From a1e1e27f6755899f50a68a1dc0826237248bd73f Mon Sep 17 00:00:00 2001 From: kevinmenden Date: Mon, 25 Jan 2021 15:00:18 +0100 Subject: [PATCH] updated test md5sums --- .github/workflows/star_align.yml | 40 +++++++++++ .github/workflows/star_genomegenerate.yml | 2 +- tests/software/star/main.nf | 30 +++----- tests/software/star/test.yml | 85 ++++++++++++++++++++++- 4 files changed, 133 insertions(+), 24 deletions(-) create mode 100644 .github/workflows/star_align.yml diff --git a/.github/workflows/star_align.yml b/.github/workflows/star_align.yml new file mode 100644 index 00000000..94e87e7d --- /dev/null +++ b/.github/workflows/star_align.yml @@ -0,0 +1,40 @@ +name: star_genomegenerate +on: + push: + paths: + - software/star/align/** + - .github/workflows/star_align.yml + - tests/software/star/** + pull_request: + paths: + - software/star/index/** + - .github/workflows/star_align.yml + - tests/software/star/** + +jobs: + ci_test: + runs-on: ubuntu-latest + strategy: + matrix: + nxf_version: [20.11.0-edge] + env: + NXF_ANSI_LOG: false + steps: + - uses: actions/checkout@v2 + + - name: Install Nextflow + env: + NXF_VER: ${{ matrix.nxf_version }} + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow + + # Test the module + - run: pytest --tag star_genomegenerate --symlink --wt 2 diff --git a/.github/workflows/star_genomegenerate.yml b/.github/workflows/star_genomegenerate.yml index a9a8a530..dcd3884e 100644 --- a/.github/workflows/star_genomegenerate.yml +++ b/.github/workflows/star_genomegenerate.yml @@ -7,7 +7,7 @@ on: - tests/software/star/** pull_request: paths: - - software/star/index/** + - software/star/genomegenerate/** - .github/workflows/star_genomegenerate.yml - tests/software/star/** diff --git a/tests/software/star/main.nf b/tests/software/star/main.nf index 8bfed839..d6f1d6ee 100644 --- a/tests/software/star/main.nf +++ b/tests/software/star/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow nextflow.enable.dsl = 2 -def options_align = [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted SortedByCoordinate'] +def options_align = [args: '--readFilesCommand zcat'] def options_gg = [args: '--genomeSAindexNbases 9'] include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align ) include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg ) @@ -23,24 +23,14 @@ workflow test_star_alignment_single_end { STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf) } -// workflow test_star_alignment_single_end { +workflow test_star_alignment_paired_end { + fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true) + gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true) + STAR_GENOMEGENERATE ( fasta, gtf ) -// fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) -// BOWTIE_INDEX ( fasta ) + input = [ [ id:'test', single_end:false ], // meta map + [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), + file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] -// def input = [] -// input = [ [ id:'test', single_end:true ], // meta map -// [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ] -// BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) -// } - -// workflow test_star_alignment_paired_end { -// fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) -// BOWTIE_INDEX ( fasta ) - -// def input = [] -// input = [ [ id:'test', single_end:false ], // meta map -// [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true), -// file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ] -// BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index ) -// } + STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf) +} diff --git a/tests/software/star/test.yml b/tests/software/star/test.yml index 2690956e..f566afcd 100644 --- a/tests/software/star/test.yml +++ b/tests/software/star/test.yml @@ -9,20 +9,19 @@ - path: output/star/star/SA md5sum: 3e70e4fc6d031e1915bb510727f2c559 - path: output/star/star/SAindex - md5sum: 05a7baf30bda37f42f9fcf187a6e8247 + md5sum: a94198b95a245d4f64af2a7133b6ec7b - path: output/star/star/chrLength.txt md5sum: f2bea3725fe1c01420c57fb73bdeb31a - path: output/star/star/chrNameLength.txt md5sum: c7ceb0a8827b2ea91c386933bee48742 - path: output/star/star/chrStart.txt md5sum: faf5c55020c99eceeef3e34188ac0d2f - - path: output/star/star/exonGeTrInfo.tab md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 - path: output/star/star/exonInfo.tab md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 - path: output/star/star/genomeParameters.txt - md5sum: ba83e83fc204d48534a1bb11f378076c + md5sum: ed47b8b034cae2fefcdb39321aea47cd - path: output/star/star/sjdbInfo.txt md5sum: 1082ab459363b3f2f7aabcef0979c1ed - path: output/star/star/sjdbList.fromGTF.out.tab @@ -31,3 +30,83 @@ md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/star/star/transcriptInfo.tab md5sum: 8fbe69abbbef4f89da3854873984dbac + +- name: Run star single-end alignment + command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_single_end -c tests/config/nextflow.config + tags: + - star + - star_align + - star_alignment_single_end + files: + - path: output/star/star/Genome + md5sum: 323c992bac354f93073ce0fc43f222f8 + - path: output/star/star/SA + md5sum: 3e70e4fc6d031e1915bb510727f2c559 + - path: output/star/star/SAindex + md5sum: a94198b95a245d4f64af2a7133b6ec7b + - path: output/star/star/chrLength.txt + md5sum: f2bea3725fe1c01420c57fb73bdeb31a + - path: output/star/star/chrNameLength.txt + md5sum: c7ceb0a8827b2ea91c386933bee48742 + - path: output/star/star/chrStart.txt + md5sum: faf5c55020c99eceeef3e34188ac0d2f + - path: output/star/star/exonGeTrInfo.tab + md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 + - path: output/star/star/exonInfo.tab + md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 + - path: output/star/star/genomeParameters.txt + md5sum: ed47b8b034cae2fefcdb39321aea47cd + - path: output/star/star/sjdbInfo.txt + md5sum: 1082ab459363b3f2f7aabcef0979c1ed + - path: output/star/star/sjdbList.fromGTF.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/sjdbList.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/transcriptInfo.tab + md5sum: 8fbe69abbbef4f89da3854873984dbac + - path: output/star/test.Aligned.out.bam + md5sum: d7f59c1728482e76a18e3f6eb9c66c25 + - path: output/star/test.Log.progress.out + md5sum: b2bd061d6cbaaf3d6d3b1fed547f69b8 + - path: output/star/test.SJ.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + +- name: Run star paired-end alignment + command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_paired_end -c tests/config/nextflow.config + tags: + - star + - star_align + - star_alignment_paired_end + files: + - path: output/star/star/Genome + md5sum: 323c992bac354f93073ce0fc43f222f8 + - path: output/star/star/SA + md5sum: 3e70e4fc6d031e1915bb510727f2c559 + - path: output/star/star/SAindex + md5sum: a94198b95a245d4f64af2a7133b6ec7b + - path: output/star/star/chrLength.txt + md5sum: f2bea3725fe1c01420c57fb73bdeb31a + - path: output/star/star/chrNameLength.txt + md5sum: c7ceb0a8827b2ea91c386933bee48742 + - path: output/star/star/chrStart.txt + md5sum: faf5c55020c99eceeef3e34188ac0d2f + - path: output/star/star/exonGeTrInfo.tab + md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 + - path: output/star/star/exonInfo.tab + md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 + - path: output/star/star/genomeParameters.txt + md5sum: ed47b8b034cae2fefcdb39321aea47cd + - path: output/star/star/sjdbInfo.txt + md5sum: 1082ab459363b3f2f7aabcef0979c1ed + - path: output/star/star/sjdbList.fromGTF.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/sjdbList.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: output/star/star/transcriptInfo.tab + md5sum: 8fbe69abbbef4f89da3854873984dbac + - path: output/star/test.Aligned.out.bam + md5sum: 5c52bcaa15e86914ad6b895638235166 + - path: output/star/test.Log.progress.out + md5sum: b2bd061d6cbaaf3d6d3b1fed547f69b8 + - path: output/star/test.SJ.out.tab + md5sum: d41d8cd98f00b204e9800998ecf8427e