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Merge pull request #293 from nf-core/dev
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Patch release v2.5.1
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grst authored Jan 23, 2024
2 parents e03cd46 + 737ef17 commit 90cb6a4
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8 changes: 4 additions & 4 deletions .devcontainer/devcontainer.json
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Expand Up @@ -18,11 +18,11 @@
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.linting.pylintPath": "/opt/conda/bin/pylint",
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
},
},
}
8 changes: 4 additions & 4 deletions .github/workflows/ci.yml
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Expand Up @@ -26,13 +26,13 @@ jobs:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile:
[
profile: [
"test,docker --aligner alevin",
"test,docker --aligner kallisto",
"test,docker --aligner star",
"test,docker --aligner cellranger -stub",
"test,docker --aligner universc -stub",
"test,docker --aligner cellranger",
# "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
# "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
]
steps:
- name: Free some space
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,11 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v2.5.1

- Fix that cellranger workflow couldn't be run and enable CI for this workflow ([#288](https://github.com/nf-core/scrnaseq/pull/288)).
- Update modules ([#288]()https://github.com/nf-core/scrnaseq/pull/288).

## v2.5.0 - 2024-01-02

- Update template to v2.11.1 ([#279](https://github.com/nf-core/scrnaseq/pull/279))
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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,7 +1,7 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.5.0" target="_blank">nf-core/scrnaseq</a>
This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.5.1" target="_blank">nf-core/scrnaseq</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/scrnaseq/2.5.0/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/scrnaseq/2.5.1/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-scrnaseq-methods-description":
order: -1000
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25 changes: 20 additions & 5 deletions modules.json
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Expand Up @@ -20,24 +20,39 @@
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"cellrangerarc/count": {
"branch": "master",
"git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
"installed_by": ["modules"]
},
"cellrangerarc/mkgtf": {
"branch": "master",
"git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
"installed_by": ["modules"]
},
"cellrangerarc/mkref": {
"branch": "master",
"git_sha": "4196b1b2e7ce265892f3979eabf7a9ddc030702f",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"git_sha": "617777a807a1770f73deb38c80004bac06807eef",
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
"git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8",
"git_sha": "b8858b10356b87db4325341872816f9672541b7b",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "3a5fef109d113b4997c9822198664ca5f2716208",
"installed_by": ["modules"]
},
"kallistobustools/count": {
Expand All @@ -52,7 +67,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "4ab13872435962dadc239979554d13709e20bf29",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": ["modules"]
},
"star/genomegenerate": {
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6 changes: 3 additions & 3 deletions modules/local/mtx_to_seurat.nf
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Expand Up @@ -20,9 +20,9 @@ process MTX_TO_SEURAT {
script:
def aligner = params.aligner
if (params.aligner in [ 'cellranger', 'cellrangerarc' ]) {
matrix = "filtered_feature_bc_matrix/matrix.mtx.gz"
barcodes = "filtered_feature_bc_matrix/barcodes.tsv.gz"
features = "filtered_feature_bc_matrix/features.tsv.gz"
matrix = "matrix.mtx.gz"
barcodes = "barcodes.tsv.gz"
features = "features.tsv.gz"
} else if (params.aligner == "kallisto") {
matrix = "*count/counts_unfiltered/*.mtx"
barcodes = "*count/counts_unfiltered/*.barcodes.txt"
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84 changes: 84 additions & 0 deletions modules/nf-core/cellranger/count/templates/cellranger_count.py

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4 changes: 2 additions & 2 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf

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50 changes: 28 additions & 22 deletions modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap

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