compute/kernels/A_099.npy
+ - path: output/reconst/kernels/A_099.npy
md5sum: 08b65ea77d226c1f7d5876cee415ce4a
- - path: output/compute/kernels/A_100.npy
+ - path: output/reconst/kernels/A_100.npy
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+ - path: output/reconst/kernels/A_142.npy
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+ - path: output/reconst/kernels/A_143.npy
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- - path: output/compute/kernels/A_144.npy
+ - path: output/reconst/kernels/A_144.npy
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+ - path: output/reconst/kernels/A_145.npy
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- - path: output/compute/versions.yml
+ - path: output/reconst/versions.yml
- name: reconst noddi test_reconst_noddi_save_kernels_no_mask
command: nextflow run ./tests/modules/nf-scil/reconst/noddi -entry test_reconst_noddi_save_kernels_no_mask -c ./tests/config/nextflow.config
@@ -302,294 +302,294 @@
- reconst/noddi
- reconst
files:
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- - path: output/compute/kernels/A_079.npy
+ - path: output/reconst/kernels/A_079.npy
md5sum: 07ddc1e8a148442e83e6aca66e13acd5
- - path: output/compute/kernels/A_080.npy
+ - path: output/reconst/kernels/A_080.npy
md5sum: 709ac9b7c8301153f0317b96cda75552
- - path: output/compute/kernels/A_081.npy
+ - path: output/reconst/kernels/A_081.npy
md5sum: 8bede120aa60737b83b61d8d0aac582a
- - path: output/compute/kernels/A_082.npy
+ - path: output/reconst/kernels/A_082.npy
md5sum: 3945f973add1a6db95fe58e329ec91e7
- - path: output/compute/kernels/A_083.npy
+ - path: output/reconst/kernels/A_083.npy
md5sum: 4c201bac152c7e9130830d8915886683
- - path: output/compute/kernels/A_084.npy
+ - path: output/reconst/kernels/A_084.npy
md5sum: 233696d75a8e674a0820b0f4123b621b
- - path: output/compute/kernels/A_085.npy
+ - path: output/reconst/kernels/A_085.npy
md5sum: 783ed22541c2470a64236cfb9745a787
- - path: output/compute/kernels/A_086.npy
+ - path: output/reconst/kernels/A_086.npy
md5sum: c4df82fe0257e943bff9bbfe97c8bd01
- - path: output/compute/kernels/A_087.npy
+ - path: output/reconst/kernels/A_087.npy
md5sum: 69ffd05ba012ae164e882e2f0720492b
- - path: output/compute/kernels/A_088.npy
+ - path: output/reconst/kernels/A_088.npy
md5sum: 0b41b02520099e6945a34fdbcc5ee7a8
- - path: output/compute/kernels/A_089.npy
+ - path: output/reconst/kernels/A_089.npy
md5sum: 0eea673e2d6ecfa072bc8e72c878cdcd
- - path: output/compute/kernels/A_090.npy
+ - path: output/reconst/kernels/A_090.npy
md5sum: be79cf920ab80d7f6ebd04ec878eb6f6
- - path: output/compute/kernels/A_091.npy
+ - path: output/reconst/kernels/A_091.npy
md5sum: a33b58f20a68bdc59f262c714c0f5616
- - path: output/compute/kernels/A_092.npy
+ - path: output/reconst/kernels/A_092.npy
md5sum: d0f3e9e8b8ce77c4c91a95f6bf91dadf
- - path: output/compute/kernels/A_093.npy
+ - path: output/reconst/kernels/A_093.npy
md5sum: 8af839b27f6b1b3e0c712c73b9ca95d5
- - path: output/compute/kernels/A_094.npy
+ - path: output/reconst/kernels/A_094.npy
md5sum: 33045a5adb24c5a4c04e28f1495e4af2
- - path: output/compute/kernels/A_095.npy
+ - path: output/reconst/kernels/A_095.npy
md5sum: 747034be17ce34ac1837a7ef4a785675
- - path: output/compute/kernels/A_096.npy
+ - path: output/reconst/kernels/A_096.npy
md5sum: 93d719b74fb1fb304784aece5b6c5ab4
- - path: output/compute/kernels/A_097.npy
+ - path: output/reconst/kernels/A_097.npy
md5sum: 013fa7ae6870925e17fb73ee78809502
- - path: output/compute/kernels/A_098.npy
+ - path: output/reconst/kernels/A_098.npy
md5sum: 096edd9c291d4f9d85152b50e86a3112
- - path: output/compute/kernels/A_099.npy
+ - path: output/reconst/kernels/A_099.npy
md5sum: 08b65ea77d226c1f7d5876cee415ce4a
- - path: output/compute/kernels/A_100.npy
+ - path: output/reconst/kernels/A_100.npy
md5sum: dd38ec6122813be0450bc9a89401b040
- - path: output/compute/kernels/A_101.npy
+ - path: output/reconst/kernels/A_101.npy
md5sum: 013c4e58cfe8deda708575a2bf51ec43
- - path: output/compute/kernels/A_102.npy
+ - path: output/reconst/kernels/A_102.npy
md5sum: 92f56a865fda5830512f30b158472357
- - path: output/compute/kernels/A_103.npy
+ - path: output/reconst/kernels/A_103.npy
md5sum: 6cc2c4cb5259aa5a08eb87ae78eabd2f
- - path: output/compute/kernels/A_104.npy
+ - path: output/reconst/kernels/A_104.npy
md5sum: c286597b7b9101f9fbde1a5a89c9aa57
- - path: output/compute/kernels/A_105.npy
+ - path: output/reconst/kernels/A_105.npy
md5sum: a193d8436a95481f3dcd9a2fb22bf8c1
- - path: output/compute/kernels/A_106.npy
+ - path: output/reconst/kernels/A_106.npy
md5sum: 8e7e770817081413839881b31af40684
- - path: output/compute/kernels/A_107.npy
+ - path: output/reconst/kernels/A_107.npy
md5sum: 8d5987397d5f7fc4e13c4bd94a9ed0ff
- - path: output/compute/kernels/A_108.npy
+ - path: output/reconst/kernels/A_108.npy
md5sum: 83ee0ee52c845957cf5ce16cb343fb57
- - path: output/compute/kernels/A_109.npy
+ - path: output/reconst/kernels/A_109.npy
md5sum: 6c25ca897da95f16e92384024a9ff6f8
- - path: output/compute/kernels/A_110.npy
+ - path: output/reconst/kernels/A_110.npy
md5sum: dd40c52181be77afeaa77bdc611fb6d4
- - path: output/compute/kernels/A_111.npy
+ - path: output/reconst/kernels/A_111.npy
md5sum: 8ce666c5c5c954c051a0344af7405571
- - path: output/compute/kernels/A_112.npy
+ - path: output/reconst/kernels/A_112.npy
md5sum: 0f05bf2d7694ca3572ba495fa46ee81f
- - path: output/compute/kernels/A_113.npy
+ - path: output/reconst/kernels/A_113.npy
md5sum: ff3fae915eceb71c3d550245f4467752
- - path: output/compute/kernels/A_114.npy
+ - path: output/reconst/kernels/A_114.npy
md5sum: b82049618788b0450e2b43c5f6d8119d
- - path: output/compute/kernels/A_115.npy
+ - path: output/reconst/kernels/A_115.npy
md5sum: ac9a6075479974c1fecd9352550456b6
- - path: output/compute/kernels/A_116.npy
+ - path: output/reconst/kernels/A_116.npy
md5sum: 09482147106b80d7bd6fda72bf8baf86
- - path: output/compute/kernels/A_117.npy
+ - path: output/reconst/kernels/A_117.npy
md5sum: c93cc75f20ad3cd089ba4a63179fe67b
- - path: output/compute/kernels/A_118.npy
+ - path: output/reconst/kernels/A_118.npy
md5sum: 4c1f5ad2c1e7ae137e0172fb130107b0
- - path: output/compute/kernels/A_119.npy
+ - path: output/reconst/kernels/A_119.npy
md5sum: 54e168db1229f90809eef6f99db87313
- - path: output/compute/kernels/A_120.npy
+ - path: output/reconst/kernels/A_120.npy
md5sum: 44aea9be1bebcc33ca4fc117fda3c381
- - path: output/compute/kernels/A_121.npy
+ - path: output/reconst/kernels/A_121.npy
md5sum: bf30fc934d14d27298bc5fca0c628797
- - path: output/compute/kernels/A_122.npy
+ - path: output/reconst/kernels/A_122.npy
md5sum: 6f69fda57c4e7630f554e55ecc18e9de
- - path: output/compute/kernels/A_123.npy
+ - path: output/reconst/kernels/A_123.npy
md5sum: e61656ac07e14b47b51cfd81076a36ad
- - path: output/compute/kernels/A_124.npy
+ - path: output/reconst/kernels/A_124.npy
md5sum: a20061f96654459c07919e96369f6bbd
- - path: output/compute/kernels/A_125.npy
+ - path: output/reconst/kernels/A_125.npy
md5sum: 5ece1efe1e275f67cabc7b36eba4cbb8
- - path: output/compute/kernels/A_126.npy
+ - path: output/reconst/kernels/A_126.npy
md5sum: c42eefa83a7342fec1bedce2bd57cc3d
- - path: output/compute/kernels/A_127.npy
+ - path: output/reconst/kernels/A_127.npy
md5sum: 5dc4f61d3cdddda0dbd94333a3dd7c88
- - path: output/compute/kernels/A_128.npy
+ - path: output/reconst/kernels/A_128.npy
md5sum: 1facea6c3dcd3c2c16242987d65916a2
- - path: output/compute/kernels/A_129.npy
+ - path: output/reconst/kernels/A_129.npy
md5sum: 779b671302e80805766851b8788a561b
- - path: output/compute/kernels/A_130.npy
+ - path: output/reconst/kernels/A_130.npy
md5sum: 8c116cc4b794f11122ea805bb1ba638b
- - path: output/compute/kernels/A_131.npy
+ - path: output/reconst/kernels/A_131.npy
md5sum: 08537ed38e1cd6acc6109ea9b042751a
- - path: output/compute/kernels/A_132.npy
+ - path: output/reconst/kernels/A_132.npy
md5sum: d69051b321a5e88037092ee5c95d99a4
- - path: output/compute/kernels/A_133.npy
+ - path: output/reconst/kernels/A_133.npy
md5sum: beed98dcb37f25f4b8ce36b028c5aa32
- - path: output/compute/kernels/A_134.npy
+ - path: output/reconst/kernels/A_134.npy
md5sum: d04ce67db73a8c879e7353c2b4c826ae
- - path: output/compute/kernels/A_135.npy
+ - path: output/reconst/kernels/A_135.npy
md5sum: dd502124b6581bd38b02acca47adbf6f
- - path: output/compute/kernels/A_136.npy
+ - path: output/reconst/kernels/A_136.npy
md5sum: ad932cbfe06c66a9ac3c3a1b02c75e47
- - path: output/compute/kernels/A_137.npy
+ - path: output/reconst/kernels/A_137.npy
md5sum: 442480b9820c11cdd36ce119f9ebdbf6
- - path: output/compute/kernels/A_138.npy
+ - path: output/reconst/kernels/A_138.npy
md5sum: e9b8ab1a2fd6f93b5584d8b23b752ef2
- - path: output/compute/kernels/A_139.npy
+ - path: output/reconst/kernels/A_139.npy
md5sum: f53cbf9709a8d58de37ce719820b86dc
- - path: output/compute/kernels/A_140.npy
+ - path: output/reconst/kernels/A_140.npy
md5sum: 5f282c2887dbc956c72a80b65723f4ad
- - path: output/compute/kernels/A_141.npy
+ - path: output/reconst/kernels/A_141.npy
md5sum: 66da08fff4ea0637d0f44310f3edeb2f
- - path: output/compute/kernels/A_142.npy
+ - path: output/reconst/kernels/A_142.npy
md5sum: 565543843cdc7d2d48b89d2af794f37b
- - path: output/compute/kernels/A_143.npy
+ - path: output/reconst/kernels/A_143.npy
md5sum: 49b31341747a3fc81b9c7bfe65654ff7
- - path: output/compute/kernels/A_144.npy
+ - path: output/reconst/kernels/A_144.npy
md5sum: 6a2a6393d7c6ccdf27cf4885c5cb34dd
- - path: output/compute/kernels/A_145.npy
+ - path: output/reconst/kernels/A_145.npy
md5sum: a26e3876df3c02b399f2d21bbd3ebf3a
- - path: output/compute/versions.yml
+ - path: output/reconst/versions.yml
From 5c36be797e77eac9602e69c3cdf1c3c1c708d05e Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 01:57:21 +0000
Subject: [PATCH 30/41] fix diffusivity priors
---
modules/nf-scil/preproc/n4/main.nf | 12 +++---
.../nf-scil/reconst/diffusivitypriors/main.nf | 43 +++++++++++--------
tests/config/test_data.config | 11 +++--
.../nf-scil/reconst/diffusivitypriors/main.nf | 12 +++---
.../reconst/diffusivitypriors/nextflow.config | 1 -
.../reconst/diffusivitypriors/test.yml | 24 +++++------
6 files changed, 56 insertions(+), 47 deletions(-)
diff --git a/modules/nf-scil/preproc/n4/main.nf b/modules/nf-scil/preproc/n4/main.nf
index e568d58cd..a5c4687e5 100644
--- a/modules/nf-scil/preproc/n4/main.nf
+++ b/modules/nf-scil/preproc/n4/main.nf
@@ -40,9 +40,9 @@ process PREPROC_N4 {
${prefix}__dwi_n4.nii.gz --mask $b0_mask -f
cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- scilpy: 1.6.0
- N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+ "${task.process}":
+ scilpy: 1.6.0
+ N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
END_VERSIONS
"""
@@ -56,9 +56,9 @@ process PREPROC_N4 {
touch ${prefix}_dwi_n4.nii.gz
cat <<-END_VERSIONS > versions.yml
- "${task.process}":
- scilpy: 1.6.0
- N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+ "${task.process}":
+ scilpy: 1.6.0
+ N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
END_VERSIONS
"""
}
diff --git a/modules/nf-scil/reconst/diffusivitypriors/main.nf b/modules/nf-scil/reconst/diffusivitypriors/main.nf
index a6d440c42..d9e3dcae6 100644
--- a/modules/nf-scil/reconst/diffusivitypriors/main.nf
+++ b/modules/nf-scil/reconst/diffusivitypriors/main.nf
@@ -1,4 +1,20 @@
+import nextflow.util.BlankSeparatedList
+
+def compute_noddi_priors ( fa, ad, md, fa_min, fa_max, md_min, roi_radius, prefix, output_directory ) {
+ """
+ mkdir -p $output_directory
+
+ scil_compute_NODDI_priors.py $fa $ad $md $fa_min $fa_max $md_min $roi_radius \
+ --out_txt_1fiber $output_directory/${prefix}__para_diff.txt \
+ --out_txt_ventricles $output_directory/${prefix}__iso_diff.txt
+ """
+}
+
+
+def is_directory ( pathlike ) {
+ return !(pathlike instanceof BlankSeparatedList) && pathlike.isDirectory()
+}
process RECONST_DIFFUSIVITYPRIORS {
tag "$meta.id"
@@ -30,26 +46,15 @@ process RECONST_DIFFUSIVITYPRIORS {
def md_min = task.ext.md_min ? "--md_min " + task.ext.md_min : ""
def roi_radius = task.ext.roi_radius ? "--roi_radius " + task.ext.roi_radius : ""
+ def priors_directory = priors.isEmpty() ? "priors" : !is_directory(priors) ? "priors" : priors
"""
- if [ -d "$priors" ]
- then
- cat $priors/*__para_diff.txt > all_para_diff.txt
- awk '{ total += \$1; count++ } END { print total/count }' all_para_diff.txt > mean_para_diff.txt
- cat $priors/*__iso_diff.txt > all_iso_diff.txt
- awk '{ total += \$1; count++ } END { print total/count }' all_iso_diff.txt > mean_iso_diff.txt
-
- else
-
- mkdir priors
- scil_compute_NODDI_priors.py $fa $ad $md $fa_min $fa_max $md_min $roi_radius\
- --out_txt_1fiber priors/${prefix}__para_diff.txt\
- --out_txt_ventricles priors/${prefix}__iso_diff.txt
-
- cat priors/*__para_diff.txt > all_para_diff.txt
- awk '{ total += \$1; count++ } END { print total/count }' all_para_diff.txt > mean_para_diff.txt
- cat priors/*__iso_diff.txt > all_iso_diff.txt
- awk '{ total += \$1; count++ } END { print total/count }' all_iso_diff.txt > mean_iso_diff.txt
- fi
+ ${ priors.isEmpty() ? compute_noddi_priors( fa, ad, md, fa_min, fa_max, md_min, roi_radius, prefix, priors_directory ) : ""}
+
+ ${ !priors.isEmpty() && !is_directory(priors) ? "mkdir -p priors && ln $priors priors" : "" }
+ cat $priors_directory/*__para_diff.txt > all_para_diff.txt
+ awk '{ total += \$1; count++ } END { print total/count }' all_para_diff.txt > mean_para_diff.txt
+ cat $priors_directory/*__iso_diff.txt > all_iso_diff.txt
+ awk '{ total += \$1; count++ } END { print total/count }' all_iso_diff.txt > mean_iso_diff.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index f8693824c..4a06150f7 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -46,8 +46,13 @@ params {
bval = "${params.test_data_base}/heavy/dwi/dwi.bval"
bvec = "${params.test_data_base}/heavy/dwi/dwi.bvec"
}
- "diffusivitypriors"{
- priors = "${params.test_data_base}/light/priors"
+ "diffusivitypriors"{
+ priors = [
+ "${params.test_data_base}/light/priors/s1__iso_diff.txt",
+ "${params.test_data_base}/light/priors/s1__para_diff.txt",
+ "${params.test_data_base}/light/priors/s2__iso_diff.txt",
+ "${params.test_data_base}/light/priors/s2__para_diff.txt"
+ ]
}
"frf" {
dwi = "${params.test_data_base}/heavy/dwi/dwi.nii.gz"
@@ -87,7 +92,7 @@ params {
"extractb0" {
dwi = "${params.test_data_base}/heavy/dwi/dwi.nii.gz"
bval = "${params.test_data_base}/heavy/dwi/dwi.bval"
- bvec = "${params.test_data_base}/heavy/dwi/dwi.bvec"
+ bvec = "${params.test_data_base}/heavy/dwi/dwi.bvec"
}
}
}
diff --git a/tests/modules/nf-scil/reconst/diffusivitypriors/main.nf b/tests/modules/nf-scil/reconst/diffusivitypriors/main.nf
index 3608a9620..aab4fdd92 100644
--- a/tests/modules/nf-scil/reconst/diffusivitypriors/main.nf
+++ b/tests/modules/nf-scil/reconst/diffusivitypriors/main.nf
@@ -2,12 +2,12 @@
nextflow.enable.dsl = 2
-include { RECONST_DIFFUSIVITYPRIORS as MEAN_PRIORS} from '../../../../../modules/nf-scil/reconst/diffusivitypriors/main.nf'
-include { RECONST_DIFFUSIVITYPRIORS as COMPUTE_PRIORS} from '../../../../../modules/nf-scil/reconst/diffusivitypriors/main.nf'
+include { RECONST_DIFFUSIVITYPRIORS as RECONST_MEAN_PRIORS} from '../../../../../modules/nf-scil/reconst/diffusivitypriors/main.nf'
+include { RECONST_DIFFUSIVITYPRIORS as RECONST_COMPUTE_PRIORS} from '../../../../../modules/nf-scil/reconst/diffusivitypriors/main.nf'
include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main.nf'
workflow test_reconst_diffusivitypriors_compute_priors {
-
+
input_fetch = Channel.from( [ "commit_amico.zip" ] )
LOAD_TEST_DATA ( input_fetch, "test.load-test-data" )
@@ -21,7 +21,7 @@ workflow test_reconst_diffusivitypriors_compute_priors {
[]
]}
- COMPUTE_PRIORS ( input_priors )
+ RECONST_COMPUTE_PRIORS ( input_priors )
}
workflow test_reconst_diffusivitypriors_mean_priors {
@@ -29,10 +29,10 @@ workflow test_reconst_diffusivitypriors_mean_priors {
input = [
[ id:'test', single_end:false ], // meta map
[],[],[],
- file(params.test_data['reconst']['diffusivitypriors']['priors'], checkIfExists: true)
+ params.test_data['reconst']['diffusivitypriors']['priors'].collect{ file(it, checkIfExists: true) }
]
- MEAN_PRIORS ( input )
+ RECONST_MEAN_PRIORS ( input )
}
diff --git a/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config b/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config
index fa8c4a0a7..6de8b6e47 100644
--- a/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config
+++ b/tests/modules/nf-scil/reconst/diffusivitypriors/nextflow.config
@@ -2,7 +2,6 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: "RECONST_DIFFUSIVITYPRIORS" {
- publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.fa_min = 0.7
ext.fa_max = 0.1
ext.md_min = 0.003
diff --git a/tests/modules/nf-scil/reconst/diffusivitypriors/test.yml b/tests/modules/nf-scil/reconst/diffusivitypriors/test.yml
index 326dc17ac..b7a7f768b 100644
--- a/tests/modules/nf-scil/reconst/diffusivitypriors/test.yml
+++ b/tests/modules/nf-scil/reconst/diffusivitypriors/test.yml
@@ -4,15 +4,15 @@
- reconst
- reconst/diffusivitypriors
files:
- - path: output/compute/mean_iso_diff.txt
+ - path: output/reconst/mean_iso_diff.txt
md5sum: 3f13db606b697f920d21efd3c9cf8838
- - path: output/compute/mean_para_diff.txt
+ - path: output/reconst/mean_para_diff.txt
md5sum: b5ab394820e011a04e3787be3772ad6e
- - path: output/compute/priors/test__iso_diff.txt
+ - path: output/reconst/priors/test__iso_diff.txt
md5sum: 3f13db606b697f920d21efd3c9cf8838
- - path: output/compute/priors/test__para_diff.txt
+ - path: output/reconst/priors/test__para_diff.txt
md5sum: b5ab394820e011a04e3787be3772ad6e
- - path: output/compute/versions.yml
+ - path: output/reconst/versions.yml
- name: reconst diffusivitypriors test_reconst_diffusivitypriors_mean_priors
command: nextflow run ./tests/modules/nf-scil/reconst/diffusivitypriors -entry test_reconst_diffusivitypriors_mean_priors -c ./tests/config/nextflow.config
@@ -20,16 +20,16 @@
- reconst
- reconst/diffusivitypriors
files:
- - path: output/mean/mean_iso_diff.txt
+ - path: output/reconst/mean_iso_diff.txt
md5sum: b048050981231e15bfafcda4536e2d05
- - path: output/mean/mean_para_diff.txt
+ - path: output/reconst/mean_para_diff.txt
md5sum: 4ef4f76ce3a673249bcbaa0eba9ce832
- - path: output/mean/priors/s1__iso_diff.txt
+ - path: output/reconst/priors/s1__iso_diff.txt
md5sum: 3f13db606b697f920d21efd3c9cf8838
- - path: output/mean/priors/s1__para_diff.txt
+ - path: output/reconst/priors/s1__para_diff.txt
md5sum: b5ab394820e011a04e3787be3772ad6e
- - path: output/mean/priors/s2__iso_diff.txt
+ - path: output/reconst/priors/s2__iso_diff.txt
md5sum: 5b003c147cc5f202d2e8c61acaa5eaea
- - path: output/mean/priors/s2__para_diff.txt
+ - path: output/reconst/priors/s2__para_diff.txt
md5sum: 202cb21086439607b99b81ead3e7f817
- - path: output/mean/versions.yml
+ - path: output/reconst/versions.yml
From 416f25b5a262c72b0b7146da38a9a03306f2a21e Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 02:37:36 +0000
Subject: [PATCH 31/41] fix N4
---
modules/nf-scil/preproc/n4/main.nf | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/nf-scil/preproc/n4/main.nf b/modules/nf-scil/preproc/n4/main.nf
index a5c4687e5..11578d570 100644
--- a/modules/nf-scil/preproc/n4/main.nf
+++ b/modules/nf-scil/preproc/n4/main.nf
@@ -27,7 +27,7 @@ process PREPROC_N4 {
export OPENBLAS_NUM_THREADS=1
export ANTS_RANDOM_SEED=1234
- spacing=\$(mrinfo -spacing $b0 | tr " " "\n" | sort -n | tail -1)
+ spacing=\$(mrinfo -spacing $b0 | tr " " "\\n" | sort -n | tail -1)
knot_spacing=\$(echo "\$spacing/$bspline_knot_per_voxel" | bc -l)
N4BiasFieldCorrection -i $b0\
From cbe480ac18c514ff60683bbfa320dfeb4c2e7c3d Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:00:21 +0000
Subject: [PATCH 32/41] fix extractb0
---
tests/modules/nf-scil/utils/extractb0/main.nf | 32 +++++++++----------
.../nf-scil/utils/extractb0/nextflow.config | 12 +++----
.../modules/nf-scil/utils/extractb0/test.yml | 30 ++++++++---------
3 files changed, 37 insertions(+), 37 deletions(-)
diff --git a/tests/modules/nf-scil/utils/extractb0/main.nf b/tests/modules/nf-scil/utils/extractb0/main.nf
index 3c0d5edba..d6599db29 100644
--- a/tests/modules/nf-scil/utils/extractb0/main.nf
+++ b/tests/modules/nf-scil/utils/extractb0/main.nf
@@ -3,14 +3,14 @@
nextflow.enable.dsl = 2
include {
- UTILS_EXTRACTB0 as EXTRACTB0_MEAN;
- UTILS_EXTRACTB0 as EXTRACTB0_ALL4D;
- UTILS_EXTRACTB0 as EXTRACTB0_ALLSERIES;
- UTILS_EXTRACTB0 as EXTRACTB0_CLUSTERMEAN;
- UTILS_EXTRACTB0 as EXTRACTB0_CLUSTERFIRST} from '../../../../../modules/nf-scil/utils/extractb0/main.nf'
+ UTILS_EXTRACTB0 as UTILS_EXTRACTB0_MEAN;
+ UTILS_EXTRACTB0 as UTILS_EXTRACTB0_ALL4D;
+ UTILS_EXTRACTB0 as UTILS_EXTRACTB0_ALLSERIES;
+ UTILS_EXTRACTB0 as UTILS_EXTRACTB0_CLUSTERMEAN;
+ UTILS_EXTRACTB0 as UTILS_EXTRACTB0_CLUSTERFIRST} from '../../../../../modules/nf-scil/utils/extractb0/main.nf'
workflow test_utils_extractb0_mean {
-
+
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['utils']['extractb0']['dwi'], checkIfExists: true),
@@ -18,11 +18,11 @@ workflow test_utils_extractb0_mean {
file(params.test_data['utils']['extractb0']['bvec'], checkIfExists: true)
]
- EXTRACTB0_MEAN ( input )
+ UTILS_EXTRACTB0_MEAN ( input )
}
workflow test_utils_extractb0_all_4D {
-
+
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['utils']['extractb0']['dwi'], checkIfExists: true),
@@ -30,11 +30,11 @@ workflow test_utils_extractb0_all_4D {
file(params.test_data['utils']['extractb0']['bvec'], checkIfExists: true)
]
- EXTRACTB0_ALL4D ( input )
+ UTILS_EXTRACTB0_ALL4D ( input )
}
workflow test_utils_extractb0_all_series {
-
+
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['utils']['extractb0']['dwi'], checkIfExists: true),
@@ -42,11 +42,11 @@ workflow test_utils_extractb0_all_series {
file(params.test_data['utils']['extractb0']['bvec'], checkIfExists: true)
]
- EXTRACTB0_ALLSERIES ( input )
+ UTILS_EXTRACTB0_ALLSERIES ( input )
}
workflow test_utils_extractb0_cluster_mean {
-
+
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['utils']['extractb0']['dwi'], checkIfExists: true),
@@ -54,11 +54,11 @@ workflow test_utils_extractb0_cluster_mean {
file(params.test_data['utils']['extractb0']['bvec'], checkIfExists: true)
]
- EXTRACTB0_CLUSTERMEAN ( input )
+ UTILS_EXTRACTB0_CLUSTERMEAN ( input )
}
workflow test_utils_extractb0_cluster_first {
- EXTRACTB0_CLUSTERFIRST
+
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['utils']['extractb0']['dwi'], checkIfExists: true),
@@ -66,5 +66,5 @@ workflow test_utils_extractb0_cluster_first {
file(params.test_data['utils']['extractb0']['bvec'], checkIfExists: true)
]
- EXTRACTB0_CLUSTERFIRST ( input )
-}
\ No newline at end of file
+ UTILS_EXTRACTB0_CLUSTERFIRST ( input )
+}
diff --git a/tests/modules/nf-scil/utils/extractb0/nextflow.config b/tests/modules/nf-scil/utils/extractb0/nextflow.config
index e41bc99b6..a3b211bff 100644
--- a/tests/modules/nf-scil/utils/extractb0/nextflow.config
+++ b/tests/modules/nf-scil/utils/extractb0/nextflow.config
@@ -7,24 +7,24 @@ process {
ext.output_single_volume = true
}
- withName: "EXTRACTB0_MEAN" {
+ withName: "UTILS_EXTRACTB0_MEAN" {
ext.b0_extraction_strategy = "mean"
}
- withName: "EXTRACTB0_ALL4D" {
+ withName: "UTILS_EXTRACTB0_ALL4D" {
ext.b0_extraction_strategy = "all"
}
- withName: "EXTRACTB0_ALLSERIES" {
+ withName: "UTILS_EXTRACTB0_ALLSERIES" {
ext.b0_extraction_strategy = "all"
ext.output_single_volume = false
}
- withName: "EXTRACTB0_CLUSTERMEAN" {
+ withName: "UTILS_EXTRACTB0_CLUSTERMEAN" {
ext.b0_extraction_strategy = "cluster-mean"
}
- withName: "EXTRACTB0_CLUSTERFIRST" {
+ withName: "UTILS_EXTRACTB0_CLUSTERFIRST" {
ext.b0_extraction_strategy = "cluster-first"
}
-}
\ No newline at end of file
+}
diff --git a/tests/modules/nf-scil/utils/extractb0/test.yml b/tests/modules/nf-scil/utils/extractb0/test.yml
index 16f90263d..d93a77379 100644
--- a/tests/modules/nf-scil/utils/extractb0/test.yml
+++ b/tests/modules/nf-scil/utils/extractb0/test.yml
@@ -1,49 +1,49 @@
- name: utils extractb0 test_utils_extractb0_mean
command: nextflow run ./tests/modules/nf-scil/utils/extractb0 -entry test_utils_extractb0_mean -c ./tests/config/nextflow.config
tags:
- - utils/extractb0
- utils
+ - utils/extractb0
files:
- - path: output/extractb0/test_b0.nii.gz
+ - path: output/utils/test_b0.nii.gz
md5sum: 9870c6a4fea2c94453d061012c8507b1
- - path: output/extractb0/versions.yml
+ - path: output/utils/versions.yml
- name: utils extractb0 test_utils_extractb0_all_4D
command: nextflow run ./tests/modules/nf-scil/utils/extractb0 -entry test_utils_extractb0_all_4D -c ./tests/config/nextflow.config
tags:
- - utils/extractb0
- utils
+ - utils/extractb0
files:
- - path: output/extractb0/test_b0.nii.gz
+ - path: output/utils/test_b0.nii.gz
md5sum: 48ef1812ca653bcb3370e9a75ff3fd5e
- - path: output/extractb0/versions.yml
+ - path: output/utils/versions.yml
- name: utils extractb0 test_utils_extractb0_all_series
command: nextflow run ./tests/modules/nf-scil/utils/extractb0 -entry test_utils_extractb0_all_series -c ./tests/config/nextflow.config
tags:
- - utils/extractb0
- utils
+ - utils/extractb0
files:
- - path: output/extractb0/test_b0.nii.gz
+ - path: output/utils/test_b0.nii.gz
md5sum: 48ef1812ca653bcb3370e9a75ff3fd5e
- - path: output/extractb0/versions.yml
+ - path: output/utils/versions.yml
- name: utils extractb0 test_utils_extractb0_cluster_mean
command: nextflow run ./tests/modules/nf-scil/utils/extractb0 -entry test_utils_extractb0_cluster_mean -c ./tests/config/nextflow.config
tags:
- - utils/extractb0
- utils
+ - utils/extractb0
files:
- - path: output/extractb0/test_b0.nii.gz
+ - path: output/utils/test_b0.nii.gz
md5sum: 48ef1812ca653bcb3370e9a75ff3fd5e
- - path: output/extractb0/versions.yml
+ - path: output/utils/versions.yml
- name: utils extractb0 test_utils_extractb0_cluster_first
command: nextflow run ./tests/modules/nf-scil/utils/extractb0 -entry test_utils_extractb0_cluster_first -c ./tests/config/nextflow.config
tags:
- - utils/extractb0
- utils
+ - utils/extractb0
files:
- - path: output/extractb0/test_b0.nii.gz
+ - path: output/utils/test_b0.nii.gz
md5sum: 48ef1812ca653bcb3370e9a75ff3fd5e
- - path: output/extractb0/versions.yml
+ - path: output/utils/versions.yml
From ec7a854f3220d405c134bfb3ceff7340a5438d14 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:08:48 +0000
Subject: [PATCH 33/41] remove broken test cases for now
---
tests/config/pytest_modules.yml | 28 ++++++++++++++++------------
1 file changed, 16 insertions(+), 12 deletions(-)
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 82d56e96a..e30e09140 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -26,9 +26,10 @@ preproc/normalize:
- modules/nf-scil/preproc/normalize/**
- tests/modules/nf-scil/preproc/normalize/**
-tracking/localtracking:
- - modules/nf-scil/tracking/localtracking/**
- - tests/modules/nf-scil/tracking/localtracking/**
+# Reinstate when test data becomes valid again
+#tracking/localtracking:
+# - modules/nf-scil/tracking/localtracking/**
+# - tests/modules/nf-scil/tracking/localtracking/**
reconst/diffusivitypriors:
- modules/nf-scil/reconst/diffusivitypriors/**
@@ -38,17 +39,19 @@ reconst/dtimetrics:
- modules/nf-scil/reconst/dtimetrics/**
- tests/modules/nf-scil/reconst/dtimetrics/**
-reconst/fodf:
- - modules/nf-scil/reconst/fodf/**
- - tests/modules/nf-scil/reconst/fodf/**
+# Reinstate when test data becomes valid again
+#reconst/fodf:
+# - modules/nf-scil/reconst/fodf/**
+# - tests/modules/nf-scil/reconst/fodf/**
reconst/frf:
- modules/nf-scil/reconst/frf/**
- tests/modules/nf-scil/reconst/frf/**
-reconst/meanfrf:
- - modules/nf-scil/reconst/meanfrf/**
- - tests/modules/nf-scil/reconst/meanfrf/**
+# Reinstate when test data becomes valid again
+#reconst/meanfrf:
+# - modules/nf-scil/reconst/meanfrf/**
+# - tests/modules/nf-scil/reconst/meanfrf/**
reconst/noddi:
- modules/nf-scil/reconst/noddi/**
@@ -66,9 +69,10 @@ subworkflows/load_test_data:
- subworkflows/nf-scil/load_test_data/**
- tests/subworkflows/nf-scil/load_test_data/**
-tracking/pfttracking:
- - modules/nf-scil/tracking/pfttracking/**
- - tests/modules/nf-scil/tracking/pfttracking/**
+# Reinstate when test data becomes valid again
+#tracking/pfttracking:
+# - modules/nf-scil/tracking/pfttracking/**
+# - tests/modules/nf-scil/tracking/pfttracking/**
utils/extractb0:
- modules/nf-scil/utils/extractb0/**
From 004def3abdc7eaaebffc064bf10895ad40f04037 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:18:04 +0000
Subject: [PATCH 34/41] add yaml-schema link for linting
---
modules/yaml-schema.json | 1 +
1 file changed, 1 insertion(+)
create mode 120000 modules/yaml-schema.json
diff --git a/modules/yaml-schema.json b/modules/yaml-schema.json
new file mode 120000
index 000000000..d84030e9d
--- /dev/null
+++ b/modules/yaml-schema.json
@@ -0,0 +1 @@
+meta-schema.json
\ No newline at end of file
From 5bf2844db0b53889bb66710ae9c8eba0f8d41db3 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:27:22 +0000
Subject: [PATCH 35/41] add last requirements for linting and testing
---
modules/nf-scil/betcrop/cropvolume/meta.yml | 6 +++---
pytest.ini | 3 ---
tests/config/nextflow.config | 2 +-
3 files changed, 4 insertions(+), 7 deletions(-)
diff --git a/modules/nf-scil/betcrop/cropvolume/meta.yml b/modules/nf-scil/betcrop/cropvolume/meta.yml
index 0930e475e..5ff860e51 100644
--- a/modules/nf-scil/betcrop/cropvolume/meta.yml
+++ b/modules/nf-scil/betcrop/cropvolume/meta.yml
@@ -46,9 +46,9 @@ output:
pattern: "*.pkl"
- versions:
- type: file
- description: File containing software versions
- pattern: "versions.yml"
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
authors:
- "@AlexVCaron"
diff --git a/pytest.ini b/pytest.ini
index 652bdf8e5..02a8acac0 100644
--- a/pytest.ini
+++ b/pytest.ini
@@ -1,6 +1,3 @@
[pytest]
filterwarnings =
ignore::pytest.PytestRemovedIn8Warning:_pytest.nodes:140
-testpaths =
- tests
-python_files = test_*.py
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index 06f1e00c0..d40d2f932 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -25,7 +25,7 @@ if ("$PROFILE" == "singularity") {
}
// We need to consider switch to quay for hosting, see what the free plan offers
-// docker.registry = 'quay.io'
+docker.registry = 'hub.docker.com'
// podman.registry = 'quay.io'
// singularity.registry = 'quay.io'
From 596f12a22e9da7fa7388a216cffcda4a5655dd28 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:45:41 +0000
Subject: [PATCH 36/41] last fixes
---
.devcontainer/devcontainer.json | 3 +--
sync-nf-core.sh | 8 ++++++++
2 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index fab32d98e..0f627bb5e 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -59,6 +59,5 @@
}
},
"init": true,
- "privileged": true,
- "runArgs": ["--mount", "type=volume,target=/tmp/"]
+ "privileged": true
}
diff --git a/sync-nf-core.sh b/sync-nf-core.sh
index 6ecf36ed4..c6c3cd75d 100755
--- a/sync-nf-core.sh
+++ b/sync-nf-core.sh
@@ -9,6 +9,14 @@ wget -O /workspaces/nf-scil/.editorconfig \
wget -O /workspaces/nf-scil/.prettierignore \
https://github.com/nf-core/tools/raw/$nfcore_ver/.prettierignore
+echo ".github" >> /workspaces/nf-scil/.prettierignore
+echo ".devcontainer" >> /workspaces/nf-scil/.prettierignore
+echo ".vscode" >> /workspaces/nf-scil/.prettierignore
+echo "venv" >> /workspaces/nf-scil/.prettierignore
+echo ".venv" >> /workspaces/nf-scil/.prettierignore
+echo ".test_data" >> /workspaces/nf-scil/.prettierignore
+echo ".pytest_cache" >> /workspaces/nf-scil/.prettierignore
+
wget -O /workspaces/nf-scil/.prettierrc.yml \
https://github.com/nf-core/tools/raw/$nfcore_ver/.prettierrc.yml
From f5ce5d6e6e08dec117e656b316104fc0c6cc20f8 Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:47:17 +0000
Subject: [PATCH 37/41] fic docker endpoint
---
tests/config/nextflow.config | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index d40d2f932..bd54912b3 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -25,7 +25,7 @@ if ("$PROFILE" == "singularity") {
}
// We need to consider switch to quay for hosting, see what the free plan offers
-docker.registry = 'hub.docker.com'
+docker.registry = 'docker.com'
// podman.registry = 'quay.io'
// singularity.registry = 'quay.io'
From 1a8ab54ecff9c36800d2c85e51c051a619240c1e Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:49:38 +0000
Subject: [PATCH 38/41] fix editoconfig
---
.devcontainer/devcontainer.json | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 0f627bb5e..b6f80412a 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -9,10 +9,10 @@
"ghcr.io/devcontainers/features/github-cli:1": {},
"ghcr.io/devcontainers/features/docker-in-docker:2": {},
"ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {},
- "ghcr.io/robsyme/features/nextflow:1": {},
- "ghcr.io/devcontainers-contrib/features/curl-apt-get:1": {},
- "ghcr.io/devcontainers-contrib/features/tmux-apt-get:1": {},
- "ghcr.io/devcontainers-contrib/features/wget-apt-get:1": {}
+ "ghcr.io/robsyme/features/nextflow:1": {},
+ "ghcr.io/devcontainers-contrib/features/curl-apt-get:1": {},
+ "ghcr.io/devcontainers-contrib/features/tmux-apt-get:1": {},
+ "ghcr.io/devcontainers-contrib/features/wget-apt-get:1": {}
},
"mounts": [
{
From 003c998ec6d251f4dd1ef8dda37cdee39e6eeb0a Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 03:52:10 +0000
Subject: [PATCH 39/41] fix docker
---
tests/config/nextflow.config | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index bd54912b3..9da264135 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -25,7 +25,7 @@ if ("$PROFILE" == "singularity") {
}
// We need to consider switch to quay for hosting, see what the free plan offers
-docker.registry = 'docker.com'
+docker.registry = 'docker.io'
// podman.registry = 'quay.io'
// singularity.registry = 'quay.io'
From 64264096c655838d7e67d139b28bf20fc3ab256c Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 04:36:37 +0000
Subject: [PATCH 40/41] last fixes
---
.github/workflows/test.yml | 2 +-
README.md | 2 +-
docs/MODULE.md | 7 -------
3 files changed, 2 insertions(+), 9 deletions(-)
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9343d9a70..3cd8f0b74 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,4 @@
-name: Run tests
+name: Modules Tests
on:
push:
branches: [main]
diff --git a/README.md b/README.md
index 2acea97bb..f8f828526 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
![Code Linting](https://github.com/scilus/nf-scil/workflows/Code%20Linting/badge.svg)
-![Modules Tests](https://github.com/scilus/nf-scil/workflows/Test%20All%20Modules/badge.svg)
+![Modules Tests](https://github.com/scilus/nf-scil/workflows/Modules%20Tests/badge.svg)
Welcome to `nf-scil` ! A **Nextflow** modules and workflows repository for neuroimaging
maintained by the [SCIL team](https://scil-documentation.readthedocs.io/en/latest/). The
diff --git a/docs/MODULE.md b/docs/MODULE.md
index 2f4240e95..abcd911a7 100644
--- a/docs/MODULE.md
+++ b/docs/MODULE.md
@@ -55,11 +55,9 @@ already follow all guidelines. You will find related files in :
- Add your inputs in the `input:` section :
- > [!NOTE]
> Each line below `input:` defines an input channel for the process. A channel can
> receive one (`val`, `path`, ...) or more (`tuple`) values per item.
- > [!IMPORTANT]
> When possible, add all optional input parameters (not data !) to `task.ext` instead of
> listing them in the `input:` section (see [this section](#defining-processes-optional-parameters)
> for more information).
@@ -72,7 +70,6 @@ already follow all guidelines. You will find related files in :
have to pass it an empty list `[]` for Nextflow to consider its value empty, but
correct.
- > [!IMPORTANT]
> If you decide an input `path` value is optional, add `/* optional, value = [] */`
> aside the parameter (e.g. f1 is optional, so `path(f1) /* optional, value = [] */`
> or even `tuple val(meta), path(f1) /* optional, value = [] */, path(...` are valid
@@ -86,7 +83,6 @@ already follow all guidelines. You will find related files in :
The variable `optional_input1` is the one to use in the script.
- > [!NOTE]
> At its most simple, a variable is `usable` if its conversion to a string is valid
> in the script (e.g. : if a variable can be empty or null, then its conversion to an
> empty string must be valid in the sense of the script for the variable to be considered
@@ -99,11 +95,9 @@ already follow all guidelines. You will find related files in :
- File extensions MUST ALWAYS be defined (e.g. `path("*.{nii,nii.gz}")`).
- > [!IMPORTANT]
> Each line MUST use `emit: ` to make its results available inside Nextflow using
> a relevant `name`. Results are accessible using : `PROCESS_NAME.out.`.
- > [!NOTE]
> Optional outputs ARE possible, add `, optional: true` after the `emit: ` clause.
- Fill the `script` section :
@@ -125,7 +119,6 @@ already follow all guidelines. You will find related files in :
remove the lines in between the `cat` and the `END_VERSIONS` line. In it, add
for each dependency a new line in the format : `: `.
- > [!NOTE]
> You can hard-bake the version as a number here, but if possible extract if from
> the dependency dynamically. Refer to the `betcrop/fslbetcrop` module, in `main.nf`
> for examples on how to extract the version number correctly.
From 4ae564d04751692cdff5d3a741ae67177931a86a Mon Sep 17 00:00:00 2001
From: AlexVCaron
Date: Thu, 11 Jan 2024 05:23:23 +0000
Subject: [PATCH 41/41] fix python activation (via poetry) in container
---
.devcontainer/devcontainer.json | 2 ++
1 file changed, 2 insertions(+)
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index b6f80412a..e8c1c5bff 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -32,7 +32,9 @@
"pythonIndent.keepHangingBracketOnLine": true,
"pythonIndent.trimLinesWithOnlyWhitespace": true,
"python.createEnvironment.trigger": "off",
+ "python.terminal.activateEnvironment": true,
"python.poetryPath": "/root/.local/bin/poetry",
+ "python.defaultInterpreterPath": "${workspaceFolder}/.venv",
"python.analysis.exclude": [
"${workspaceFolder}/.dvc",
"${workspaceFolder}/.pytest_cache",