diff --git a/.gitignore b/.gitignore index a42ce0162..a534a6e0f 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ testing/ testing* *.pyc null/ + +.nf-test* diff --git a/docs/output.md b/docs/output.md index a1336953a..0fc9a1784 100644 --- a/docs/output.md +++ b/docs/output.md @@ -321,7 +321,6 @@ Once installed, open IGV, go to `File > Open Session` and select the `igv_sessio - `genome/` - A number of genome-specific files are generated by the pipeline in order to aid in the filtering of the data, and because they are required by standard tools such as BEDTools. These can be found in this directory along with the genome fasta file which is required by IGV. If using a genome from AWS iGenomes and if it exists a `README.txt` file containing information about the annotation version will also be saved in this directory. - `genome/index/` - - `bwa/`: Directory containing BWA indices. - `bowtie2/`: Directory containing BOWTIE2 indices. - `chromap/`: Directory containing Chromap indices. diff --git a/modules/local/bam_remove_orphans.nf b/modules/local/bam_remove_orphans.nf index 2bfb7dfd1..6d43011d6 100644 --- a/modules/local/bam_remove_orphans.nf +++ b/modules/local/bam_remove_orphans.nf @@ -43,4 +43,15 @@ process BAM_REMOVE_ORPHANS { END_VERSIONS """ } + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/local/bamtools_filter.nf b/modules/local/bamtools_filter.nf index a1e8feede..49349ddec 100644 --- a/modules/local/bamtools_filter.nf +++ b/modules/local/bamtools_filter.nf @@ -40,4 +40,16 @@ process BAMTOOLS_FILTER { bamtools: \$(echo \$(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + bamtools: \$(echo \$(bamtools --version 2>&1) | sed 's/^.*bamtools //; s/Part .*\$//') + END_VERSIONS + """ } diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf index fb274631a..23cdf4cbc 100644 --- a/modules/local/bedtools_genomecov.nf +++ b/modules/local/bedtools_genomecov.nf @@ -40,4 +40,16 @@ process BEDTOOLS_GENOMECOV { bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bedGraph + touch ${prefix}.scale_factor.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ } diff --git a/modules/local/frip_score.nf b/modules/local/frip_score.nf index 77f856bc0..ae304d56a 100644 --- a/modules/local/frip_score.nf +++ b/modules/local/frip_score.nf @@ -31,4 +31,16 @@ process FRIP_SCORE { samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.FRiP.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ } diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf index b2273c704..620529ce0 100644 --- a/modules/local/multiqc.nf +++ b/modules/local/multiqc.nf @@ -71,4 +71,16 @@ process MULTIQC { multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) END_VERSIONS """ + + stub: + """ + mkdir -p multiqc_data + touch multiqc_report.html + touch multiqc_data/multiqc.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) + END_VERSIONS + """ } diff --git a/modules/local/multiqc_custom_phantompeakqualtools.nf b/modules/local/multiqc_custom_phantompeakqualtools.nf index c8d1346f5..57341b532 100644 --- a/modules/local/multiqc_custom_phantompeakqualtools.nf +++ b/modules/local/multiqc_custom_phantompeakqualtools.nf @@ -33,4 +33,17 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS { r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.spp_nsc_mqc.tsv + touch ${prefix}.spp_rsc_mqc.tsv + touch ${prefix}.spp_correlation_mqc.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/nf-test.config b/nf-test.config index 3a1fff59f..b3f60e800 100644 --- a/nf-test.config +++ b/nf-test.config @@ -19,6 +19,6 @@ config { // load the necessary plugins plugins { - load "nft-utils@0.0.3" + load "nft-utils@0.0.5" } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 34d7c8f9b..60dcda02a 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2025-07-08T11:38:17+00:00", - "description": "

\n \n \n \"nf-core/chipseq\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/chipseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/chipseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23chipseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/chipseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/chipseq** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/chipseq \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/chipseq/usage) and the [parameter documentation](https://nf-co.re/chipseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/chipseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/chipseq/output).\n\n## Credits\n\nnf-core/chipseq was originally written by Espinosa-Carrasco J, Patel H, Wang C, Ewels P.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#chipseq` channel](https://nfcore.slack.com/channels/chipseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-04-30T12:25:55+00:00", + "description": "

\n \n \n \"nf-core/chipseq\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/chipseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/chipseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/chipseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/chipseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3240506-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3240506)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/chipseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23chipseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/chipseq)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nfcore/chipseq** is a bioinformatics analysis pipeline used for Chromatin ImmunoPrecipitation sequencing (ChIP-seq) data.\n\nOn release, automated continuous integration tests run the pipeline on a [full-sized dataset](https://github.com/nf-core/test-datasets/tree/chipseq#full-test-dataset-origin) on the AWS cloud infrastructure. The dataset consists of FoxA1 (transcription factor) and EZH2 (histone,mark) IP experiments from _Franco et al. 2015_ ([GEO: GSE59530](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59530), [PMID: 25752574](https://pubmed.ncbi.nlm.nih.gov/25752574/)) and _Popovic et al. 2014_ ([GEO: GSE57632](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57632), [PMID: 25188243](https://pubmed.ncbi.nlm.nih.gov/25188243/)), respectively. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from running the full-sized tests can be viewed on the [nf-core website](https://nf-co.re/chipseq/results).\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\n## Online videos\n\nA short talk about the history, current status and functionality on offer in this pipeline was given by Jose Espinosa-Carrasco ([@joseespinosa](https://github.com/joseespinosa)) on [26th July 2022](https://nf-co.re/events/2022/bytesize-chipseq) as part of the nf-core/bytesize series.\n\nYou can find numerous talks on the [nf-core events page](https://nf-co.re/events) from various topics including writing pipelines/modules in Nextflow DSL2, using nf-core tooling, running nf-core pipelines as well as more generic content like contributing to Github. Please check them out!\n\n## Pipeline summary\n\n![nf-core/chipseq metro map](docs/images/nf-core-chipseq_metro_map_grey.png)\n\n1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))\n3. Choice of multiple aligners\n 1.([`BWA`](https://sourceforge.net/projects/bio-bwa/files/))\n 2.([`Chromap`](https://github.com/haowenz/chromap))\n 3.([`Bowtie2`](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))\n 4.([`STAR`](https://github.com/alexdobin/STAR))\n4. Mark duplicates ([`picard`](https://broadinstitute.github.io/picard/))\n5. Merge alignments from multiple libraries of the same sample ([`picard`](https://broadinstitute.github.io/picard/))\n 1. Re-mark duplicates ([`picard`](https://broadinstitute.github.io/picard/))\n 2. Filtering to remove:\n - reads mapping to blacklisted regions ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/), [`BEDTools`](https://github.com/arq5x/bedtools2/))\n - reads that are marked as duplicates ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n - reads that are not marked as primary alignments ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n - reads that are unmapped ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n - reads that map to multiple locations ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/))\n - reads containing > 4 mismatches ([`BAMTools`](https://github.com/pezmaster31/bamtools))\n - reads that have an insert size > 2kb ([`BAMTools`](https://github.com/pezmaster31/bamtools); _paired-end only_)\n - reads that map to different chromosomes ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)\n - reads that arent in FR orientation ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)\n - reads where only one read of the pair fails the above criteria ([`Pysam`](http://pysam.readthedocs.io/en/latest/installation.html); _paired-end only_)\n 3. Alignment-level QC and estimation of library complexity ([`picard`](https://broadinstitute.github.io/picard/), [`Preseq`](http://smithlabresearch.org/software/preseq/))\n 4. Create normalised bigWig files scaled to 1 million mapped reads ([`BEDTools`](https://github.com/arq5x/bedtools2/), [`bedGraphToBigWig`](http://hgdownload.soe.ucsc.edu/admin/exe/))\n 5. Generate gene-body meta-profile from bigWig files ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html))\n 6. Calculate genome-wide IP enrichment relative to control ([`deepTools`](https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html))\n 7. Calculate strand cross-correlation peak and ChIP-seq quality measures including NSC and RSC ([`phantompeakqualtools`](https://github.com/kundajelab/phantompeakqualtools))\n 8. Call broad/narrow peaks ([`MACS3`](https://github.com/macs3-project/MACS))\n 9. Annotate peaks relative to gene features ([`HOMER`](http://homer.ucsd.edu/homer/download.html))\n 10. Create consensus peakset across all samples and create tabular file to aid in the filtering of the data ([`BEDTools`](https://github.com/arq5x/bedtools2/))\n 11. Count reads in consensus peaks ([`featureCounts`](http://bioinf.wehi.edu.au/featureCounts/))\n 12. PCA and clustering ([`R`](https://www.r-project.org/), [`DESeq2`](https://bioconductor.org/packages/release/bioc/html/DESeq2.html))\n6. Create IGV session file containing bigWig tracks, peaks and differential sites for data visualisation ([`IGV`](https://software.broadinstitute.org/software/igv/)).\n7. Present QC for raw read, alignment, peak-calling and differential binding results ([`MultiQC`](http://multiqc.info/), [`R`](https://www.r-project.org/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\nTo run on your data, prepare a tab-separated samplesheet with your input data. Please follow the [documentation on samplesheets](https://nf-co.re/chipseq/usage#samplesheet-input) for more details. An example samplesheet for running the pipeline looks as follows:\n\n```csv title=\"samplesheet.csv\"\nsample,fastq_1,fastq_2,replicate,antibody,control,control_replicate\nWT_BCATENIN_IP,BLA203A1_S27_L006_R1_001.fastq.gz,,1,BCATENIN,WT_INPUT,1\nWT_BCATENIN_IP,BLA203A25_S16_L001_R1_001.fastq.gz,,2,BCATENIN,WT_INPUT,2\nWT_BCATENIN_IP,BLA203A25_S16_L002_R1_001.fastq.gz,,2,BCATENIN,WT_INPUT,2\nWT_BCATENIN_IP,BLA203A25_S16_L003_R1_001.fastq.gz,,2,BCATENIN,WT_INPUT,2\nWT_BCATENIN_IP,BLA203A49_S40_L001_R1_001.fastq.gz,,3,BCATENIN,WT_INPUT,3\nWT_INPUT,BLA203A6_S32_L006_R1_001.fastq.gz,,1,,,\nWT_INPUT,BLA203A30_S21_L001_R1_001.fastq.gz,,2,,,\nWT_INPUT,BLA203A30_S21_L002_R1_001.fastq.gz,,2,,,\nWT_INPUT,BLA203A31_S21_L003_R1_001.fastq.gz,,3,,,\n```\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/chipseq --input samplesheet.csv --outdir --genome GRCh37 -profile \n```\n\nSee [usage docs](https://nf-co.re/chipseq/usage) for all of the available options when running the pipeline.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/chipseq/usage) and the [parameter documentation](https://nf-co.re/chipseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/chipseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/chipseq/output).\n\n## Credits\n\nThese scripts were originally written by Chuan Wang ([@chuan-wang](https://github.com/chuan-wang)) and Phil Ewels ([@ewels](https://github.com/ewels)) for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. The pipeline was re-implemented by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/) and converted to Nextflow DSL2 by Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/).\n\nThe pipeline workflow diagram was designed by Sarah Guinchard ([@G-Sarah](https://github.com/G-Sarah)).\n\nMany thanks to others who have helped out and contributed along the way too, including (but not limited to): [@apeltzer](https://github.com/apeltzer), [@bc2zb](https://github.com/bc2zb), [@bjlang](https://github.com/bjlang), [@crickbabs](https://github.com/crickbabs), [@drejom](https://github.com/drejom), [@houghtos](https://github.com/houghtos), [@KevinMenden](https://github.com/KevinMenden), [@mashehu](https://github.com/mashehu), [@pditommaso](https://github.com/pditommaso), [@Rotholandus](https://github.com/Rotholandus), [@sofiahaglund](https://github.com/sofiahaglund), [@tiagochst](https://github.com/tiagochst) and [@winni2k](https://github.com/winni2k).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#chipseq` channel](https://nfcore.slack.com/channels/chipseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/chipseq for your analysis, please cite it using the following doi: [10.5281/zenodo.3240506](https://doi.org/10.5281/zenodo.3240506)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#8595f74e-7192-47f7-9803-8db8f194fc47" + "@id": "#be26b39c-8ae7-447d-a6dd-8b423bd521ec" } ], "name": "nf-core/chipseq" @@ -121,9 +121,13 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "dateCreated": "", - "dateModified": "2025-07-08T11:38:17Z", + "dateModified": "2025-04-30T12:25:55Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -134,16 +138,25 @@ "macs2", "peak-calling" ], - "license": ["MIT"], - "name": ["nf-core/chipseq"], + "license": [ + "MIT" + ], + "name": [ + "nf-core/chipseq" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/chipseq", "https://nf-co.re/chipseq/dev/"], - "version": ["2.2.0dev"] + "url": [ + "https://github.com/nf-core/chipseq", + "https://nf-co.re/chipseq/dev/" + ], + "version": [ + "2.2.0dev" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -155,14 +168,14 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=24.10.5" + "version": "!>=24.04.2" }, { - "@id": "#8595f74e-7192-47f7-9803-8db8f194fc47", + "@id": "#be26b39c-8ae7-447d-a6dd-8b423bd521ec", "@type": "TestSuite", "instance": [ { - "@id": "#f6b83786-2342-48cb-b471-8f6554ca1da9" + "@id": "#ab6a8ea3-81bb-44bf-a564-11b2997ed6d3" } ], "mainEntity": { @@ -171,10 +184,10 @@ "name": "Test suite for nf-core/chipseq" }, { - "@id": "#f6b83786-2342-48cb-b471-8f6554ca1da9", + "@id": "#ab6a8ea3-81bb-44bf-a564-11b2997ed6d3", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/chipseq", - "resource": "repos/nf-core/chipseq/actions/workflows/nf-test.yml", + "resource": "repos/nf-core/chipseq/actions/workflows/ci.yml", "runsOn": { "@id": "https://w3id.org/ro/terms/test#GithubService" }, @@ -300,4 +313,4 @@ "url": "https://nf-co.re/" } ] -} +} \ No newline at end of file diff --git a/tests/.nftignore b/tests/.nftignore index 158c83c59..6b5473db1 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,11 +1,84 @@ +# === SYSTEM FILES === .DS_Store +**/.DS_Store + +# === PIPELINE EXECUTION METADATA === +pipeline_info/*.{html,json,txt,yml} + +# === MULTIQC OUTPUTS === +# MultiQC files contain timestamps, system paths, and run-specific data multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt multiqc/multiqc_data/BETA-multiqc.parquet -multiqc/multiqc_data/multiqc.log -multiqc/multiqc_data/multiqc_data.json +**/multiqc.log +**/multiqc_data.json +**/multiqc_report.html multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} -multiqc/multiqc_report.html + +# === QC TOOL OUTPUTS === fastqc/*_fastqc.{html,zip} -pipeline_info/*.{html,json,txt,yml} +**/*_fastqc.html +**/*_val_*_fastqc.html + +# === BINARY AND COMPRESSED FILES === +**/*.{pdf,png,svg,gz,bam,bai,bigWig,zip,RData,rds} + +# === TOOL-SPECIFIC METRICS FILES === +# Picard metrics +**/*.quality_distribution_metrics +**/*.quality_by_cycle_metrics +**/*.insert_size_metrics +**/*.alignment_summary_metrics +**/*.base_distribution_by_cycle_metrics +**/*.MarkDuplicates.metrics.txt + +# Trimming reports +**/*_trimming_report.txt + +# Generic outputs +**/*.out + +# === ANALYSIS RESULTS (FLOATING-POINT VARIATIONS) === +# DeepTools outputs +**/*.plotFingerprint.raw.txt +**/*.plotFingerprint.qcmetrics.txt +**/*.computeMatrix.vals.mat.tab +**/*.plotHeatmap.mat.tab +**/*.computeMatrix.mat.gz +**/*.plotProfile.tab + +# Peak calling and annotation +**/*.annotatePeaks.txt +**/*.boolean.annotatePeaks.txt +**/macs3_peak.summary.txt + +# Feature counting +**/*.featureCounts.txt +**/*.featureCounts.txt.summary + +# Statistical analysis +**/*.pca.vals.txt +**/*.pca.vals_mqc.tsv +**/*.sample.dists.txt +**/*.sample.dists_mqc.tsv + +# === YAML CONFIGURATION FILES === +**/deeptools_plot_profile_mlib_deeptools.yaml +**/multiqc_deseq2_clustering_1.yaml +**/multiqc_deseq2_pca_1.yaml +**/multiqc_sources.yaml +**/read_distribution_profile.yaml +**/deeptools_fingerprint_plot.yaml +**/deeptools_plot_fingerprint_counts_mlib_deeptools.yaml + +# === CHIP-SEQ SPECIFIC OUTPUTS === +# PhantomPeakQualTools outputs (contain variable correlation data) +**/*.spp_correlation_mqc.tsv +**/*.spp_nsc_mqc.tsv +**/*.spp_rsc_mqc.tsv + +# === IGV SESSION FILES === +# IGV session files contain absolute paths and timestamps +**/igv_files.txt +**/igv_session.xml diff --git a/tests/bowtie2.nf.test b/tests/bowtie2.nf.test new file mode 100644 index 000000000..47a61beda --- /dev/null +++ b/tests/bowtie2.nf.test @@ -0,0 +1,57 @@ +nextflow_pipeline { + + name "Test pipeline with bowtie2 aligner" + script "../main.nf" + tag "bowtie2" + + test("bowtie2") { + + when { + params { + outdir = "$outputDir" + aligner = "bowtie2" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + + test("bowtie2 with stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + aligner = "bowtie2" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.succeeded().size() + ).match() } + ) + } + } +} diff --git a/tests/bowtie2.nf.test.snap b/tests/bowtie2.nf.test.snap new file mode 100644 index 000000000..91c2f2284 --- /dev/null +++ b/tests/bowtie2.nf.test.snap @@ -0,0 +1,990 @@ +{ + "bowtie2": { + "content": [ + 215, + { + "ANNOTATE_BOOLEAN_PEAKS": { + "sed": 4.7 + }, + "BAMTOOLS_FILTER": { + "bamtools": "2.5.2", + "samtools": "1.15.1" + }, + "BAM_REMOVE_ORPHANS": { + "samtools": "1.15.1" + }, + "BEDTOOLS_GENOMECOV": { + "bedtools": "2.30.0" + }, + "BOWTIE2_ALIGN": { + "bowtie2": "2.5.2", + "pigz": 2.6, + "samtools": 1.18 + }, + "BOWTIE2_BUILD": { + "bowtie2": "2.5.2" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "DEEPTOOLS_COMPUTEMATRIX": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTFINGERPRINT": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTHEATMAP": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTPROFILE": { + "deeptools": "3.5.5" + }, + "DESEQ2_QC": { + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FRIP_SCORE": { + "bedtools": "2.30.0", + "samtools": "1.15.1" + }, + "GENOME_BLACKLIST_REGIONS": { + "bedtools": "2.30.0" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "HOMER_ANNOTATEPEAKS": { + "homer": 4.11 + }, + "IGV": { + "python": "3.8.3" + }, + "MACS3_CALLPEAK": { + "macs3": "3.0.1" + }, + "MACS3_CONSENSUS": { + "python": "3.10.0", + "r-base": "4.1.1" + }, + "MULTIQC_CUSTOM_PEAKS": { + "sed": 4.7 + }, + "PHANTOMPEAKQUALTOOLS": { + "phantompeakqualtools": "1.2.2" + }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MERGESAMFILES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PLOT_HOMER_ANNOTATEPEAKS": { + "r-base": "4.0.3" + }, + "PLOT_MACS3_QC": { + "r-base": "4.0.3" + }, + "SAMPLESHEET_CHECK": { + "python": "3.8.3" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TRIMGALORE": { + "cutadapt": 3.4, + "trimgalore": "0.6.7" + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "Workflow": { + "nf-core/chipseq": "v2.2.0dev" + } + }, + [ + "bowtie2", + "bowtie2/merged_library", + "bowtie2/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", + "bowtie2/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam.bai", + "bowtie2/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam", + "bowtie2/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam.bai", + "bowtie2/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam", + "bowtie2/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam.bai", + "bowtie2/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam", + "bowtie2/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam.bai", + "bowtie2/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam", + "bowtie2/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam.bai", + "bowtie2/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", + "bowtie2/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", + "bowtie2/merged_library/bigwig", + "bowtie2/merged_library/bigwig/SPT5_INPUT_REP1.mLb.clN.bigWig", + "bowtie2/merged_library/bigwig/SPT5_INPUT_REP2.mLb.clN.bigWig", + "bowtie2/merged_library/bigwig/SPT5_T0_REP1.mLb.clN.bigWig", + "bowtie2/merged_library/bigwig/SPT5_T0_REP2.mLb.clN.bigWig", + "bowtie2/merged_library/bigwig/SPT5_T15_REP1.mLb.clN.bigWig", + "bowtie2/merged_library/bigwig/SPT5_T15_REP2.mLb.clN.bigWig", + "bowtie2/merged_library/bigwig/scale", + "bowtie2/merged_library/bigwig/scale/SPT5_INPUT_REP1.mLB.clN.scale_factor.txt", + "bowtie2/merged_library/bigwig/scale/SPT5_INPUT_REP2.mLB.clN.scale_factor.txt", + "bowtie2/merged_library/bigwig/scale/SPT5_T0_REP1.mLB.clN.scale_factor.txt", + "bowtie2/merged_library/bigwig/scale/SPT5_T0_REP2.mLB.clN.scale_factor.txt", + "bowtie2/merged_library/bigwig/scale/SPT5_T15_REP1.mLB.clN.scale_factor.txt", + "bowtie2/merged_library/bigwig/scale/SPT5_T15_REP2.mLB.clN.scale_factor.txt", + "bowtie2/merged_library/deepTools", + "bowtie2/merged_library/deepTools/plotFingerprint", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.pdf", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.qcmetrics.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP1.mLb.clN.plotFingerprint.raw.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP2.mLb.clN.plotFingerprint.pdf", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP2.mLb.clN.plotFingerprint.qcmetrics.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T0_REP2.mLb.clN.plotFingerprint.raw.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T15_REP1.mLb.clN.plotFingerprint.pdf", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T15_REP1.mLb.clN.plotFingerprint.qcmetrics.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T15_REP1.mLb.clN.plotFingerprint.raw.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T15_REP2.mLb.clN.plotFingerprint.pdf", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T15_REP2.mLb.clN.plotFingerprint.qcmetrics.txt", + "bowtie2/merged_library/deepTools/plotFingerprint/SPT5_T15_REP2.mLb.clN.plotFingerprint.raw.txt", + "bowtie2/merged_library/deepTools/plotProfile", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP1.mLb.clN.computeMatrix.mat.gz", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP1.mLb.clN.computeMatrix.vals.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP1.mLb.clN.plotHeatmap.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP1.mLb.clN.plotHeatmap.pdf", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP1.mLb.clN.plotProfile.pdf", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP1.mLb.clN.plotProfile.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP2.mLb.clN.computeMatrix.mat.gz", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP2.mLb.clN.computeMatrix.vals.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP2.mLb.clN.plotHeatmap.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP2.mLb.clN.plotHeatmap.pdf", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP2.mLb.clN.plotProfile.pdf", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_INPUT_REP2.mLb.clN.plotProfile.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP1.mLb.clN.computeMatrix.mat.gz", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP1.mLb.clN.computeMatrix.vals.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP1.mLb.clN.plotHeatmap.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP1.mLb.clN.plotHeatmap.pdf", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP1.mLb.clN.plotProfile.pdf", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP1.mLb.clN.plotProfile.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP2.mLb.clN.computeMatrix.mat.gz", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP2.mLb.clN.computeMatrix.vals.mat.tab", + "bowtie2/merged_library/deepTools/plotProfile/SPT5_T0_REP2.mLb.clN.plotHeatmap.mat.tab", 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"fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3", + "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c", + "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2", + "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678", + "fastqc_sequence_length_distribution_plot.yaml:md5,f1d36d9bed4b85e0ae349b514ab788fc", + "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d", + "featureCounts_assignment_plot.yaml:md5,83f65e024cdcf840199ff56dfdbbc0fc", + "multiqc_citations.yaml:md5,fca5dc7cb20162434c714d26b11161f3", + "multiqc_cutadapt.yaml:md5,25f32008ccf0041ac74bb82d744d6eda", + "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9", + "multiqc_fastqc_1.yaml:md5,dd7981fa28827b895ef844011053eeff", + "multiqc_featurecounts.yaml:md5,b04c61a636508a406a40d532c3841474", + "multiqc_frip_score.yaml:md5,ac21032eb4978f8bc2ef2d03dfc7c04c", + "multiqc_nsc_coefficient.yaml:md5,63db816351d46b1420aa35dca04a4a3f", + "multiqc_peak_annotation.yaml:md5,eed4fb1ce72c9dfcf28b33143a5f63c5", + "multiqc_peak_count.yaml:md5,b595892dcd65c4f233597c17b0d982f1", + "multiqc_phantompeakqualtools.yaml:md5,ddadca49d172a77ea491675930155413", + "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,86347cb87e66b56dfa591568ebfd4c24", + "multiqc_picard-1_insertSize.yaml:md5,e0fb94ddfce5be120711660801850972", + "multiqc_picard-1_quality_by_cycle.yaml:md5,2478f6aac43166b2c6b3cc653288579e", + "multiqc_picard-1_quality_score_distribution.yaml:md5,63f6a752be596fb6ad1a8b1c8bbdf17a", + "multiqc_picard_baseContent.yaml:md5,8fe24fbc195b032c064f9267349a8826", + "multiqc_picard_dups.yaml:md5,daf7f91937e15046c525c6032813bc75", + "multiqc_rsc_coefficient.yaml:md5,70d442b344556b9fd6ab591d38423004", + "multiqc_samtools_flagstat.yaml:md5,7f49f4aeeaa0b33a6a56403ef4e511ba", + "multiqc_samtools_flagstat_1.yaml:md5,e7826d97bcb600953a58814996f864e6", + 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"picard-1_histogram_1.yaml:md5,2478f6aac43166b2c6b3cc653288579e", + "picard-1_histogram_2.yaml:md5,63f6a752be596fb6ad1a8b1c8bbdf17a", + "picard-1_insert_size_Counts.yaml:md5,8fcef0700ff63df7dbb2a0594f3294a9", + "picard-1_insert_size_Percentages.yaml:md5,ba621b3cb07eb930b769e24461a62482", + "picard-1_quality_by_cycle.yaml:md5,0432b05602d754b5f03b34c15058ed6f", + "picard-1_quality_score_distribution.yaml:md5,426e031acc10eeb8b7977401ed731dfa", + "picard_base_distribution_by_cycle__Adenine.yaml:md5,0ad2885a20e408e41c3515afecdd6ea9", + "picard_base_distribution_by_cycle__Cytosine.yaml:md5,3e6dbfb300937eabb098c65071597abd", + "picard_base_distribution_by_cycle__Guanine.yaml:md5,71b8c3f5ced0393f3b4a2dac8ee53402", + "picard_base_distribution_by_cycle__Thymine.yaml:md5,05ba2b40801888464d8e17e349387d4f", + "picard_base_distribution_by_cycle__Undetermined.yaml:md5,ecd12bd2e8698c090f06e6c6bcf37188", + "picard_deduplication.yaml:md5,f0123e6449274c09a0158657b549d861", + 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"samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,7dbbc39984c5dc6421e68711d9f0732c", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,b7266c4e8bc759932521d0abeefccf8f", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,9e69299aa94e930736eb6d58a99e32ab", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,5823a0a1231681d8887007bd2659ee8e", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,df06db1e3a0e492bdbcef799730c2cd9", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,b210ce5a055931fd94328750454df24d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,f594898789d8f354ce7720e5cbdcb1d3", + "samtools-stats-dp.yaml:md5,a17797e8a52aff0c17051735099629fe", + "samtools_alignment_plot.yaml:md5,21e19a3581f28089acffd00121442ffc", + "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T20:18:53.73805" + }, + "bowtie2 with stub": { + "content": [ + 20 + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T20:19:29.013062" + } +} \ No newline at end of file diff --git a/tests/chromap.nf.test b/tests/chromap.nf.test new file mode 100644 index 000000000..a23af1a9f --- /dev/null +++ b/tests/chromap.nf.test @@ -0,0 +1,57 @@ +nextflow_pipeline { + + name "Test pipeline with chromap aligner" + script "../main.nf" + tag "chromap" + + test("chromap") { + + when { + params { + outdir = "$outputDir" + aligner = "chromap" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + + test("chromap with stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + aligner = "chromap" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.succeeded().size() + ).match() } + ) + } + } +} diff --git a/tests/chromap.nf.test.snap b/tests/chromap.nf.test.snap new file mode 100644 index 000000000..0767d57ed --- /dev/null +++ b/tests/chromap.nf.test.snap @@ -0,0 +1,993 @@ +{ + "chromap": { + "content": [ + 215, + { + 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"multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml", + "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml", + "multiqc/broad_peak/multiqc_data/picard_histogram.yaml", + "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml", + "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml", + "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml", + 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"multiqc_featurecounts.yaml:md5,f3859f6c8dce0e1acd116f516e814fbc", + "multiqc_frip_score.yaml:md5,70f0eb1370581c57537cdd650fc7af92", + "multiqc_nsc_coefficient.yaml:md5,6befd2c9a2a88d80d84225b282de3857", + "multiqc_peak_annotation.yaml:md5,807711a8de90b96350cdb704713f377c", + "multiqc_peak_count.yaml:md5,9febb685e0995e635c0d34644aef1c22", + "multiqc_phantompeakqualtools.yaml:md5,8b98fb4f8b51f22c6d688b0f69fa8af6", + "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,4131380513ad07ea9d03bf07ee580b21", + "multiqc_picard-1_insertSize.yaml:md5,e0db1e0acb304b399940e0597f0b2fc7", + "multiqc_picard-1_quality_by_cycle.yaml:md5,04701f440eb72e4adfa5334472db84fc", + "multiqc_picard-1_quality_score_distribution.yaml:md5,c3891e6ac941eecca13a57383c909510", + "multiqc_picard_baseContent.yaml:md5,f696b1a8fa5d664c674812d78c08956d", + "multiqc_picard_dups.yaml:md5,3a2202c3af4eb47216a1343a2cf4bce9", + "multiqc_rsc_coefficient.yaml:md5,8461f0178d38bdb58cfad7dad7bfdb88", + "multiqc_samtools_flagstat.yaml:md5,2833155ed2487f9cb7829f8264fed339", + "multiqc_samtools_flagstat_1.yaml:md5,e0deba4fd1bb7f802549e95fba444cdc", + "multiqc_samtools_flagstat_2.yaml:md5,18245e4474861a2f45f54ca9afa8828a", + "multiqc_samtools_idxstats.yaml:md5,86f0b32ebd9494aea700d24b78f4785f", + "multiqc_samtools_idxstats_1.yaml:md5,2a83a1a9f1a66e90b9f73181a5a196c6", + "multiqc_samtools_idxstats_2.yaml:md5,e9cd19da34eac4fd2c9196fc303da4e2", + "multiqc_samtools_stats.yaml:md5,c75c982cdca8a83186d345bf66b365e0", + "multiqc_samtools_stats_1.yaml:md5,33531055d31307925f94f5e6460463fc", + "multiqc_samtools_stats_2.yaml:md5,e538f9993283ee9f2a056f279d3a8dca", + "multiqc_software_versions.yaml:md5,f1c1f63a7fd92a16ae9ae5659a6ff6c0", + "multiqc_strand_shift_correlation.yaml:md5,9a9a859ce75534a8074811ee1ca80f71", + "picard-1_alignment_readlength_plot.yaml:md5,fc25da4e9daefd74134d960adde48951", + "picard-1_alignment_summary_Aligned_Bases.yaml:md5,c174cd7cabe80cedf2c6e11b0091b7cb", + "picard-1_alignment_summary_Aligned_Reads.yaml:md5,afc30230b330fd55b13de82100976be6", + "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard-1_histogram_1.yaml:md5,04701f440eb72e4adfa5334472db84fc", + "picard-1_histogram_2.yaml:md5,c3891e6ac941eecca13a57383c909510", + "picard-1_insert_size_Counts.yaml:md5,95be371f6c22ce55e0f6915a1e45fb43", + "picard-1_insert_size_Percentages.yaml:md5,9e7b10d0267a86a55938108c20dbbe93", + "picard-1_quality_by_cycle.yaml:md5,bebc4523218048e1d1957cd70397bb61", + "picard-1_quality_score_distribution.yaml:md5,e80f658b3eb4c4737c774b0060941bfc", + "picard_base_distribution_by_cycle__Adenine.yaml:md5,8d020ac49d29295b49a11dd53ba453aa", + "picard_base_distribution_by_cycle__Cytosine.yaml:md5,26f8572c29758c423562abdaa03b7a34", + "picard_base_distribution_by_cycle__Guanine.yaml:md5,58aea7e2c0eed31250b5f86a1188d737", + "picard_base_distribution_by_cycle__Thymine.yaml:md5,1a4b97ac690abe12d5513d0d3a40cc11", + "picard_base_distribution_by_cycle__Undetermined.yaml:md5,4c2feab0a1a94826c53fabe7a3274dda", + "picard_deduplication.yaml:md5,c5e459b5774f23a7b0e398e5cb86bd56", + "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,823114a992da2bab04eb4edd903746d8", + "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,a97c37a9d95494fe0d02d6e16e6057a6", + "samtools-flagstat-dp_Percentage_of_total.yaml:md5,9c2b32dc86d09eeb870c8fb63d46f9e5", + "samtools-flagstat-dp_Read_counts-1.yaml:md5,d5dfeebe9bff8dd3fcdfdbf32adb106b", + "samtools-flagstat-dp_Read_counts-2.yaml:md5,c3cbc20287333e65b0053c0c644d81f3", + "samtools-flagstat-dp_Read_counts.yaml:md5,265762d51681a3cc1ad8aeb85c71a4e0", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,8837b9900307d0e626f08864e5bdf2cd", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,969627a72da77f241fcca5c19547f6cb", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,55e93fb7b4a86e11fbc2cc0381f4cec3", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,1b97bc9b6f2d353285aa0f873a433754", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,be4649e0e75abcf2d3f8b7cdfce34506", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,63ed0a2b79eb80512305f288c837054d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,ec7d25c50ae159832a8ce0cb8630a03d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,12259c95d8a4038e99ccdaf583695592", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,5e3a88d956ac7dcc1b7a6d5ae3f3b814", + "samtools-stats-dp.yaml:md5,25a63e73197b0fb5a9c3663698b08589", + "samtools_alignment_plot.yaml:md5,f05cae90c4fb4ff66c4e92eaabd2caf2", + "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T21:19:39.042131" + } +} \ No newline at end of file diff --git a/tests/nextflow.config b/tests/nextflow.config index bed87c26b..21fe2997c 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -4,8 +4,15 @@ ======================================================================================== */ -// TODO nf-core: Specify any additional parameters here -// Or any resources requirements +// Limit resources so that this can run on GitHub Actions +process { + resourceLimits = [ + cpus: 2, + memory: '6.GB', + time: '6.h' + ] +} + params { modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/chipseq' diff --git a/tests/skip_consensus_peaks.nf.test b/tests/skip_consensus_peaks.nf.test new file mode 100644 index 000000000..aaa7202fb --- /dev/null +++ b/tests/skip_consensus_peaks.nf.test @@ -0,0 +1,57 @@ +nextflow_pipeline { + + name "Test pipeline with --skip_consensus_peaks" + script "../main.nf" + tag "skip_consensus_peaks" + + test("skip_consensus_peaks") { + + when { + params { + outdir = "$outputDir" + skip_consensus_peaks = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + + test("skip_consensus_peaks with stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + skip_consensus_peaks = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.succeeded().size() + ).match() } + ) + } + } +} diff --git a/tests/skip_consensus_peaks.nf.test.snap b/tests/skip_consensus_peaks.nf.test.snap new file mode 100644 index 000000000..2354afc6a --- /dev/null +++ b/tests/skip_consensus_peaks.nf.test.snap @@ -0,0 +1,920 @@ +{ + "skip_consensus_peaks with stub": { + "content": [ + 20 + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T21:50:26.130655" + }, + "skip_consensus_peaks": { + "content": [ + 210, + { + "BAMTOOLS_FILTER": { + "bamtools": "2.5.2", + "samtools": "1.15.1" + }, + "BAM_REMOVE_ORPHANS": { + "samtools": "1.15.1" + }, + "BEDTOOLS_GENOMECOV": { + "bedtools": "2.30.0" + }, + "BWA_INDEX": { + "bwa": "0.7.18-r1243-dirty" + }, + "BWA_MEM": { + "bwa": "0.7.18-r1243-dirty", + "samtools": 1.2 + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "DEEPTOOLS_COMPUTEMATRIX": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTFINGERPRINT": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTHEATMAP": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTPROFILE": { + "deeptools": "3.5.5" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FRIP_SCORE": { + "bedtools": "2.30.0", + "samtools": "1.15.1" + }, + "GENOME_BLACKLIST_REGIONS": { + "bedtools": "2.30.0" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "HOMER_ANNOTATEPEAKS": { + "homer": 4.11 + }, + "IGV": { + "python": "3.8.3" + }, + "MACS3_CALLPEAK": { + "macs3": "3.0.1" + }, + "MULTIQC_CUSTOM_PEAKS": { + "sed": 4.7 + }, + "PHANTOMPEAKQUALTOOLS": { + "phantompeakqualtools": "1.2.2" + }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MERGESAMFILES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PLOT_HOMER_ANNOTATEPEAKS": { + "r-base": "4.0.3" + }, + "PLOT_MACS3_QC": { + "r-base": "4.0.3" + }, + "SAMPLESHEET_CHECK": { + "python": "3.8.3" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "TRIMGALORE": { + "cutadapt": 3.4, + "trimgalore": "0.6.7" + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "Workflow": { + "nf-core/chipseq": "v2.2.0dev" + } + }, + [ + "bwa", + "bwa/merged_library", + "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", + 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"fastqc-status-check-heatmap.yaml:md5,1e473e0f9140b718607d8c72cf3c0b45", + "fastqc_adapter_content_plot.yaml:md5,591991daf3e3c49873f4a51a3710b072", + "fastqc_per_base_n_content_plot.yaml:md5,c16a4af177b9ad9694a9535023906927", + "fastqc_per_base_sequence_quality_plot.yaml:md5,20fc07ce2bc8e369d5fdd18afc6e60e9", + "fastqc_per_sequence_gc_content_plot_Counts.yaml:md5,ab233171fb8fd4e717886b01868ebcf2", + "fastqc_per_sequence_gc_content_plot_Percentages.yaml:md5,db29d683777cc0742585d1c48e712bd3", + "fastqc_per_sequence_quality_scores_plot.yaml:md5,351b55974af5ee21294ebf5deb850d7c", + "fastqc_sequence_counts_plot.yaml:md5,5522b2b42f0b3753dd359aad1565d7c2", + "fastqc_sequence_duplication_levels_plot.yaml:md5,e883323380f2880c81ea36dc91ad8678", + "fastqc_sequence_length_distribution_plot.yaml:md5,f1d36d9bed4b85e0ae349b514ab788fc", + "fastqc_top_overrepresented_sequences_table.yaml:md5,443e161371f73cebf63c14f7a9f3580d", + "multiqc_citations.yaml:md5,c4cdebc20cfc52eb2eee741a36323b3e", + "multiqc_cutadapt.yaml:md5,25f32008ccf0041ac74bb82d744d6eda", + "multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9", + "multiqc_fastqc_1.yaml:md5,dd7981fa28827b895ef844011053eeff", + "multiqc_frip_score.yaml:md5,70f0eb1370581c57537cdd650fc7af92", + "multiqc_nsc_coefficient.yaml:md5,6befd2c9a2a88d80d84225b282de3857", + "multiqc_peak_annotation.yaml:md5,807711a8de90b96350cdb704713f377c", + "multiqc_peak_count.yaml:md5,9febb685e0995e635c0d34644aef1c22", + "multiqc_phantompeakqualtools.yaml:md5,8b98fb4f8b51f22c6d688b0f69fa8af6", + "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,4131380513ad07ea9d03bf07ee580b21", + "multiqc_picard-1_insertSize.yaml:md5,e0db1e0acb304b399940e0597f0b2fc7", + "multiqc_picard-1_quality_by_cycle.yaml:md5,04701f440eb72e4adfa5334472db84fc", + "multiqc_picard-1_quality_score_distribution.yaml:md5,c3891e6ac941eecca13a57383c909510", + "multiqc_picard_baseContent.yaml:md5,f696b1a8fa5d664c674812d78c08956d", + "multiqc_picard_dups.yaml:md5,3a2202c3af4eb47216a1343a2cf4bce9", + "multiqc_rsc_coefficient.yaml:md5,8461f0178d38bdb58cfad7dad7bfdb88", + "multiqc_samtools_flagstat.yaml:md5,2833155ed2487f9cb7829f8264fed339", + "multiqc_samtools_flagstat_1.yaml:md5,e0deba4fd1bb7f802549e95fba444cdc", + "multiqc_samtools_flagstat_2.yaml:md5,18245e4474861a2f45f54ca9afa8828a", + "multiqc_samtools_idxstats.yaml:md5,86f0b32ebd9494aea700d24b78f4785f", + "multiqc_samtools_idxstats_1.yaml:md5,2a83a1a9f1a66e90b9f73181a5a196c6", + "multiqc_samtools_idxstats_2.yaml:md5,e9cd19da34eac4fd2c9196fc303da4e2", + "multiqc_samtools_stats.yaml:md5,c75c982cdca8a83186d345bf66b365e0", + "multiqc_samtools_stats_1.yaml:md5,33531055d31307925f94f5e6460463fc", + "multiqc_samtools_stats_2.yaml:md5,e538f9993283ee9f2a056f279d3a8dca", + "multiqc_software_versions.yaml:md5,86ec45886fd8ca55da7be24e41a70b4b", + "multiqc_strand_shift_correlation.yaml:md5,9a9a859ce75534a8074811ee1ca80f71", + "picard-1_alignment_readlength_plot.yaml:md5,fc25da4e9daefd74134d960adde48951", + "picard-1_alignment_summary_Aligned_Bases.yaml:md5,c174cd7cabe80cedf2c6e11b0091b7cb", + "picard-1_alignment_summary_Aligned_Reads.yaml:md5,afc30230b330fd55b13de82100976be6", + "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard-1_histogram_1.yaml:md5,04701f440eb72e4adfa5334472db84fc", + "picard-1_histogram_2.yaml:md5,c3891e6ac941eecca13a57383c909510", + "picard-1_insert_size_Counts.yaml:md5,95be371f6c22ce55e0f6915a1e45fb43", + "picard-1_insert_size_Percentages.yaml:md5,9e7b10d0267a86a55938108c20dbbe93", + "picard-1_quality_by_cycle.yaml:md5,bebc4523218048e1d1957cd70397bb61", + "picard-1_quality_score_distribution.yaml:md5,e80f658b3eb4c4737c774b0060941bfc", + "picard_base_distribution_by_cycle__Adenine.yaml:md5,8d020ac49d29295b49a11dd53ba453aa", + "picard_base_distribution_by_cycle__Cytosine.yaml:md5,26f8572c29758c423562abdaa03b7a34", + "picard_base_distribution_by_cycle__Guanine.yaml:md5,58aea7e2c0eed31250b5f86a1188d737", + "picard_base_distribution_by_cycle__Thymine.yaml:md5,1a4b97ac690abe12d5513d0d3a40cc11", + "picard_base_distribution_by_cycle__Undetermined.yaml:md5,4c2feab0a1a94826c53fabe7a3274dda", + "picard_deduplication.yaml:md5,c5e459b5774f23a7b0e398e5cb86bd56", + "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,823114a992da2bab04eb4edd903746d8", + "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,a97c37a9d95494fe0d02d6e16e6057a6", + "samtools-flagstat-dp_Percentage_of_total.yaml:md5,9c2b32dc86d09eeb870c8fb63d46f9e5", + "samtools-flagstat-dp_Read_counts-1.yaml:md5,d5dfeebe9bff8dd3fcdfdbf32adb106b", + "samtools-flagstat-dp_Read_counts-2.yaml:md5,c3cbc20287333e65b0053c0c644d81f3", + "samtools-flagstat-dp_Read_counts.yaml:md5,265762d51681a3cc1ad8aeb85c71a4e0", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,8837b9900307d0e626f08864e5bdf2cd", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,969627a72da77f241fcca5c19547f6cb", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,55e93fb7b4a86e11fbc2cc0381f4cec3", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,1b97bc9b6f2d353285aa0f873a433754", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,be4649e0e75abcf2d3f8b7cdfce34506", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,63ed0a2b79eb80512305f288c837054d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,ec7d25c50ae159832a8ce0cb8630a03d", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,12259c95d8a4038e99ccdaf583695592", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,5e3a88d956ac7dcc1b7a6d5ae3f3b814", + "samtools-stats-dp.yaml:md5,25a63e73197b0fb5a9c3663698b08589", + "samtools_alignment_plot.yaml:md5,f05cae90c4fb4ff66c4e92eaabd2caf2", + "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T21:48:44.371756" + } +} \ No newline at end of file diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test new file mode 100644 index 000000000..e3502859d --- /dev/null +++ b/tests/skip_trimming.nf.test @@ -0,0 +1,57 @@ +nextflow_pipeline { + + name "Test pipeline with --skip_trimming" + script "../main.nf" + tag "skip_trimming" + + test("skip_trimming") { + + when { + params { + outdir = "$outputDir" + skip_trimming = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + + test("skip_trimming with stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + skip_trimming = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.succeeded().size() + ).match() } + ) + } + } +} diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap new file mode 100644 index 000000000..9cb6070a9 --- /dev/null +++ b/tests/skip_trimming.nf.test.snap @@ -0,0 +1,870 @@ +{ + "skip_trimming": { + "content": [ + 209, + { + "ANNOTATE_BOOLEAN_PEAKS": { + "sed": 4.7 + }, + "BAMTOOLS_FILTER": { + "bamtools": "2.5.2", + "samtools": "1.15.1" + }, + "BAM_REMOVE_ORPHANS": { + "samtools": "1.15.1" + }, + "BEDTOOLS_GENOMECOV": { + "bedtools": "2.30.0" + }, + "BWA_INDEX": { + "bwa": "0.7.18-r1243-dirty" + }, + "BWA_MEM": { + "bwa": "0.7.18-r1243-dirty", + "samtools": 1.2 + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "DEEPTOOLS_COMPUTEMATRIX": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTFINGERPRINT": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTHEATMAP": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTPROFILE": { + "deeptools": "3.5.5" + }, + "DESEQ2_QC": { + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FRIP_SCORE": { + "bedtools": "2.30.0", + "samtools": "1.15.1" + }, + "GENOME_BLACKLIST_REGIONS": { + "bedtools": "2.30.0" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "HOMER_ANNOTATEPEAKS": { + "homer": 4.11 + }, + "IGV": { + "python": "3.8.3" + }, + "MACS3_CALLPEAK": { + "macs3": "3.0.1" + }, + "MACS3_CONSENSUS": { + "python": "3.10.0", + "r-base": "4.1.1" + }, + "MULTIQC_CUSTOM_PEAKS": { + "sed": 4.7 + }, + "PHANTOMPEAKQUALTOOLS": { + "phantompeakqualtools": "1.2.2" + }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MERGESAMFILES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PLOT_HOMER_ANNOTATEPEAKS": { + "r-base": "4.0.3" + }, + "PLOT_MACS3_QC": { + "r-base": "4.0.3" + }, + "SAMPLESHEET_CHECK": { + "python": "3.8.3" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "Workflow": { + "nf-core/chipseq": "v2.2.0dev" + } + }, + [ + "bwa", + "bwa/merged_library", + "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_INPUT_REP1.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_INPUT_REP2.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T0_REP1.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T0_REP2.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T15_REP1.mLb.clN.sorted.bam.bai", + "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam", + "bwa/merged_library/SPT5_T15_REP2.mLb.clN.sorted.bam.bai", + 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"multiqc_fastqc.yaml:md5,30fe6d1a5e5c04695dda81294b828ec9", + "multiqc_featurecounts.yaml:md5,ced4c5eba074f83ff81de10775aff55f", + "multiqc_frip_score.yaml:md5,68a0bf27565f380e121d4861fd35ed67", + "multiqc_nsc_coefficient.yaml:md5,167f8d2ff0b5c54265ef70e727257348", + "multiqc_peak_annotation.yaml:md5,91cbb7d9660d47c3de8771deb1ee5192", + "multiqc_peak_count.yaml:md5,a90be51b16c07f36278cc0a5948159a1", + "multiqc_phantompeakqualtools.yaml:md5,4acbd2e598839f94376040108a6ff2b7", + "multiqc_picard-1_AlignmentSummaryMetrics.yaml:md5,99a15cd2e0477f4338a2f31713c58681", + "multiqc_picard-1_insertSize.yaml:md5,4468b6ca00b3be89426b1319b309bc62", + "multiqc_picard-1_quality_by_cycle.yaml:md5,5cb2257bf0ad79b5ae628c7cdf9c4e46", + "multiqc_picard-1_quality_score_distribution.yaml:md5,4012d180f127ee70efe233a816cbb97f", + "multiqc_picard_baseContent.yaml:md5,5ad8bb85fe50da94430bed46337305c8", + "multiqc_picard_dups.yaml:md5,c56ed89e6fca1ddb83d8072c462ae9ff", + 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"picard-1_alignment_summary_Aligned_Bases.yaml:md5,86717ca1bbeef507046dee670543c763", + "picard-1_alignment_summary_Aligned_Reads.yaml:md5,c8559ff41529868f4e419cd22c41ba6f", + "picard-1_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard-1_histogram_1.yaml:md5,5cb2257bf0ad79b5ae628c7cdf9c4e46", + "picard-1_histogram_2.yaml:md5,4012d180f127ee70efe233a816cbb97f", + "picard-1_insert_size_Counts.yaml:md5,465abea2c884be140e89c8cf3ad309c3", + "picard-1_insert_size_Percentages.yaml:md5,fb6c20e3a3f3020c209b5f806904082f", + "picard-1_quality_by_cycle.yaml:md5,fb474b70c11f8fe81f72369c08b8054c", + "picard-1_quality_score_distribution.yaml:md5,903baf5e71843524678485a8705c6617", + "picard_base_distribution_by_cycle__Adenine.yaml:md5,42d1afd748eae02fa3e752d324e6a374", + "picard_base_distribution_by_cycle__Cytosine.yaml:md5,54924614f53ea4cd0869f6c778b69999", + "picard_base_distribution_by_cycle__Guanine.yaml:md5,dd0dde5afd7b5b921adb9649ea138ceb", + "picard_base_distribution_by_cycle__Thymine.yaml:md5,fa6581e44811ce0cb14a34a89541ce15", + "picard_base_distribution_by_cycle__Undetermined.yaml:md5,4139649de017250f52cf86e4a9b44e00", + "picard_deduplication.yaml:md5,3b3298251d41828d79d76eb75188d368", + "picard_histogram.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard_histogram_1.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "picard_histogram_2.yaml:md5,8a80554c91d9fca8acb82f023de02f11", + "samtools-flagstat-dp_Percentage_of_total-1.yaml:md5,0c14d9c586f29e6b576ad273032eea58", + "samtools-flagstat-dp_Percentage_of_total-2.yaml:md5,0c814013444b7866198be9f3a421475d", + "samtools-flagstat-dp_Percentage_of_total.yaml:md5,78b526c2c4712e47690c336a5b0980ed", + "samtools-flagstat-dp_Read_counts-1.yaml:md5,2368c79bd7b994ac9055dc7b62fd5c17", + "samtools-flagstat-dp_Read_counts-2.yaml:md5,fb0e11473916f2cd1d7ec502f57f39ff", + "samtools-flagstat-dp_Read_counts.yaml:md5,a20c997bdd2aff3e21e12aca5dd43c61", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml:md5,48a345c40ec8f84e90b2a4a5aaf3db7c", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml:md5,1fcc4a8f8aa7de6e54ec1f3ea610ed4b", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml:md5,4692f35c7b651a040aae2cf92744a1ea", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml:md5,1f4e1d615529ad05be46adbfd13ad6a0", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml:md5,af055d9f7409215eaf77b090ca57413b", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml:md5,78f10a87fd257421174bad50cfe72412", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml:md5,972b5bd2f63137965c322ed8c5b6e245", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml:md5,35f42b24afe3b25a093c78d8610cd732", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml:md5,c035319353bb52655028940619e48afd", + "samtools-stats-dp.yaml:md5,a589756f342eea833dfb9c4f7f925427", + "samtools_alignment_plot.yaml:md5,a33df285c13ab5b360d9eb5282471908", + "samplesheet.valid.csv:md5,276425084544b3baf533e2f17207a384" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T22:14:43.613805" + }, + "skip_trimming with stub": { + "content": [ + 190 + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-04T22:18:55.08725" + } +} \ No newline at end of file diff --git a/tests/star.nf.test b/tests/star.nf.test new file mode 100644 index 000000000..42def49cf --- /dev/null +++ b/tests/star.nf.test @@ -0,0 +1,57 @@ +nextflow_pipeline { + + name "Test pipeline with STAR aligner" + script "../main.nf" + tag "star" + + test("star") { + + when { + params { + outdir = "$outputDir" + aligner = "star" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_chipseq_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } + + test("star with stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + aligner = "star" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.trace.succeeded().size() + ).match() } + ) + } + } +} diff --git a/tests/star.nf.test.snap b/tests/star.nf.test.snap new file mode 100644 index 000000000..f148ae007 --- /dev/null +++ b/tests/star.nf.test.snap @@ -0,0 +1,1020 @@ +{ + "star": { + "content": [ + 215, + { + "ANNOTATE_BOOLEAN_PEAKS": { + "sed": 4.7 + }, + "BAMTOOLS_FILTER": { + "bamtools": "2.5.2", + "samtools": "1.15.1" + }, + "BAM_REMOVE_ORPHANS": { + "samtools": "1.15.1" + }, + "BEDTOOLS_GENOMECOV": { + "bedtools": "2.30.0" + }, + "CUSTOM_GETCHROMSIZES": { + "getchromsizes": 1.2 + }, + "DEEPTOOLS_COMPUTEMATRIX": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTFINGERPRINT": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTHEATMAP": { + "deeptools": "3.5.5" + }, + "DEEPTOOLS_PLOTPROFILE": { + "deeptools": "3.5.5" + }, + "DESEQ2_QC": { + "bioconductor-deseq2": "1.28.0", + "r-base": "4.0.3" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "FRIP_SCORE": { + "bedtools": "2.30.0", + "samtools": "1.15.1" + }, + "GENOME_BLACKLIST_REGIONS": { + "bedtools": "2.30.0" + }, + "GTF2BED": { + "perl": "5.26.2" + }, + "HOMER_ANNOTATEPEAKS": { + "homer": 4.11 + }, + "IGV": { + "python": "3.8.3" + }, + "MACS3_CALLPEAK": { + "macs3": "3.0.1" + }, + "MACS3_CONSENSUS": { + "python": "3.10.0", + "r-base": "4.1.1" + }, + "MULTIQC_CUSTOM_PEAKS": { + "sed": 4.7 + }, + "PHANTOMPEAKQUALTOOLS": { + "phantompeakqualtools": "1.2.2" + }, + "PICARD_COLLECTMULTIPLEMETRICS": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MARKDUPLICATES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PICARD_MERGESAMFILES": { + "picard": "3.2.0-1-g3948afb6b" + }, + "PLOT_HOMER_ANNOTATEPEAKS": { + "r-base": "4.0.3" + }, + "PLOT_MACS3_QC": { + "r-base": "4.0.3" + }, + "SAMPLESHEET_CHECK": { + "python": "3.8.3" + }, + "SAMTOOLS_FLAGSTAT": { + "samtools": 1.2 + }, + "SAMTOOLS_IDXSTATS": { + "samtools": 1.2 + }, + "SAMTOOLS_INDEX": { + "samtools": 1.2 + }, + "SAMTOOLS_SORT": { + "samtools": 1.2 + }, + "SAMTOOLS_STATS": { + "samtools": 1.2 + }, + "STAR_ALIGN": { + "star": "2.6.1d" + }, + "STAR_GENOMEGENERATE": { + "star": "2.6.1d" + }, + "SUBREAD_FEATURECOUNTS": { + "subread": "2.0.1" + }, + "TRIMGALORE": { + "cutadapt": 3.4, + "trimgalore": "0.6.7" + }, + "UCSC_BEDGRAPHTOBIGWIG": { + "ucsc": 445 + }, + "Workflow": { + "nf-core/chipseq": "v2.2.0dev" + } + }, + [ + "fastqc", + "fastqc/SPT5_INPUT_REP1_T1_1_fastqc.html", + "fastqc/SPT5_INPUT_REP1_T1_2_fastqc.html", + "fastqc/SPT5_INPUT_REP2_T1_1_fastqc.html", + "fastqc/SPT5_INPUT_REP2_T1_2_fastqc.html", + "fastqc/SPT5_T0_REP1_T1_1_fastqc.html", + "fastqc/SPT5_T0_REP1_T1_2_fastqc.html", + "fastqc/SPT5_T0_REP2_T1_1_fastqc.html", + "fastqc/SPT5_T0_REP2_T1_2_fastqc.html", + "fastqc/SPT5_T15_REP1_T1_1_fastqc.html", + "fastqc/SPT5_T15_REP1_T1_2_fastqc.html", + "fastqc/SPT5_T15_REP2_T1_1_fastqc.html", + "fastqc/SPT5_T15_REP2_T1_2_fastqc.html", + "fastqc/zips", + "fastqc/zips/SPT5_INPUT_REP1_T1_1_fastqc.zip", + "fastqc/zips/SPT5_INPUT_REP1_T1_2_fastqc.zip", + "fastqc/zips/SPT5_INPUT_REP2_T1_1_fastqc.zip", + "fastqc/zips/SPT5_INPUT_REP2_T1_2_fastqc.zip", + "fastqc/zips/SPT5_T0_REP1_T1_1_fastqc.zip", + "fastqc/zips/SPT5_T0_REP1_T1_2_fastqc.zip", + "fastqc/zips/SPT5_T0_REP2_T1_1_fastqc.zip", + "fastqc/zips/SPT5_T0_REP2_T1_2_fastqc.zip", + "fastqc/zips/SPT5_T15_REP1_T1_1_fastqc.zip", + "fastqc/zips/SPT5_T15_REP1_T1_2_fastqc.zip", + "fastqc/zips/SPT5_T15_REP2_T1_1_fastqc.zip", + "fastqc/zips/SPT5_T15_REP2_T1_2_fastqc.zip", + "genome", + "genome/genome.fa", + "genome/genome.fa.fai", + "genome/genome.fa.sizes", + "igv", + "igv/broad_peak", + "igv/broad_peak/igv_files.txt", + "igv/broad_peak/igv_session.xml", + "multiqc", + "multiqc/broad_peak", + "multiqc/broad_peak/multiqc_data", + "multiqc/broad_peak/multiqc_data/cutadapt_filtered_reads_plot.yaml", + "multiqc/broad_peak/multiqc_data/cutadapt_trimmed_sequences_plot_3_Counts.yaml", + "multiqc/broad_peak/multiqc_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.yaml", + "multiqc/broad_peak/multiqc_data/deeptools_fingerprint_plot.yaml", + "multiqc/broad_peak/multiqc_data/deeptools_plot_fingerprint_counts_mlib_deeptools.yaml", + "multiqc/broad_peak/multiqc_data/deeptools_plot_profile_mlib_deeptools.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1-status-check-heatmap.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_per_base_n_content_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_per_base_sequence_quality_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Counts.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_per_sequence_gc_content_plot_Percentages.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_per_sequence_quality_scores_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_sequence_counts_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_sequence_duplication_levels_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-1_top_overrepresented_sequences_table.yaml", + "multiqc/broad_peak/multiqc_data/fastqc-status-check-heatmap.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_adapter_content_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_per_base_n_content_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_per_base_sequence_quality_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_per_sequence_quality_scores_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_sequence_counts_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_sequence_duplication_levels_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_sequence_length_distribution_plot.yaml", + "multiqc/broad_peak/multiqc_data/fastqc_top_overrepresented_sequences_table.yaml", + "multiqc/broad_peak/multiqc_data/featureCounts_assignment_plot.yaml", + "multiqc/broad_peak/multiqc_data/multiqc.log", + "multiqc/broad_peak/multiqc_data/multiqc_citations.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_cutadapt.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_data.json", + "multiqc/broad_peak/multiqc_data/multiqc_deseq2_clustering_1.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_deseq2_pca_1.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_fastqc.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_fastqc_1.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_featurecounts.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_frip_score.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_nsc_coefficient.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_peak_annotation.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_peak_count.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_phantompeakqualtools.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_picard-1_AlignmentSummaryMetrics.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_picard-1_insertSize.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_by_cycle.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_picard-1_quality_score_distribution.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_picard_baseContent.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_picard_dups.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_rsc_coefficient.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_1.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_flagstat_2.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_1.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_idxstats_2.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_1.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_samtools_stats_2.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_software_versions.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_sources.yaml", + "multiqc/broad_peak/multiqc_data/multiqc_strand_shift_correlation.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_alignment_readlength_plot.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Bases.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_alignment_summary_Aligned_Reads.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_histogram.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_histogram_1.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_histogram_2.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Counts.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_insert_size_Percentages.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_quality_by_cycle.yaml", + "multiqc/broad_peak/multiqc_data/picard-1_quality_score_distribution.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Adenine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Cytosine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Guanine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Thymine.yaml", + "multiqc/broad_peak/multiqc_data/picard_base_distribution_by_cycle__Undetermined.yaml", + "multiqc/broad_peak/multiqc_data/picard_deduplication.yaml", + "multiqc/broad_peak/multiqc_data/picard_histogram.yaml", + "multiqc/broad_peak/multiqc_data/picard_histogram_1.yaml", + "multiqc/broad_peak/multiqc_data/picard_histogram_2.yaml", + "multiqc/broad_peak/multiqc_data/read_distribution_profile.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-1.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total-2.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Percentage_of_total.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-1.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts-2.yaml", + "multiqc/broad_peak/multiqc_data/samtools-flagstat-dp_Read_counts.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-1.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts-2.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-1.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-2.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts-1.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts-2.yaml", + "multiqc/broad_peak/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.yaml", + "multiqc/broad_peak/multiqc_data/samtools-stats-dp.yaml", + "multiqc/broad_peak/multiqc_data/samtools_alignment_plot.yaml", + "multiqc/broad_peak/multiqc_plots", + "multiqc/broad_peak/multiqc_plots/pdf", + "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deeptools_fingerprint_plot.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_clustering_1.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/deseq2_pca_1.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1-status-check-heatmap.pdf", + "multiqc/broad_peak/multiqc_plots/pdf/fastqc-1_per_base_n_content_plot.pdf", + 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