From 86d73c75cd770b52870b729a49f8eec4e6c8ce62 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Mon, 12 Jun 2023 14:33:56 -0400 Subject: [PATCH 01/34] bump version 2.5.0dev --- CHANGELOG.md | 6 ++++++ nextflow.config | 2 +- tests/pipeline/bismark/main.nf.test.snap | 8 ++++---- tests/pipeline/bismark_hisat/main.nf.test.snap | 4 ++-- tests/pipeline/bwameth/main.nf.test.snap | 4 ++-- 5 files changed, 15 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 696d7219..9ea33412 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # nf-core/methylseq +## [v2.5.0] - [date] + +### Pipeline Updates + +### Bug fixes & refactoring + ## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02 ### Pipeline Updates diff --git a/nextflow.config b/nextflow.config index 7e1f1b86..f3f3a59e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -287,7 +287,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.4.0' + version = '2.5.0dev' doi = '10.5281/zenodo.1343417' } diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 27cf8920..64d7422f 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,19 +1,19 @@ { "clipping_params_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.4.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-06-01T02:27:54+0000" }, "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.4.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-06-01T02:27:54+0000" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.4.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-06-01T02:27:54+0000" }, @@ -30,7 +30,7 @@ }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.4.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-06-01T02:27:54+0000" }, diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index c016095d..aab97792 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.4.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-06-01T02:43:30+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.4.0}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-06-01T02:43:30+0000" }, diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 146f52e1..0f3e3671 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.4.0}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-05-28T00:53:43+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.4.0}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.5.0dev}}" ], "timestamp": "2023-05-28T00:53:43+0000" }, From 5ece807ee1104304d07e4ece3d997ded7f689b52 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:13:52 +0000 Subject: [PATCH 02/34] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CHANGELOG.md | 2 +- CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-methylseq_logo_light.png | Bin 11886 -> 76621 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowMain.groovy | 37 -- lib/WorkflowMethylseq.groovy | 45 +- main.nf | 16 + nextflow.config | 54 ++- nextflow_schema.json | 36 +- workflows/methylseq.nf | 25 +- 23 files changed, 177 insertions(+), 639 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 73c4a2ed..ec1edd1a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 1e3f7273..2c3f5ece 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 07a95b0a..045b5e63 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 51d93888..73a8cce2 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 57954d55..0a7b78af 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CHANGELOG.md b/CHANGELOG.md index a368ff6b..99290858 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v2.4.0dev - [date] +## v2.5.0dev - [date] Initial release of nf-core/methylseq, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index a3f26d76..2de30894 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index 45359e82..1e1e887a 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![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/) @@ -66,11 +66,11 @@ nextflow run nf-core/methylseq \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 4f40505b..642f22e7 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/methylseq Methods Description" section_href: "https://github.com/nf-core/methylseq" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/methylseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/methylseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
+

${tool_citations}

References

Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d1145e96..f6332716 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq + This report has been generated by the nf-core/methylseq analysis pipeline. 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"https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index 27911fa0..e1595836 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 39849f26..78ffb19f 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/methylseq --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/methylseq --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/methylseq -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index b86d8184..423aafad 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } // Print workflow version and exit on --version if (params.version) { @@ -62,14 +33,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/lib/WorkflowMethylseq.groovy b/lib/WorkflowMethylseq.groovy index 29066a19..87a43851 100755 --- a/lib/WorkflowMethylseq.groovy +++ b/lib/WorkflowMethylseq.groovy @@ -11,6 +11,7 @@ class WorkflowMethylseq { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowMethylseq { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/main.nf b/main.nf index d90e67c2..706abfcd 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index 51614373..a364ca80 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/methylseq profiles: ${params.custom_config_base}/pipeline/methylseq.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -219,8 +227,8 @@ manifest { homePage = 'https://github.com/nf-core/methylseq' description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' - version = '2.4.0dev' + nextflowVersion = '!>=23.04.0' + version = '2.5.0dev' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index acacb847..47d1a108 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/methylseq/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,12 +256,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/methylseq.nf b/workflows/methylseq.nf index 3908717d..bbb226ba 100644 --- a/workflows/methylseq.nf +++ b/workflows/methylseq.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowMethylseq.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowMethylseq.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow METHYLSEQ { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow METHYLSEQ { workflow_summary = WorkflowMethylseq.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowMethylseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowMethylseq.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 9e2d80f541e4723d4079ffbe49f09cf09efbd62e Mon Sep 17 00:00:00 2001 From: Felix Krueger Date: Tue, 25 Jul 2023 15:51:21 +0200 Subject: [PATCH 03/34] Update modules.config Adding publish mode for coverage2cytosine NOMe-seq filtered GpC coverage files. --- conf/modules.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/modules.config b/conf/modules.config index 50017087..71be35bb 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -256,6 +256,11 @@ process { path: { "${params.outdir}/bismark/coverage2cytosine/reports" }, mode: params.publish_dir_mode, pattern: "*_report.txt.gz" + ], + publishDir = [ + path: { "${params.outdir}/bismark/coverage2cytosine/coverage" }, + mode: params.publish_dir_mode, + pattern: "*cov.gz" ] ] } From 107f736dcb5ce58e311495fd8284a6a41951813e Mon Sep 17 00:00:00 2001 From: Felix Krueger Date: Tue, 25 Jul 2023 15:55:30 +0200 Subject: [PATCH 04/34] Update CHANGELOG.md Added comment for coverage2cytosine publishing of files. --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9ea33412..e35dc720 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,8 @@ ### Bug fixes & refactoring +- 🛠️ Added publishing of coverage (`*cov.gz`) files for NOMe-seq filtered reads for `coverage2cytosine` + ## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02 ### Pipeline Updates From e0487109f2ffb14c393c784646571aacbf54a2fa Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 31 Jul 2023 13:48:03 +0200 Subject: [PATCH 05/34] Apply easy module updates Some other module updates are available, but those will require changes to the pipeline code. --- modules.json | 6 +++--- modules/nf-core/fastqc/main.nf | 6 +++++- modules/nf-core/samtools/flagstat/main.nf | 11 +++++++++++ modules/nf-core/samtools/sort/main.nf | 2 -- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/modules.json b/modules.json index 2b51dee0..318b4e71 100644 --- a/modules.json +++ b/modules.json @@ -62,7 +62,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", "installed_by": ["modules"] }, "methyldackel/extract": { @@ -107,7 +107,7 @@ }, "samtools/flagstat": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c", "installed_by": ["modules"] }, "samtools/index": { @@ -117,7 +117,7 @@ }, "samtools/sort": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", "installed_by": ["modules"] }, "samtools/stats": { diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 07d5e433..249f9064 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -29,7 +29,11 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - fastqc $args --threads $task.cpus $renamed_files + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index eb7e72fc..b75707ec 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -32,4 +32,15 @@ process SAMTOOLS_FLAGSTAT { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.flagstat + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 1e5181d4..2b7753fd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -21,13 +21,11 @@ process SAMTOOLS_SORT { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sort_memory = (task.memory.mega/task.cpus).intValue() if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools sort \\ $args \\ -@ $task.cpus \\ - -m ${sort_memory}M \\ -o ${prefix}.bam \\ -T $prefix \\ $bam From ace1a391c9976a16ec4decebb412cf4a8dace62c Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 31 Jul 2023 13:50:58 +0200 Subject: [PATCH 06/34] Changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9ea33412..0cb85852 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,9 @@ ### Pipeline Updates +- Updated nf-core modules for FastQC, samtools sort, samtools flagstat + - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81) + ### Bug fixes & refactoring ## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02 From 2caf09ecb9794e59aa96dd27a72cb5a2b60e65e8 Mon Sep 17 00:00:00 2001 From: Wassim Salam <97744975+wassimsalam01@users.noreply.github.com> Date: Thu, 17 Aug 2023 02:39:34 +0200 Subject: [PATCH 07/34] Update nextflow_schema.json Updated zymo preset "--clip_r2" argument value from 15 to 10. --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 57ede4cc..5bdb022b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -220,7 +220,7 @@ "type": "boolean", "fa_icon": "fas fa-cut", "description": "Trimming preset for the Zymo kit.", - "help_text": "Equivalent to `--clip_r1 10` `--clip_r2 15` `--three_prime_clip_r1 10` `--three_prime_clip_r2 10`.\n\nAlso sets the `--non_directional` flag for Bismark." + "help_text": "Equivalent to `--clip_r1 10` `--clip_r2 10` `--three_prime_clip_r1 10` `--three_prime_clip_r2 10`.\n\nAlso sets the `--non_directional` flag for Bismark." } }, "fa_icon": "fas fa-prescription-bottle" From 591cc41edd1327bbe190c792946f0e868b42045e Mon Sep 17 00:00:00 2001 From: Wassim Salam <97744975+wassimsalam01@users.noreply.github.com> Date: Thu, 17 Aug 2023 02:44:34 +0200 Subject: [PATCH 08/34] Update nextflow_schema.json Updated all em_seq preset argument values from 8 to 10. --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 5bdb022b..5f6a0865 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -190,7 +190,7 @@ "type": "boolean", "fa_icon": "fas fa-cubes", "description": "Preset for EM-seq libraries.", - "help_text": "Equivalent to `--clip_r1 8` `--clip_r2 8` `--three_prime_clip_r1 8` `--three_prime_clip_r2 8`.\n\nAlso sets the `--maxins` flag to `1000` for Bismark." + "help_text": "Equivalent to `--clip_r1 10` `--clip_r2 10` `--three_prime_clip_r1 10` `--three_prime_clip_r2 10`.\n\nAlso sets the `--maxins` flag to `1000` for Bismark." }, "single_cell": { "type": "boolean", From 7910cc1fd2a3a7c08366552871ba4b84ed19bc6e Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 25 Aug 2023 13:18:47 -0500 Subject: [PATCH 09/34] refactor: Use fromSamplesheet instead of input_check --- assets/schema_input.json | 3 +- modules/local/samplesheet_check.nf | 32 ---------------------- subworkflows/local/input_check.nf | 44 ------------------------------ workflows/methylseq.nf | 44 ++++++++++++++++-------------- 4 files changed, 25 insertions(+), 98 deletions(-) delete mode 100644 modules/local/samplesheet_check.nf delete mode 100644 subworkflows/local/input_check.nf diff --git a/assets/schema_input.json b/assets/schema_input.json index e50fcf2e..070ee510 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -10,7 +10,8 @@ "sample": { "type": "string", "pattern": "^\\S+$", - "errorMessage": "Sample name must be provided and cannot contain spaces" + "errorMessage": "Sample name must be provided and cannot contain spaces", + "meta": ["id"] }, "fastq_1": { "type": "string", diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 3043b83b..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,32 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in nf-core/methylseq/bin/ - // def reference = params.fasta ? "--genome ${params.fasta}" : "" - """ - check_samplesheet.py \\ - $samplesheet \\ - samplesheet.valid.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf deleted file mode 100644 index 0aecf87f..00000000 --- a/subworkflows/local/input_check.nf +++ /dev/null @@ -1,44 +0,0 @@ -// -// Check input samplesheet and get read channels -// - -include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' - -workflow INPUT_CHECK { - take: - samplesheet // file: /path/to/samplesheet.csv - - main: - SAMPLESHEET_CHECK ( samplesheet ) - .csv - .splitCsv ( header:true, sep:',' ) - .map { create_fastq_channel(it) } - .set { reads } - - emit: - reads // channel: [ val(meta), [ reads ] ] - versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] -} - -// Function to get list of [ meta, [ fastq_1, fastq_2 ] ] -def create_fastq_channel(LinkedHashMap row) { - // create meta map - def meta = [:] - meta.id = row.sample - meta.single_end = row.single_end.toBoolean() - - // add path(s) of the fastq file(s) to the meta map - def fastq_meta = [] - if (!file(row.fastq_1).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" - } - if (meta.single_end) { - fastq_meta = [ meta, [ file(row.fastq_1) ] ] - } else { - if (!file(row.fastq_2).exists()) { - exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" - } - fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] - } - return fastq_meta -} diff --git a/workflows/methylseq.nf b/workflows/methylseq.nf index cf2bcca0..40b9ec60 100644 --- a/workflows/methylseq.nf +++ b/workflows/methylseq.nf @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' +include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet } from 'plugin/nf-validation' def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) def citation = '\n' + WorkflowMain.citation(workflow) + '\n' @@ -35,7 +35,6 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil // // SUBWORKFLOWS: Consisting of a mix of local and nf-core/modules // -include { INPUT_CHECK } from '../subworkflows/local/input_check' include { PREPARE_GENOME } from '../subworkflows/local/prepare_genome' // Aligner: bismark or bismark_hisat @@ -84,31 +83,34 @@ workflow METHYLSEQ { ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) // - // SUBWORKFLOW: Read in samplesheet, validate and stage input files + // Create input channel from input file provided through params.input // - INPUT_CHECK ( - file(params.input) - ) - .reads - .map { - meta, fastq -> + Channel + .fromSamplesheet("input") + .map { + meta, fastq_1, fastq_2 -> + if (!fastq_2) { + return [ meta + [ single_end:true ], [ fastq_1 ] ] + } else { + return [ meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] + } + } + .groupTuple() + .map { + meta, fastq -> def meta_clone = meta.clone() meta_clone.id = meta_clone.id.split('_')[0..-2].join('_') [ meta_clone, fastq ] - } - .groupTuple(by: [0]) - .branch { - meta, fastq -> + } + .groupTuple(by: [0]) + .branch { + meta, fastq -> single: fastq.size() == 1 - return [ meta, fastq.flatten() ] + return [ meta, fastq.flatten() ] multiple: fastq.size() > 1 - return [ meta, fastq.flatten() ] - } - .set { ch_fastq } - ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema + return [ meta, fastq.flatten() ] + } + .set { ch_fastq } // // MODULE: Concatenate FastQ files from same sample if required From 47d631c4a4e47af6655bbec54ffdcaa4a3153b1f Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 25 Aug 2023 13:20:02 -0500 Subject: [PATCH 10/34] fix: Add some magic from rnaseq --- assets/schema_input.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/assets/schema_input.json b/assets/schema_input.json index 070ee510..9e51e2e9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -15,11 +15,16 @@ }, "fastq_1": { "type": "string", + "format": "file-path", + "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", + "type": "string", + "format": "file-path", + "exists": true, "anyOf": [ { "type": "string", From b6bb69f3caffd3c486c359a9fce01b753c446540 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 25 Aug 2023 13:24:40 -0500 Subject: [PATCH 11/34] chore: Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0078f30..f591a8fe 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Updated template to nf-core/tools v2.9 - Updated nf-core modules for FastQC, samtools sort, samtools flagstat - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81) +- Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341) ### Bug fixes & refactoring From 675f73cad8c9947ce904a53c246c84c29129c0b0 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 25 Aug 2023 15:19:18 -0500 Subject: [PATCH 12/34] chore: Update snapshots --- tests/pipeline/bismark/main.nf.test.snap | 22 +++++++++---------- .../pipeline/bismark_hisat/main.nf.test.snap | 12 +++++----- tests/pipeline/bwameth/main.nf.test.snap | 12 +++++----- 3 files changed, 23 insertions(+), 23 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index 64d7422f..bb19a6da 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,21 +1,21 @@ { "clipping_params_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" }, "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" }, "single_end_nomeseq": { "content": [ @@ -26,13 +26,13 @@ "genome_results.txt:md5,79287f69ff6c8a308f0bb988c97f0e15", "genome_results.txt:md5,29e911b75d7160e964530e9607110164" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" }, "single_end": { "content": [ @@ -43,7 +43,7 @@ "genome_results.txt:md5,79287f69ff6c8a308f0bb988c97f0e15", "genome_results.txt:md5,29e911b75d7160e964530e9607110164" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" }, "single_end_rrbs": { "content": [ @@ -54,6 +54,6 @@ "genome_results.txt:md5,7a86634fd1c768d8302e071088641815", "genome_results.txt:md5,9e9b6841f3b3a46a299c61c516aa125e" ], - "timestamp": "2023-06-01T02:27:54+0000" + "timestamp": "2023-08-25T19:47:04+0000" } } \ No newline at end of file diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index aab97792..733cf6e1 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,15 +1,15 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-06-01T02:43:30+0000" + "timestamp": "2023-08-25T19:31:06+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-06-01T02:43:30+0000" + "timestamp": "2023-08-25T19:31:06+0000" }, "single_end": { "content": [ @@ -20,7 +20,7 @@ "genome_results.txt:md5,9956ed1dcf51e6975f4a6ab8fe156aba", "genome_results.txt:md5,1133ea5d1376389c6a17def89d2e90ec" ], - "timestamp": "2023-06-01T02:43:30+0000" + "timestamp": "2023-08-25T19:31:06+0000" }, "single_end_rrbs": { "content": [ @@ -31,6 +31,6 @@ "genome_results.txt:md5,58a2aeeb5eacca4c766bb23fee8f9013", "genome_results.txt:md5,473022a29cf12d97e75451a4eea67c02" ], - "timestamp": "2023-06-01T02:43:30+0000" + "timestamp": "2023-08-25T19:31:06+0000" } } \ No newline at end of file diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 0f3e3671..35463979 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,15 +1,15 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-05-28T00:53:43+0000" + "timestamp": "2023-08-25T19:53:02+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, SAMPLESHEET_CHECK={python=3.8.3}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-05-28T00:53:43+0000" + "timestamp": "2023-08-25T19:53:02+0000" }, "single_end": { "content": [ @@ -23,7 +23,7 @@ "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", "genome_results.txt:md5,3c7d14ea070df510941c55f72706a7a0" ], - "timestamp": "2023-05-28T00:53:43+0000" + "timestamp": "2023-08-25T19:53:02+0000" }, "single_end_rrbs": { "content": [ @@ -37,6 +37,6 @@ "genome_results.txt:md5,f01c68dd46ca9ec0af3d6ec926763b75", "genome_results.txt:md5,f4513f5aa1622937ccdcfe92a6f877c0" ], - "timestamp": "2023-05-28T00:53:43+0000" + "timestamp": "2023-08-25T19:53:02+0000" } } \ No newline at end of file From 0cd09ec35247039ca94b69621b5dcfbe56cf0799 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Mon, 28 Aug 2023 06:44:07 -0400 Subject: [PATCH 13/34] update tests, snapshots and ci --- .github/workflows/ci.yml | 47 ++-- tests/pipeline/bismark/main.nf.test | 138 +++++++++--- tests/pipeline/bismark/main.nf.test.snap | 207 +++++++++++++++--- tests/pipeline/bismark_hisat/main.nf.test | 65 ++++-- .../pipeline/bismark_hisat/main.nf.test.snap | 72 ++++-- tests/pipeline/bwameth/main.nf.test | 63 ++++-- tests/pipeline/bwameth/main.nf.test.snap | 74 +++++-- 7 files changed, 518 insertions(+), 148 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dcd9ff10..699e5287 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -21,42 +21,45 @@ concurrency: cancel-in-progress: true jobs: + define_nxf_versions: + name: Choose nextflow versions to test against depending on target branch + runs-on: ubuntu-latest + outputs: + matrix: ${{ steps.nxf_versions.outputs.matrix }} + steps: + - id: nxf_versions + run: | + if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then + echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT + else + echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT + fi + test: name: Run pipeline with test data + needs: define_nxf_versions runs-on: ubuntu-latest strategy: fail-fast: false matrix: - NXF_VER: - - "23.04.0" - - "latest-everything" - aligner: + NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} + test_tags: - "bismark" - "bismark_hisat" - "bwameth" profile: - "docker" - steps: - # Skip if it's a pull_request to dev and NXF_VER is '22.10.1' - - name: Skip condition - id: condition - run: | - if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then - echo "skip=true" >> $GITHUB_OUTPUT - fi + steps: - name: Check out pipeline code - if: steps.condition.outputs.skip != 'true' uses: actions/checkout@v3 - name: Hash Github Workspace - if: steps.condition.outputs.skip != 'true' id: hash_workspace run: | echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT - name: Cache test data - if: steps.condition.outputs.skip != 'true' id: cache-testdata uses: actions/cache@v3 with: @@ -64,7 +67,6 @@ jobs: key: ${{ steps.hash_workspace.outputs.digest }} - name: Check out test data - if: steps.cache-testdata.outputs.cache-hit != 'true' && steps.condition.outputs.skip != 'true' uses: actions/checkout@v3 with: repository: nf-core/test-datasets @@ -72,7 +74,6 @@ jobs: path: test-datasets/ - name: Replace remote paths in samplesheets - if: steps.condition.outputs.skip != 'true' run: | for f in ./test-datasets/samplesheet/*csv; do sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f @@ -83,25 +84,27 @@ jobs: done; - name: Install Nextflow - if: steps.condition.outputs.skip != 'true' uses: nf-core/setup-nextflow@v1 with: version: "${{ matrix.NXF_VER }}" - name: Install nf-test - if: steps.condition.outputs.skip != 'true' run: | wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER sudo mv nf-test /usr/local/bin/ - name: Run nf-test - if: steps.condition.outputs.skip != 'true' run: | - nf-test test tests/pipeline/${{ matrix.aligner }}/ --profile "test,${{ matrix.profile }}" --tap=test.tap + nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml - # If the test fails, output the software_versions.yml using the 'batcat' utility - name: Output log on failure if: failure() run: | sudo apt install bat > /dev/null batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml + + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: test.xml diff --git a/tests/pipeline/bismark/main.nf.test b/tests/pipeline/bismark/main.nf.test index 2bd75c9c..72af7acd 100644 --- a/tests/pipeline/bismark/main.nf.test +++ b/tests/pipeline/bismark/main.nf.test @@ -29,14 +29,34 @@ nextflow_pipeline { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end") }, + { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() } + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } } @@ -71,14 +91,31 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_bismark_bt2_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2.merged_bismark_bt2_splitting_report.txt"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end_rrbs") }, + { assert snapshot(path("$outputDir/bismark/alignments/Ecoli_10K_methylated_R1_bismark_bt2_pe.bam"), + path("$outputDir/bismark/alignments/SRR389222.merged_bismark_bt2.bam"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222.merged_bismark_bt2.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222.merged_bismark_bt2.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222.merged_bismark_bt2.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222.merged_bismark_bt2_splitting_report.txt"), + path("$outputDir/bismark/reference_genome/BismarkIndex/").list(), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() } + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222.merged_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222.merged_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() } ) } } @@ -113,19 +150,43 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end_nomeseq") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_nomeseq_software_versions") }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() } + { assert snapshot(path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli_10K.NOMe.CpG.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/Ecoli_10K.NOMe.GpC.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.CpG.cov.gz"), + path("$outputDir/bismark/coverage2cytosine/coverage/SRR389222.NOMe.GpC.cov.gz"), + path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_nomeseq") }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end__nomeseq_software_versions") }, + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } } - test("Bismark Clipping Params") { + test("Bismark Clip R1 - 2") { when { params { aligner = "bismark" @@ -138,10 +199,35 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("clipping_params_software_versions") }, - { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() } + { assert snapshot(path("$outputDir/bismark/deduplicated/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam"), + path("$outputDir/bismark/deduplicated/SRR389222_trimmed_bismark_bt2.deduplicated.bam"), + path("$outputDir/bismark/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/bedGraph/SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/mbias/SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark/methylation_calls/methylation_calls/").list(), + path("$outputDir/bismark/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark/methylation_calls/splitting_report/SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt"), + path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("clip_r1") }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("clip_r1_software_versions") }, + { assert new File("$outputDir/bismark/alignments/logs/Ecoli_10K_1_val_1_bismark_bt2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark/alignments/logs/SRR389222_trimmed_bismark_bt2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark/reports/Ecoli_10K_1_val_1_bismark_bt2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark/reports/SRR389222_trimmed_bismark_bt2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.html").exists() }, + { assert new File("$outputDir/bismark/summary/bismark_summary_report.txt").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bismark/multiqc_report.html").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } } - } diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index bb19a6da..a746a936 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,59 +1,208 @@ { - "clipping_params_software_versions": { - "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" - ], - "timestamp": "2023-08-25T19:47:04+0000" - }, "single_end_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:47:04+0000" + "timestamp": "2023-08-28T08:46:48+0000" }, "single_end_nomeseq_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:47:04+0000" + "timestamp": "2023-08-28T08:46:48+0000" }, "single_end_nomeseq": { "content": [ - "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,5ce32b88b28766d6fa0bf91ea9df77d6", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,d70ee229a29b68db8634fa7d568b7c53", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,3038a90a6e513c3b1c0de540439eb101", - "genome_results.txt:md5,7886cc1a96ee892e49898b0d69ed66f2", - "genome_results.txt:md5,79287f69ff6c8a308f0bb988c97f0e15", - "genome_results.txt:md5,29e911b75d7160e964530e9607110164" + "Ecoli_10K.NOMe.CpG.cov.gz:md5,b172ec70bfb6607a5704c68ed27dc8e4", + "Ecoli_10K.NOMe.GpC.cov.gz:md5,c975d1cbd714f79ce900378604b460b5", + "SRR389222.NOMe.CpG.cov.gz:md5,c86cd4e0523987bbb18191aeb2d2ecfd", + "SRR389222.NOMe.GpC.cov.gz:md5,bdd5bd0a9fc8be7cbd22d7fe302e8f17", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,a7464c83416ba057387df5d85b1bc1fe", + "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,6d631d8999657816e569a7a896f423d5", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,4a1bee24f279542dad02b167fabc6997", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", + "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,5a358982536d476e962319b6656441da", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,b08b8d4dc026106345ca6108e27ed601", + [ + "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,bca8572c7cd3cd45e148ba722ad4b12d", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,b0f6e9284b65d1bf3c813008c08656cc", + "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,ddc200fe98155bf88be3d98073a37238", + "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,e67409a20a141077edc1dc61972bb278", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,aca84c4d6fffb7bf72f4dcd4371dc89b", + "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a23e78b714eb1ef1810714d29557c620", + "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c3d32d42c00d94ea8322487aa0a20787", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d", + "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,288062a6b71f04688afad75dcd2230f9" + ], + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,79ebef1c474ff5bdb5f79b955208bb04", + "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", + "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", + "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], - "timestamp": "2023-08-25T19:47:04+0000" + "timestamp": "2023-08-28T08:46:48+0000" }, "single_end_rrbs_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:47:04+0000" + "timestamp": "2023-08-28T08:46:48+0000" + }, + "single_end__nomeseq_software_versions": { + "content": [ + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + ], + "timestamp": "2023-08-28T08:46:48+0000" + }, + "clip_r1_software_versions": { + "content": [ + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + ], + "timestamp": "2023-08-28T08:46:48+0000" }, "single_end": { "content": [ - "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,5ce32b88b28766d6fa0bf91ea9df77d6", - "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,d70ee229a29b68db8634fa7d568b7c53", - "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,3038a90a6e513c3b1c0de540439eb101", - "genome_results.txt:md5,7886cc1a96ee892e49898b0d69ed66f2", - "genome_results.txt:md5,79287f69ff6c8a308f0bb988c97f0e15", - "genome_results.txt:md5,29e911b75d7160e964530e9607110164" + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,a7464c83416ba057387df5d85b1bc1fe", + "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,7dba45955ae74159596a6ab41a9dcc87", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,66af42e52cdcaf5ceabddb33c9045a4d", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,60bf00418d5e2ede8740e3cba6c6ef61", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", + "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,bc48b8895f9ce84205a25899cf551624", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,ef5178734cdbba3326e22f8459b4db48", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,0bb6dd26908e239f695105230564b59b", + [ + "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,bca8572c7cd3cd45e148ba722ad4b12d", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,b0f6e9284b65d1bf3c813008c08656cc", + "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,ddc200fe98155bf88be3d98073a37238", + "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,e67409a20a141077edc1dc61972bb278", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,aca84c4d6fffb7bf72f4dcd4371dc89b", + "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,a23e78b714eb1ef1810714d29557c620", + "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,c3d32d42c00d94ea8322487aa0a20787", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d", + "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,288062a6b71f04688afad75dcd2230f9" + ], + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,79ebef1c474ff5bdb5f79b955208bb04", + "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,1c4a4288b3bcf1bbaa6b99e3c4b53ce9", + [ + [ + [ + "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", + "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", + "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", + "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", + "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" + ], + [ + "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", + "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", + "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", + "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", + "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", + "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] + ], + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" + ], + "genome_results.txt:md5,1e01c188f34b7d385e8b16156ab2b93e", + "genome_results.txt:md5,b99d4cfd82d21ac09ccb72865f9b3960" ], - "timestamp": "2023-08-25T19:47:04+0000" + "timestamp": "2023-08-28T08:46:48+0000" }, "single_end_rrbs": { "content": [ + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bam:md5,1497e3a06ee045cb82f834ddb4bcfe88", + "SRR389222.merged_bismark_bt2.bam:md5,c3e94ff13a934e0c78ebb6d40f7c8230", + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz:md5,66af42e52cdcaf5ceabddb33c9045a4d", + "SRR389222.merged_bismark_bt2.bedGraph.gz:md5,5d87f42769268bceb35b3341aa4dc92f", + "Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt:md5,29f3b882a51b63ce77d3d9c69b0e5f85", + "SRR389222.merged_bismark_bt2.M-bias.txt:md5,514f544046333337f0f74b7386b8afa6", + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bismark.cov.gz:md5,ef5178734cdbba3326e22f8459b4db48", + "SRR389222.merged_bismark_bt2.bismark.cov.gz:md5,b46638fd5f36fa4bce5f4f7b7247d995", + [ + "CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,bca8572c7cd3cd45e148ba722ad4b12d", + "CHG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,3fcc7974fd6c5cbacf231835f58d949b", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", + "CHG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,d80c75d6eb49f629c9f5f4c2e63588aa", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,e67409a20a141077edc1dc61972bb278", + "CHH_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,2fb870b779750951bec579ce7562736e", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", + "CHH_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,8fea7767cfe903f9671a506feaa7a8a6", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,c3d32d42c00d94ea8322487aa0a20787", + "CpG_OB_SRR389222.merged_bismark_bt2.txt.gz:md5,6537b18418e62410d9ae617480702c54", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", + "CpG_OT_SRR389222.merged_bismark_bt2.txt.gz:md5,3450512dc718e26edf13ff870cf3b159" + ], "Ecoli_10K_methylated_R1_bismark_bt2_pe_splitting_report.txt:md5,fa089f6146df9667862970b6ddc998b0", - "SRR389222_sub1_bismark_bt2_splitting_report.txt:md5,f59eac7a30ec7f1f690aac921a5591c0", - "SRR389222_sub2.merged_bismark_bt2_splitting_report.txt:md5,43ca6c76e47ce2eb1c8dd6027475b5a6", - "genome_results.txt:md5,41becdcecee6ebbdd46f472629731892", - "genome_results.txt:md5,7a86634fd1c768d8302e071088641815", - "genome_results.txt:md5,9e9b6841f3b3a46a299c61c516aa125e" + "SRR389222.merged_bismark_bt2_splitting_report.txt:md5,0ece57f8fc3aa659d2f0b7a09cf48398", + [ + [ + [ + "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", + "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", + "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", + "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", + "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", + "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" + ], + [ + "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", + "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", + "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", + "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", + "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", + "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", + "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" + ] + ], + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de" + ], + "genome_results.txt:md5,b6ba7868b12971aaad0d4a04e25acd0b", + "genome_results.txt:md5,f0d293867800a75becf2583c23729083" + ], + "timestamp": "2023-08-28T08:46:48+0000" + }, + "clip_r1": { + "content": [ + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bam:md5,388bb71e1e52628823e8b590d37cd665", + "SRR389222_trimmed_bismark_bt2.deduplicated.bam:md5,1bfe463dabf8727992e3ff6c19d8e7c1", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,4fbac770e7bf6b93e972d7e5bc494aac", + "SRR389222_trimmed_bismark_bt2.deduplicated.bedGraph.gz:md5,7b7535a28d655edaa94bcfa79957731a", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt:md5,83a004a3d957cf95f25933bcd828a8d4", + "SRR389222_trimmed_bismark_bt2.deduplicated.M-bias.txt:md5,90a6b76d41112c6de391d3a017638d95", + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.bismark.cov.gz:md5,9dc43af95c865440be68a4a41634f6c3", + "SRR389222_trimmed_bismark_bt2.deduplicated.bismark.cov.gz:md5,da2acc1e94842feee25e282575b74ce2", + [ + "CHG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,bd15affb231e6fa69f3daef1993e732f", + "CHG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,8175e992f5cd9c3cd9c2d82b36c3231b", + "CHG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,f5fee467014e215c43569efcc696a6e0", + "CHG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,9918a6c806dcb92a95e3806e8aae30f7", + "CHH_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,0c0f91367e3fd1d14710604af2cfeb1c", + "CHH_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,52dcf6c1e4e0cf4aaee2c4e42aad190f", + "CHH_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,8befa0112f299724b60eb6c5de1cdf1f", + "CHH_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,c4c864ee34ebb523d3c424b787ee9a3a", + "CpG_OB_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,50f969a02e2a50f140dedb90cdc3718d", + "CpG_OB_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,e066703e693e77ef934f64f16013c431", + "CpG_OT_Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated.txt.gz:md5,af7b19d0658a58a3a6f2632d9c0276f4", + "CpG_OT_SRR389222_trimmed_bismark_bt2.deduplicated.txt.gz:md5,b3c76b857baf4f2236137466b474cdb8" + ], + "Ecoli_10K_1_val_1_bismark_bt2_pe.deduplicated_splitting_report.txt:md5,373ac926ba4ceae1c4826f5ea4b3ada6", + "SRR389222_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,9a1a5d1e6722dda9e8a1953a01c415d0", + "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "genome_results.txt:md5,72bdf73fe97711a2ba75b5c59f3a5637", + "genome_results.txt:md5,5631f1632df00985946641cfc1601633" ], - "timestamp": "2023-08-25T19:47:04+0000" + "timestamp": "2023-08-28T08:46:48+0000" } } \ No newline at end of file diff --git a/tests/pipeline/bismark_hisat/main.nf.test b/tests/pipeline/bismark_hisat/main.nf.test index a368b722..e4bd6217 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test +++ b/tests/pipeline/bismark_hisat/main.nf.test @@ -28,14 +28,34 @@ nextflow_pipeline { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end") }, + { assert snapshot(path("$outputDir/bismark_hisat/deduplicated/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam"), + path("$outputDir/bismark_hisat/deduplicated/SRR389222_trimmed_bismark_hisat2.deduplicated.bam"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt"), + path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, - { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() } + { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_1_val_1_bismark_hisat2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222_trimmed_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_1_val_1_bismark_hisat2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222_trimmed_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() } ) } } @@ -70,14 +90,31 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub1_bismark_hisat2_splitting_report.txt"), - path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222_sub2.merged_bismark_hisat2_splitting_report.txt"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end_rrbs") }, + { assert snapshot(path("$outputDir/bismark_hisat/alignments/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam"), + path("$outputDir/bismark_hisat/alignments/SRR389222.merged_bismark_hisat2.bam"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/bedGraph/SRR389222.merged_bismark_hisat2.bedGraph.gz"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/mbias/SRR389222.merged_bismark_hisat2.M-bias.txt"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_calls/").list(), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/methylation_coverage/SRR389222.merged_bismark_hisat2.bismark.cov.gz"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt"), + path("$outputDir/bismark_hisat/methylation_calls/splitting_report/SRR389222.merged_bismark_hisat2_splitting_report.txt"), + path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, - { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() } + { assert new File("$outputDir/bismark_hisat/alignments/logs/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/alignments/logs/SRR389222.merged_bismark_hisat2_SE_report.txt").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/Ecoli_10K_methylated_R1_bismark_hisat2_PE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/reports/SRR389222.merged_bismark_hisat2_SE_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.html").exists() }, + { assert new File("$outputDir/bismark_hisat/summary/bismark_summary_report.txt").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bismark_hisat/multiqc_report.html").exists() } ) } } diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index 733cf6e1..f1fc2fe3 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -3,34 +3,76 @@ "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:31:06+0000" + "timestamp": "2023-08-28T10:04:42+0000" }, "single_end_rrbs_software_versions": { "content": [ "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:31:06+0000" + "timestamp": "2023-08-28T10:04:42+0000" }, "single_end": { "content": [ - "Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,bdec8746a4f29c56ddbe37a92f7d35dd", - "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,4020063dd8610b58b7b39c3ca62cef17", - "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,4db2155fdfae1cb9c7c758edba256e2e", - "genome_results.txt:md5,cd5d3b03821c038eb3bda24beb3ae938", - "genome_results.txt:md5,9956ed1dcf51e6975f4a6ab8fe156aba", - "genome_results.txt:md5,1133ea5d1376389c6a17def89d2e90ec" + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bam:md5,9e9b4adfeeb716e24ecba0bfad39c2e3", + "SRR389222_trimmed_bismark_hisat2.deduplicated.bam:md5,aa60cf9dcf302c185b12ced6f302a06e", + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bedGraph.gz:md5,539b06719ca6dcccaf2b86d8be571ace", + "SRR389222_trimmed_bismark_hisat2.deduplicated.bedGraph.gz:md5,dba86d0f60ad88aaeef1970ceef8376b", + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", + "SRR389222_trimmed_bismark_hisat2.deduplicated.M-bias.txt:md5,b19356395d4ae1ad83bd3ec38276e580", + [ + "CHG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,c2144bcfb7850b8c10bb8296dd2e09c1", + "CHG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,b0f6e9284b65d1bf3c813008c08656cc", + "CHG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", + "CHG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,5813137cea214c7759598ca442f29d47", + "CHH_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,4e8f5b27fbb933c572f269688004be38", + "CHH_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,aca84c4d6fffb7bf72f4dcd4371dc89b", + "CHH_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", + "CHH_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,1018c276fa14900e7b1edad0e23fc7ff", + "CpG_OB_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,3f58d13a3b47d639696dbb4478a39488", + "CpG_OB_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,0039a8c3f8971a5a99bc58bc1511fa0d", + "CpG_OT_Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", + "CpG_OT_SRR389222_trimmed_bismark_hisat2.deduplicated.txt.gz:md5,801c0dba9ca584d9c804a4254d7c4ea6" + ], + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated.bismark.cov.gz:md5,474c1291d09b023e91ed892b5a09ba80", + "SRR389222_trimmed_bismark_hisat2.deduplicated.bismark.cov.gz:md5,e58cba79f419cb411a77b656173d48ea", + "Ecoli_10K_1_val_1_bismark_hisat2_pe.deduplicated_splitting_report.txt:md5,a5dc04c52facdb5221a06ae7f3bca2e4", + "SRR389222_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,1f792e1fddb17140947f14008e1f9ffd", + "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "genome_results.txt:md5,f272f759bfed7e8a30ec2719e0b518aa", + "genome_results.txt:md5,7706d3790aee0e9244c490941ecd394f" ], - "timestamp": "2023-08-25T19:31:06+0000" + "timestamp": "2023-08-28T10:04:42+0000" }, "single_end_rrbs": { "content": [ + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bam:md5,53c34edee0bc7f34c9f4e9a3685dd706", + "SRR389222.merged_bismark_hisat2.bam:md5,204123a5f7cd77cba3a90b904443c7eb", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bedGraph.gz:md5,539b06719ca6dcccaf2b86d8be571ace", + "SRR389222.merged_bismark_hisat2.bedGraph.gz:md5,2b41ebc929eec351e21a16eec6f8fdd9", + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.M-bias.txt:md5,5fd8655f4b9dba2249a52b769fe50faf", + "SRR389222.merged_bismark_hisat2.M-bias.txt:md5,ea90b0495446d03e375aad42d598a9f9", + [ + "CHG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,c2144bcfb7850b8c10bb8296dd2e09c1", + "CHG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,3fcc7974fd6c5cbacf231835f58d949b", + "CHG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,7f49ecab1843458c28c3d6fe6a85149e", + "CHG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,e924ba0137252d4b470532cfc36524c2", + "CHH_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,4e8f5b27fbb933c572f269688004be38", + "CHH_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,2fb870b779750951bec579ce7562736e", + "CHH_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,d173808471dbb7c50ef43eb1f5f29faa", + "CHH_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,6e1d89e988f10fa528398b117a554fb1", + "CpG_OB_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,3f58d13a3b47d639696dbb4478a39488", + "CpG_OB_SRR389222.merged_bismark_hisat2.txt.gz:md5,6537b18418e62410d9ae617480702c54", + "CpG_OT_Ecoli_10K_methylated_R1_bismark_hisat2_pe.txt.gz:md5,6dfc57a2892d7cd3bebb7cbc0878196b", + "CpG_OT_SRR389222.merged_bismark_hisat2.txt.gz:md5,b07add9bb5ebc7d404e1505deb960654" + ], + "Ecoli_10K_methylated_R1_bismark_hisat2_pe.bismark.cov.gz:md5,474c1291d09b023e91ed892b5a09ba80", + "SRR389222.merged_bismark_hisat2.bismark.cov.gz:md5,626edb040f82e57c1f521bdb72618407", "Ecoli_10K_methylated_R1_bismark_hisat2_pe_splitting_report.txt:md5,76868c2015864a3f7c2b4cd1738e4765", - "SRR389222_sub1_bismark_hisat2_splitting_report.txt:md5,754ed7bf4d75acee466c48c05a11d331", - "SRR389222_sub2.merged_bismark_hisat2_splitting_report.txt:md5,0629e1f8b4727efe8fd69500783eec61", - "genome_results.txt:md5,3afd1eb7d4dc72a05e4d4de887d791e3", - "genome_results.txt:md5,58a2aeeb5eacca4c766bb23fee8f9013", - "genome_results.txt:md5,473022a29cf12d97e75451a4eea67c02" + "SRR389222.merged_bismark_hisat2_splitting_report.txt:md5,4a9e54ffb48c9bb1e5ac33aa77b25f5c", + "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "genome_results.txt:md5,13a70a3885acd9d55014aa1ad66e2bbb", + "genome_results.txt:md5,ae5b10e9a3ffa1ac7a4f4e736228ec49" ], - "timestamp": "2023-08-25T19:31:06+0000" + "timestamp": "2023-08-28T10:04:42+0000" } } \ No newline at end of file diff --git a/tests/pipeline/bwameth/main.nf.test b/tests/pipeline/bwameth/main.nf.test index 95d783c0..65b25dec 100644 --- a/tests/pipeline/bwameth/main.nf.test +++ b/tests/pipeline/bwameth/main.nf.test @@ -28,16 +28,32 @@ nextflow_pipeline { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat"), - path("$outputDir/methyldackel/Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222_sub2.markdup.sorted_CpG.bedGraph"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") } + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") }, + { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), + path("$outputDir/bwameth/deduplicated/Ecoli_10K.markdup.sorted.bam"), + path("$outputDir/bwameth/deduplicated/Ecoli_10K.markdup.sorted.bam.bai"), + path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam"), + path("$outputDir/bwameth/deduplicated/SRR389222.markdup.sorted.bam.bai"), + path("$outputDir/bwameth/reference_genome/").list(), + path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/methyldackel/Ecoli_10K.markdup.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222.markdup.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/mbias/Ecoli_10K.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end") }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_1.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/Ecoli_10K_2.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/trimgalore/logs/SRR389222.fastq.gz_trimming_report.txt").exists() }, + { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli_10K.markdup.sorted.MarkDuplicates.metrics.txt").exists() }, + { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222.markdup.sorted.MarkDuplicates.metrics.txt").exists() } ) } } @@ -73,16 +89,23 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat"), - path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat"), - path("$outputDir/methyldackel/Ecoli_10K_methylated.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222_sub1.sorted_CpG.bedGraph"), - path("$outputDir/methyldackel/SRR389222_sub2.sorted_CpG.bedGraph"), - path("$outputDir/qualimap/Ecoli_10K_methylated/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"), - path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt")).match("single_end_rrbs") }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") } + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_rrbs_software_versions") }, + { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/Ecoli_10K.stats"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.flagstat"), + path("$outputDir/bwameth/alignments/samtools_stats/SRR389222.stats"), + path("$outputDir/bwameth/reference_genome/").list(), + path("$outputDir/cat/SRR389222.merged.fastq.gz"), + path("$outputDir/methyldackel/Ecoli_10K.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/SRR389222.sorted_CpG.bedGraph"), + path("$outputDir/methyldackel/mbias/Ecoli_10K.mbias.txt"), + path("$outputDir/methyldackel/mbias/SRR389222.mbias.txt"), + path("$outputDir/qualimap/Ecoli_10K/genome_results.txt"), + path("$outputDir/qualimap/SRR389222/genome_results.txt")).match("single_end_rrbs") }, + { assert new File("$outputDir/fastqc/Ecoli_10K_1_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/Ecoli_10K_2_fastqc.html").exists() }, + { assert new File("$outputDir/fastqc/SRR389222_fastqc.html").exists() }, + { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() } ) } } diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 35463979..85e76f48 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -3,40 +3,70 @@ "content": [ "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:53:02+0000" + "timestamp": "2023-08-28T00:28:04+0000" }, "single_end_rrbs_software_versions": { "content": [ "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" ], - "timestamp": "2023-08-25T19:53:02+0000" + "timestamp": "2023-08-28T00:28:04+0000" }, "single_end": { "content": [ - "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub2.flagstat:md5,2166a52f81f9b3881e8ac060876aa2d9", - "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", - "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", - "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", - "genome_results.txt:md5,1ee2e29ac41c2cd7e6a0f00741e8d16e", - "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", - "genome_results.txt:md5,3c7d14ea070df510941c55f72706a7a0" + "Ecoli_10K.flagstat:md5,f520e87cc4050799a0dbed72909572ec", + "Ecoli_10K.stats:md5,b744221f284d3b3f5afe0b4b2d1849d7", + "SRR389222.flagstat:md5,f5a2dd6c9532bbfb8fe78aad010d8737", + "SRR389222.stats:md5,cc81b8c56d038e437a99d9c04b61ce2d", + "Ecoli_10K.markdup.sorted.bam:md5,f582d626f4b78f4e9cc63ca6e20b42cd", + "Ecoli_10K.markdup.sorted.bam.bai:md5,faa46b80545d7eb45dfc659b46f419b0", + "SRR389222.markdup.sorted.bam:md5,46b5b49280efe5d5c5d1692092e8926f", + "SRR389222.markdup.sorted.bam.bai:md5,ad6cfa0344e1ba5b9057ea39f337b3d2", + [ + [ + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", + "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", + "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", + "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", + "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", + "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", + "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" + ] + ], + "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "Ecoli_10K.markdup.sorted_CpG.bedGraph:md5,2fbe52f528b14b77380eceea8a621687", + "SRR389222.markdup.sorted_CpG.bedGraph:md5,febd0f93f46dfccabf69dbba3f518add", + "Ecoli_10K.mbias.txt:md5,3a448a2a6364b2de3129365a271c0534", + "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "genome_results.txt:md5,0f4749b54f9d923f0d4f20ad404b2062", + "genome_results.txt:md5,c786cc367645cee286360707e2624dca" ], - "timestamp": "2023-08-25T19:53:02+0000" + "timestamp": "2023-08-28T00:28:04+0000" }, "single_end_rrbs": { "content": [ - "Ecoli_10K_methylated.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", - "SRR389222_sub1.flagstat:md5,897d500a710a56a7098172167fa71108", - "SRR389222_sub2.flagstat:md5,2d680c5657fc029b703b217be4af68e2", - "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,3656c54896013b76de978ab95c3f5975", - "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", - "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", - "genome_results.txt:md5,ca30867e16c5ca25c850c81d88563d41", - "genome_results.txt:md5,f01c68dd46ca9ec0af3d6ec926763b75", - "genome_results.txt:md5,f4513f5aa1622937ccdcfe92a6f877c0" + "Ecoli_10K.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", + "Ecoli_10K.stats:md5,ff675c98abdae3c1bd83b26704d89e82", + "SRR389222.flagstat:md5,a90f1bdcb30f4d0597ccf69fe0b37b1f", + "SRR389222.stats:md5,b99800367e21a0c7c0d87e5fe29d9609", + [ + [ + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", + "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", + "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", + "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", + "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", + "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", + "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" + ] + ], + "SRR389222.merged.fastq.gz:md5,ba5df0639e25988059a6f5bf309dbb6e", + "Ecoli_10K.sorted_CpG.bedGraph:md5,513797bcafa8724fc61484e2686af517", + "SRR389222.sorted_CpG.bedGraph:md5,a754358e8b95db30602aa29835a896bd", + "Ecoli_10K.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", + "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "genome_results.txt:md5,e5e1ab8eb875aaf090b3a0d9b1927810", + "genome_results.txt:md5,199902f9d8f10f73bcb0a1ce29ceca5d" ], - "timestamp": "2023-08-25T19:53:02+0000" + "timestamp": "2023-08-28T00:28:04+0000" } } \ No newline at end of file From 1737edadee9eeb1692ecdc41efb693ddf1cab3dc Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 21 Sep 2023 12:58:29 +0200 Subject: [PATCH 14/34] Update nextflow.config support pipeline-specific configs --- nextflow.config | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 4da6ab70..cb64fcec 100644 --- a/nextflow.config +++ b/nextflow.config @@ -133,11 +133,12 @@ try { // Load nf-core/methylseq custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/methylseq.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/methylseq profiles: ${params.custom_config_base}/pipeline/methylseq.config") -// } +try { + includeConfig "${params.custom_config_base}/pipeline/methylseq.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/methylseq profiles: ${params.custom_config_base}/pipeline/methylseq.config") +} + profiles { debug { dumpHashes = true From 8e2a6f3effe10d8ca0b79be328273671e7f1b771 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 25 Sep 2023 15:16:40 +0000 Subject: [PATCH 15/34] Template update for nf-core/tools version 2.10 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcments.yml | 68 +++++++++ CITATIONS.md | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++---- README.md | 21 +-- assets/multiqc_config.yml | 4 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowMethylseq.groovy | 2 +- main.nf | 3 + modules.json | 6 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 7 +- nextflow_schema.json | 15 -- workflows/methylseq.nf | 1 + 21 files changed, 251 insertions(+), 76 deletions(-) create mode 100644 .github/workflows/release-announcments.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a584..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index ec1edd1a..88e23a1a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -> If you need help using or modifying nf-core/methylseq then the best place to ask is on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/methylseq then the best place to ask is on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 00000000..6ad33927 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/CITATIONS.md b/CITATIONS.md index 2de30894..83fe3bf1 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f..c089ec78 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/README.md b/README.md index 1e1e887a..5f858c66 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/methylseq](docs/images/nf-core-methylseq_logo_light.png#gh-light-mode-only) ![nf-core/methylseq](docs/images/nf-core-methylseq_logo_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/methylseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -29,10 +30,11 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +with `-profile test` before running the workflow on actual data. +::: + + - [Bismark](https://doi.org/10.1093/bioinformatics/btr167) > Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics, Volume 27, Issue 11, 1 June 2011, Pages 1571–1572, doi: [10.1093/bioinformatics/btr167](https://doi.org/10.1093/bioinformatics/btr167) From 157d807c60c4119c266cf1fe6ab9b7fe61d85391 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 17 Oct 2023 18:19:11 +0200 Subject: [PATCH 29/34] style: Run bib through citations --- assets/citations.bib | 67 ++++++++++++++++++++++---------------------- 1 file changed, 33 insertions(+), 34 deletions(-) diff --git a/assets/citations.bib b/assets/citations.bib index 8e41f1f0..7de27928 100644 --- a/assets/citations.bib +++ b/assets/citations.bib @@ -1,42 +1,41 @@ @misc{bwa-meth, - title={Fast and accurate alignment of long bisulfite-seq reads}, - author={Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz}, - year={2014}, - eprint={1401.1129}, - archivePrefix={arXiv}, - primaryClass={q-bio.GN} + title = {Fast and accurate alignment of long bisulfite-seq reads}, + author = {Brent S. Pedersen and Kenneth Eyring and Subhajyoti De and Ivana V. Yang and David A. Schwartz}, + year = 2014, + eprint = {1401.1129}, + archiveprefix = {arXiv}, + primaryclass = {q-bio.GN} } - @misc{Picard, - title = {Picard toolkit}, - year = {2019}, - publisher = {Broad Institute}, - journal = {Broad Institute, GitHub repository}, - howpublished = {\url{https://broadinstitute.github.io/picard/}} + title = {Picard toolkit}, + year = 2019, + journal = {Broad Institute, GitHub repository}, + publisher = {Broad Institute}, + howpublished = {\url{https://broadinstitute.github.io/picard/}} } @article{Qualimap, - author = {Okonechnikov, Konstantin and Conesa, Ana and García-Alcalde, Fernando}, - title = "{Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data}", - journal = {Bioinformatics}, - volume = {32}, - number = {2}, - pages = {292-294}, - year = {2015}, - month = {10}, - abstract = "{Motivation: Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.Results: Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.Availability and implementation: The implementation of the software along with documentation is freely available at http://www.qualimap.org.Contact:  meyer@mpiib-berlin.mpg.deSupplementary information:  Supplementary data are available at Bioinformatics online.}", - issn = {1367-4803}, - doi = {10.1093/bioinformatics/btv566}, - url = {https://doi.org/10.1093/bioinformatics/btv566}, - eprint = {https://academic.oup.com/bioinformatics/article-pdf/32/2/292/49016552/bioinformatics\_32\_2\_292.pdf}, + title = {{Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data}}, + author = {Okonechnikov, Konstantin and Conesa, Ana and García-Alcalde, Fernando}, + year = 2015, + month = 10, + journal = {Bioinformatics}, + volume = 32, + number = 2, + pages = {292--294}, + doi = {10.1093/bioinformatics/btv566}, + issn = {1367-4803}, + url = {https://doi.org/10.1093/bioinformatics/btv566}, + abstract = {{Motivation: Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.Results: Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.Availability and implementation: The implementation of the software along with documentation is freely available at http://www.qualimap.org.Contact:  meyer@mpiib-berlin.mpg.deSupplementary information:  Supplementary data are available at Bioinformatics online.}}, + eprint = {https://academic.oup.com/bioinformatics/article-pdf/32/2/292/49016552/bioinformatics\_32\_2\_292.pdf} } @article{Preseq, - title={Predicting the molecular complexity of sequencing libraries}, - author={Daley, Timothy and Smith, Andrew D}, - journal={Nature methods}, - volume={10}, - number={4}, - pages={325--327}, - year={2013}, - publisher={Nature Publishing Group US New York} - doi = {10.1038/nmeth.2375}, + title = {Predicting the molecular complexity of sequencing libraries}, + author = {Daley, Timothy and Smith, Andrew D}, + year = 2013, + journal = {Nature methods}, + publisher = {Nature Publishing Group US New York}, + volume = 10, + number = 4, + pages = {325--327}, + doi = {10.1038/nmeth.2375} } From e6db8a8e85202a6a52abbd0c8467a1dd6a3834e9 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 18 Oct 2023 10:45:15 +0200 Subject: [PATCH 30/34] chore: Add issues that were missed and add date --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a5c85b10..99f1a530 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,19 +1,23 @@ # nf-core/methylseq -## [v2.5.0] - [date] +## [v2.5.0](https://github.com/nf-core/methylseq/releases/tag/2.5.0) - 2023-10-18 ### Pipeline Updates - Updated template to nf-core/tools v2.9 +- Updated template to nf-core/tools v2.10 - Updated nf-core modules for FastQC, samtools sort, samtools flagstat - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81) - Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341) - Update Maintainers and add CODEOWNERS [#345](https://github.com/nf-core/methylseq/pull/345) - Update schema to utilize exists and add more patterns [#342](https://github.com/nf-core/methylseq/pull/342) +- Support pipeline-specific configs [#343](https://github.com/nf-core/methylseq/pull/343) ### Bug fixes & refactoring - 🛠️ Added publishing of coverage (`*cov.gz`) files for NOMe-seq filtered reads for `coverage2cytosine` +- 🛠️ Wrong display values for "zymo" and "em_seq" presets on help page [#335](https://github.com/nf-core/methylseq/pull/335) +- Use new Citation tools functions [#336](https://github.com/nf-core/methylseq/issues/336) ## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02 From ee11838f4d5415daab51a8554f7740c57a6dd39b Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 18 Oct 2023 10:46:14 +0200 Subject: [PATCH 31/34] chore: Bump version --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 6ec19d1b..141d7e5b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -299,7 +299,7 @@ manifest { description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.5.0dev' + version = '2.5.0' doi = '10.5281/zenodo.1343417' } From 45c446848e269cd4aefa41a4540124345381ecc7 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 18 Oct 2023 09:10:40 +0000 Subject: [PATCH 32/34] add emojis to changelog v2.5.0 --- CHANGELOG.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 99f1a530..9cb2dab0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,20 +4,20 @@ ### Pipeline Updates -- Updated template to nf-core/tools v2.9 -- Updated template to nf-core/tools v2.10 -- Updated nf-core modules for FastQC, samtools sort, samtools flagstat - - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81) -- Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341) -- Update Maintainers and add CODEOWNERS [#345](https://github.com/nf-core/methylseq/pull/345) -- Update schema to utilize exists and add more patterns [#342](https://github.com/nf-core/methylseq/pull/342) -- Support pipeline-specific configs [#343](https://github.com/nf-core/methylseq/pull/343) +- 🔄 Updated template to nf-core/tools v2.9 +- 🔄 Updated template to nf-core/tools v2.10 +- 🔧 Updated nf-core modules for FastQC, samtools sort, samtools flagstat + - ❌ Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81) +- 🧾 Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341) +- 🚀 Update Maintainers and add CODEOWNERS [#345](https://github.com/nf-core/methylseq/pull/345) +- ⚙️ Update schema to utilize exists and add more patterns [#342](https://github.com/nf-core/methylseq/pull/342) +- 📁 Support pipeline-specific configs [#343](https://github.com/nf-core/methylseq/pull/343) ### Bug fixes & refactoring - 🛠️ Added publishing of coverage (`*cov.gz`) files for NOMe-seq filtered reads for `coverage2cytosine` - 🛠️ Wrong display values for "zymo" and "em_seq" presets on help page [#335](https://github.com/nf-core/methylseq/pull/335) -- Use new Citation tools functions [#336](https://github.com/nf-core/methylseq/issues/336) +- 📚 Use new Citation tools functions [#336](https://github.com/nf-core/methylseq/issues/336) ## [v2.4.0](https://github.com/nf-core/methylseq/releases/tag/2.4.0) - 2023-06-02 From 18148380d32219eae71ab9aa6f2eee7418c23cb1 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Wed, 18 Oct 2023 09:23:41 +0000 Subject: [PATCH 33/34] bump snapshots for 2.5.0 release --- tests/pipeline/bismark/main.nf.test.snap | 6 +++--- tests/pipeline/bismark_hisat/main.nf.test.snap | 6 +++--- tests/pipeline/bwameth/main.nf.test.snap | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/tests/pipeline/bismark/main.nf.test.snap b/tests/pipeline/bismark/main.nf.test.snap index a746a936..86e57c54 100644 --- a/tests/pipeline/bismark/main.nf.test.snap +++ b/tests/pipeline/bismark/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, "single_end_nomeseq_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" ], "timestamp": "2023-08-28T08:46:48+0000" }, @@ -205,4 +205,4 @@ ], "timestamp": "2023-08-28T08:46:48+0000" } -} \ No newline at end of file +} diff --git a/tests/pipeline/bismark_hisat/main.nf.test.snap b/tests/pipeline/bismark_hisat/main.nf.test.snap index f1fc2fe3..5b1816cd 100644 --- a/tests/pipeline/bismark_hisat/main.nf.test.snap +++ b/tests/pipeline/bismark_hisat/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" ], "timestamp": "2023-08-28T10:04:42+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0}}" ], "timestamp": "2023-08-28T10:04:42+0000" }, @@ -75,4 +75,4 @@ ], "timestamp": "2023-08-28T10:04:42+0000" } -} \ No newline at end of file +} diff --git a/tests/pipeline/bwameth/main.nf.test.snap b/tests/pipeline/bwameth/main.nf.test.snap index 85e76f48..50a79bf2 100644 --- a/tests/pipeline/bwameth/main.nf.test.snap +++ b/tests/pipeline/bwameth/main.nf.test.snap @@ -1,13 +1,13 @@ { "single_end_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, Workflow={nf-core/methylseq=2.5.0}}" ], "timestamp": "2023-08-28T00:28:04+0000" }, "single_end_rrbs_software_versions": { "content": [ - "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0dev}}" + "{BWAMETH_ALIGN={bwameth=0.2.2}, BWAMETH_INDEX={bwameth=0.2.2}, CAT_FASTQ={cat=8.30}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, FASTQC={fastqc=0.11.9}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, Workflow={nf-core/methylseq=2.5.0}}" ], "timestamp": "2023-08-28T00:28:04+0000" }, @@ -69,4 +69,4 @@ ], "timestamp": "2023-08-28T00:28:04+0000" } -} \ No newline at end of file +} From f4fe5fd3150f323484ec04f41427ddcf55d312b6 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Wed, 18 Oct 2023 11:42:38 +0200 Subject: [PATCH 34/34] style: Ignore MultiQC config I refuse to update this every release. Co-authored-by: sateeshperi --- .nf-core.yml | 2 +- assets/multiqc_config.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 798bca42..61d85c35 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,4 +1,3 @@ -# FIXME - CI currently runs for dev and dsl2 branches, remove the latter before merging to dev repository_type: pipeline lint: files_unchanged: @@ -6,3 +5,4 @@ lint: files_exist: - bin/markdown_to_html.py actions_ci: False + multiqc_config: False diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 79b2f208..cc74e519 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/methylseq + This report has been generated by the nf-core/methylseq analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: