From aba66296a85866e00d17988e28bfb4de762b4449 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Thu, 22 Jun 2023 21:40:31 -0400 Subject: [PATCH 1/9] init nf-tests and ci for nf-test tags --- .gitattributes | 1 + .github/workflows/ci.yml | 99 +++++++++---------- .gitignore | 2 + .nf-core.yml | 4 + nf-test.config | 16 +++ tests/nextflow.config | 5 + tests/pipeline/lib/UTILS.groovy | 38 +++++++ tests/pipeline/test.nf.test | 32 ++++++ tests/pipeline/test_aligner_bowtie2.nf.test | 32 ++++++ tests/pipeline/test_aligner_chromap.nf.test | 32 ++++++ tests/pipeline/test_aligner_star.nf.test | 32 ++++++ .../test_skip_consensus_peaks.nf.test | 32 ++++++ tests/pipeline/test_skip_trimming.nf.test | 32 ++++++ 13 files changed, 307 insertions(+), 50 deletions(-) create mode 100644 nf-test.config create mode 100644 tests/nextflow.config create mode 100644 tests/pipeline/lib/UTILS.groovy create mode 100644 tests/pipeline/test.nf.test create mode 100644 tests/pipeline/test_aligner_bowtie2.nf.test create mode 100644 tests/pipeline/test_aligner_chromap.nf.test create mode 100644 tests/pipeline/test_aligner_star.nf.test create mode 100644 tests/pipeline/test_skip_consensus_peaks.nf.test create mode 100644 tests/pipeline/test_skip_trimming.nf.test diff --git a/.gitattributes b/.gitattributes index 7a2dabc2..c1c17000 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,4 +1,5 @@ *.config linguist-language=nextflow *.nf.test linguist-language=nextflow +tests/**/*nf.test.snap linguist-generated modules/nf-core/** linguist-generated subworkflows/nf-core/** linguist-generated diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d1e284f1..cdd2baf2 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,31 +1,58 @@ -name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors +name: nf-core CI on: push: branches: - dev pull_request: + branches: + - dev + - master release: - types: [published] + types: + - "published" env: NXF_ANSI_LOG: false + NFTEST_VER: "0.7.3" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" 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", "22.10.1"]' | tee -a $GITHUB_OUTPUT + fi + test: - name: Run pipeline with test data - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}" + name: nf-test + needs: define_nxf_versions runs-on: ubuntu-latest strategy: + fail-fast: false matrix: - NXF_VER: - - "22.10.1" - - "latest-everything" + NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }} + tags: + - "test_profile" + - "test_skip_trimming" + - "test_skip_consensus_peaks" + - "test_aligner_bowtie2" + - "test_aligner_chromap" + - "test_aligner_star" + profile: + - "docker" + steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -35,51 +62,23 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Run pipeline with test data + - name: Install nf-test run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + sudo mv nf-test /usr/local/bin/ - parameters: - name: Test workflow parameters - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }} - runs-on: ubuntu-latest - strategy: - matrix: - parameters: - - "--skip_trimming" - - "--skip_consensus_peaks" - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow + - name: Run nf-test run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + nf-test test --tag ${{ matrix.tags }} --profile test,${{ matrix.profile }} --junitxml=test.xml - - name: Run pipeline with various parameters + - name: Output log on failure + if: failure() run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results + sudo apt install bat > /dev/null + batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml - aligners: - name: Test available aligners - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }} - runs-on: ubuntu-latest - strategy: - matrix: - aligner: - - "bowtie2" - - "chromap" - - "star" - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - - name: Run pipeline with the different aligners available - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }} --outdir ./results + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: "*.xml" diff --git a/.gitignore b/.gitignore index 5124c9ac..935326a7 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ results/ testing/ testing* *.pyc +.nf-test/ +nf-test diff --git a/.nf-core.yml b/.nf-core.yml index 3805dc81..3b337449 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1 +1,5 @@ repository_type: pipeline +lint: + files_unchanged: + - .gitattributes + actions_ci: False diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..cd432d43 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,16 @@ +config { + // location for all nf-tests + testsDir "tests" + + // nf-test directory including temporary files for each test + workDir ".nf-test" + + // location of library folder that is added automatically to the classpath + libDir "tests/pipeline/lib/" + + // location of an optional nextflow.config file specific for executing tests + configFile "nextflow.config" + + // run all test with the defined docker profile from the main nextflow.config + profile "" +} diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 00000000..c19b1ad0 --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,5 @@ +/* +======================================================================================== + Nextflow config file for running tests +======================================================================================== +*/ diff --git a/tests/pipeline/lib/UTILS.groovy b/tests/pipeline/lib/UTILS.groovy new file mode 100644 index 00000000..28c78f75 --- /dev/null +++ b/tests/pipeline/lib/UTILS.groovy @@ -0,0 +1,38 @@ +// Helper functions for pipeline tests + +class UTILS { + + // Function to remove Nextflow version from software_versions.yml + public static String removeNextflowVersion(outputDir) { + def softwareVersions = path("$outputDir/pipeline_info/software_versions.yml").yaml + if (softwareVersions.containsKey("Workflow")) { + softwareVersions.Workflow.remove("Nextflow") + } + return softwareVersions + } + + // Function to filter lines from a file and return a new file + public static File filterLines(String inFilePath, int linesToSkip) { + if (linesToSkip >= 0) { + File inputFile = new File(inFilePath) + File outputFile = new File(inFilePath + ".filtered") + def lineCount = 0 + inputFile.eachLine { line -> + lineCount++ + if (lineCount > linesToSkip) { + outputFile.append(line + '\n') + } + } + return outputFile + } else { + File inputFile = new File(inFilePath) + File outputFile = new File(inFilePath + ".filtered") + def lines = inputFile.readLines() + def totalLines = lines.size() + lines.take(totalLines + linesToSkip).each { line -> + outputFile.append(line + '\n') + } + return outputFile + } + } +} diff --git a/tests/pipeline/test.nf.test b/tests/pipeline/test.nf.test new file mode 100644 index 00000000..66834081 --- /dev/null +++ b/tests/pipeline/test.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "test_profile" + tag "pipeline" + + test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + aassertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert new File("$outputDir/bwa/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert new File("$outputDir/genome/").exists() }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } + ) + } + + } + +} diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test b/tests/pipeline/test_aligner_bowtie2.nf.test new file mode 100644 index 00000000..c587229f --- /dev/null +++ b/tests/pipeline/test_aligner_bowtie2.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "test_aligner_bowtie2" + tag "pipeline" + + test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + aassertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert new File("$outputDir/bwa/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert new File("$outputDir/genome/").exists() }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } + ) + } + + } + +} diff --git a/tests/pipeline/test_aligner_chromap.nf.test b/tests/pipeline/test_aligner_chromap.nf.test new file mode 100644 index 00000000..d97ad6e2 --- /dev/null +++ b/tests/pipeline/test_aligner_chromap.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "test_aligner_chromap" + tag "pipeline" + + test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + aassertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert new File("$outputDir/bwa/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert new File("$outputDir/genome/").exists() }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } + ) + } + + } + +} diff --git a/tests/pipeline/test_aligner_star.nf.test b/tests/pipeline/test_aligner_star.nf.test new file mode 100644 index 00000000..07ea1ae3 --- /dev/null +++ b/tests/pipeline/test_aligner_star.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "test_aligner_star" + tag "pipeline" + + test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + aassertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert new File("$outputDir/bwa/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert new File("$outputDir/genome/").exists() }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } + ) + } + + } + +} diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test b/tests/pipeline/test_skip_consensus_peaks.nf.test new file mode 100644 index 00000000..d1d01989 --- /dev/null +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "test_skip_consensus_peaks" + tag "pipeline" + + test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + aassertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert new File("$outputDir/bwa/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert new File("$outputDir/genome/").exists() }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } + ) + } + + } + +} diff --git a/tests/pipeline/test_skip_trimming.nf.test b/tests/pipeline/test_skip_trimming.nf.test new file mode 100644 index 00000000..aa4e64a1 --- /dev/null +++ b/tests/pipeline/test_skip_trimming.nf.test @@ -0,0 +1,32 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "main.nf" + tag "test_skip_trimming" + tag "pipeline" + + test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + aassertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert new File("$outputDir/bwa/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert new File("$outputDir/genome/").exists() }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } + ) + } + + } + +} From 4d758fb48e3b228c8e7f3d8515196130c1af8ae2 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Thu, 22 Jun 2023 23:11:31 -0400 Subject: [PATCH 2/9] basic working tests --- tests/pipeline/test.nf.test | 19 ++++++++++--- tests/pipeline/test.nf.test.snap | 28 +++++++++++++++++++ tests/pipeline/test_aligner_bowtie2.nf.test | 14 ++-------- tests/pipeline/test_aligner_chromap.nf.test | 14 ++-------- tests/pipeline/test_aligner_star.nf.test | 14 ++-------- .../test_skip_consensus_peaks.nf.test | 14 ++-------- tests/pipeline/test_skip_trimming.nf.test | 14 ++-------- 7 files changed, 58 insertions(+), 59 deletions(-) create mode 100644 tests/pipeline/test.nf.test.snap diff --git a/tests/pipeline/test.nf.test b/tests/pipeline/test.nf.test index 66834081..04efbb11 100644 --- a/tests/pipeline/test.nf.test +++ b/tests/pipeline/test.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "test_profile" tag "pipeline" - test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + test("Default Test Profile") { when { params { @@ -14,12 +14,23 @@ nextflow_pipeline { } then { - aassertAll( + assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert new File("$outputDir/bwa/").exists() }, + { assert snapshot(path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/bwa/mergedLibrary/bigwig/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/deepTools/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/macs2/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/phantompeakqualtools/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/picard_metrics/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/samtools_stats/").exists() }, { assert new File("$outputDir/fastqc/").exists() }, - { assert new File("$outputDir/genome/").exists() }, + { assert snapshot(path("$outputDir/genome").list()).match("genome") }, { assert new File("$outputDir/igv/").exists() }, { assert new File("$outputDir/multiqc/").exists() }, { assert new File("$outputDir/pipeline_info/").exists() }, diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap new file mode 100644 index 00000000..8bc0edbf --- /dev/null +++ b/tests/pipeline/test.nf.test.snap @@ -0,0 +1,28 @@ +{ + "genome": { + "content": [ + "genome.fa:md5,4bad9f4b18056156a81f7f952abbe125", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" + ], + "timestamp": "2023-06-23T03:10:19+0000" + }, + "software_versions": { + "content": [ + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + ], + "timestamp": "2023-06-23T03:10:19+0000" + }, + "bwa/mergedLibrary/": { + "content": [ + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,cfe3ca6d25ea7e6bc2aaa7722da41788", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,89419543b9259872c37c13bd98d50618", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,81cdda5b11aaa901a788cc7b1bbde5c3", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,0a31e5e50e3a27775d50c76c699cd1bd", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,e532ef8339f6c927752860b1a963b52e", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,2d7e47d3384b2b349d63d57849628e72" + ], + "timestamp": "2023-06-23T03:10:19+0000" + } +} \ No newline at end of file diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test b/tests/pipeline/test_aligner_bowtie2.nf.test index c587229f..2b5b6a75 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test +++ b/tests/pipeline/test_aligner_bowtie2.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "test_aligner_bowtie2" tag "pipeline" - test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + test("Aligner - Bowtie2") { when { params { @@ -14,16 +14,8 @@ nextflow_pipeline { } then { - aassertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert new File("$outputDir/bwa/").exists() }, - { assert new File("$outputDir/fastqc/").exists() }, - { assert new File("$outputDir/genome/").exists() }, - { assert new File("$outputDir/igv/").exists() }, - { assert new File("$outputDir/multiqc/").exists() }, - { assert new File("$outputDir/pipeline_info/").exists() }, - { assert new File("$outputDir/trimgalore/").exists() } + assertAll( + { assert workflow.success } ) } diff --git a/tests/pipeline/test_aligner_chromap.nf.test b/tests/pipeline/test_aligner_chromap.nf.test index d97ad6e2..3101e5e1 100644 --- a/tests/pipeline/test_aligner_chromap.nf.test +++ b/tests/pipeline/test_aligner_chromap.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "test_aligner_chromap" tag "pipeline" - test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + test("Aligner - Chromap") { when { params { @@ -14,16 +14,8 @@ nextflow_pipeline { } then { - aassertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert new File("$outputDir/bwa/").exists() }, - { assert new File("$outputDir/fastqc/").exists() }, - { assert new File("$outputDir/genome/").exists() }, - { assert new File("$outputDir/igv/").exists() }, - { assert new File("$outputDir/multiqc/").exists() }, - { assert new File("$outputDir/pipeline_info/").exists() }, - { assert new File("$outputDir/trimgalore/").exists() } + assertAll( + { assert workflow.success } ) } diff --git a/tests/pipeline/test_aligner_star.nf.test b/tests/pipeline/test_aligner_star.nf.test index 07ea1ae3..3593f460 100644 --- a/tests/pipeline/test_aligner_star.nf.test +++ b/tests/pipeline/test_aligner_star.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "test_aligner_star" tag "pipeline" - test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + test("Aligner - STAR") { when { params { @@ -14,16 +14,8 @@ nextflow_pipeline { } then { - aassertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert new File("$outputDir/bwa/").exists() }, - { assert new File("$outputDir/fastqc/").exists() }, - { assert new File("$outputDir/genome/").exists() }, - { assert new File("$outputDir/igv/").exists() }, - { assert new File("$outputDir/multiqc/").exists() }, - { assert new File("$outputDir/pipeline_info/").exists() }, - { assert new File("$outputDir/trimgalore/").exists() } + assertAll( + { assert workflow.success } ) } diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test b/tests/pipeline/test_skip_consensus_peaks.nf.test index d1d01989..3b3e3d1f 100644 --- a/tests/pipeline/test_skip_consensus_peaks.nf.test +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "test_skip_consensus_peaks" tag "pipeline" - test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + test("Skip Consesus Peaks") { when { params { @@ -14,16 +14,8 @@ nextflow_pipeline { } then { - aassertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert new File("$outputDir/bwa/").exists() }, - { assert new File("$outputDir/fastqc/").exists() }, - { assert new File("$outputDir/genome/").exists() }, - { assert new File("$outputDir/igv/").exists() }, - { assert new File("$outputDir/multiqc/").exists() }, - { assert new File("$outputDir/pipeline_info/").exists() }, - { assert new File("$outputDir/trimgalore/").exists() } + assertAll( + { assert workflow.success } ) } diff --git a/tests/pipeline/test_skip_trimming.nf.test b/tests/pipeline/test_skip_trimming.nf.test index aa4e64a1..6008938f 100644 --- a/tests/pipeline/test_skip_trimming.nf.test +++ b/tests/pipeline/test_skip_trimming.nf.test @@ -5,7 +5,7 @@ nextflow_pipeline { tag "test_skip_trimming" tag "pipeline" - test("SPT5_T0 / SPT5_T15 / SPT5_INPUT") { + test("Skip Trimming") { when { params { @@ -14,16 +14,8 @@ nextflow_pipeline { } then { - aassertAll( - { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert new File("$outputDir/bwa/").exists() }, - { assert new File("$outputDir/fastqc/").exists() }, - { assert new File("$outputDir/genome/").exists() }, - { assert new File("$outputDir/igv/").exists() }, - { assert new File("$outputDir/multiqc/").exists() }, - { assert new File("$outputDir/pipeline_info/").exists() }, - { assert new File("$outputDir/trimgalore/").exists() } + assertAll( + { assert workflow.success } ) } From a1d12cb28a2dd7f9aca0318df53196750060ce74 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Thu, 22 Jun 2023 23:14:46 -0400 Subject: [PATCH 3/9] basic working tests --- tests/pipeline/test_aligner_bowtie2.nf.test | 1 + tests/pipeline/test_aligner_chromap.nf.test | 1 + tests/pipeline/test_aligner_star.nf.test | 3 ++- tests/pipeline/test_skip_consensus_peaks.nf.test | 3 ++- tests/pipeline/test_skip_trimming.nf.test | 3 ++- 5 files changed, 8 insertions(+), 3 deletions(-) diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test b/tests/pipeline/test_aligner_bowtie2.nf.test index 2b5b6a75..9581c3d7 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test +++ b/tests/pipeline/test_aligner_bowtie2.nf.test @@ -10,6 +10,7 @@ nextflow_pipeline { when { params { outdir = "$outputDir" + aligner = "bowtie2" } } diff --git a/tests/pipeline/test_aligner_chromap.nf.test b/tests/pipeline/test_aligner_chromap.nf.test index 3101e5e1..678a1929 100644 --- a/tests/pipeline/test_aligner_chromap.nf.test +++ b/tests/pipeline/test_aligner_chromap.nf.test @@ -10,6 +10,7 @@ nextflow_pipeline { when { params { outdir = "$outputDir" + aligner = "chromap" } } diff --git a/tests/pipeline/test_aligner_star.nf.test b/tests/pipeline/test_aligner_star.nf.test index 3593f460..250e5697 100644 --- a/tests/pipeline/test_aligner_star.nf.test +++ b/tests/pipeline/test_aligner_star.nf.test @@ -9,7 +9,8 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" + aligner = "star" } } diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test b/tests/pipeline/test_skip_consensus_peaks.nf.test index 3b3e3d1f..1da44bb5 100644 --- a/tests/pipeline/test_skip_consensus_peaks.nf.test +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test @@ -9,7 +9,8 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" + skip_consensus_peaks = true } } diff --git a/tests/pipeline/test_skip_trimming.nf.test b/tests/pipeline/test_skip_trimming.nf.test index 6008938f..43b25c7a 100644 --- a/tests/pipeline/test_skip_trimming.nf.test +++ b/tests/pipeline/test_skip_trimming.nf.test @@ -9,7 +9,8 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" + skip_trimming = true } } From a614b0975f2738b856f509032095073e5ea8a2aa Mon Sep 17 00:00:00 2001 From: Sateesh Date: Fri, 23 Jun 2023 15:08:48 +0000 Subject: [PATCH 4/9] nf-test snapshots --- tests/nextflow.config | 5 ---- tests/pipeline/test_aligner_bowtie2.nf.test | 23 +++++++++++++-- .../test_aligner_bowtie2.nf.test.snap | 28 +++++++++++++++++++ tests/pipeline/test_aligner_chromap.nf.test | 23 +++++++++++++-- .../test_aligner_chromap.nf.test.snap | 28 +++++++++++++++++++ tests/pipeline/test_aligner_star.nf.test | 21 +++++++++++++- tests/pipeline/test_aligner_star.nf.test.snap | 28 +++++++++++++++++++ .../test_skip_consensus_peaks.nf.test | 21 +++++++++++++- .../test_skip_consensus_peaks.nf.test.snap | 28 +++++++++++++++++++ tests/pipeline/test_skip_trimming.nf.test | 21 +++++++++++++- .../pipeline/test_skip_trimming.nf.test.snap | 28 +++++++++++++++++++ 11 files changed, 242 insertions(+), 12 deletions(-) delete mode 100644 tests/nextflow.config create mode 100644 tests/pipeline/test_aligner_bowtie2.nf.test.snap create mode 100644 tests/pipeline/test_aligner_chromap.nf.test.snap create mode 100644 tests/pipeline/test_aligner_star.nf.test.snap create mode 100644 tests/pipeline/test_skip_consensus_peaks.nf.test.snap create mode 100644 tests/pipeline/test_skip_trimming.nf.test.snap diff --git a/tests/nextflow.config b/tests/nextflow.config deleted file mode 100644 index c19b1ad0..00000000 --- a/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -/* -======================================================================================== - Nextflow config file for running tests -======================================================================================== -*/ diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test b/tests/pipeline/test_aligner_bowtie2.nf.test index 9581c3d7..860d78ef 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test +++ b/tests/pipeline/test_aligner_bowtie2.nf.test @@ -9,14 +9,33 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" aligner = "bowtie2" } } then { assertAll( - { assert workflow.success } + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert snapshot(path("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/bowtie2/mergedLibrary/bigwig/").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/deepTools/").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/macs2/").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/phantompeakqualtools/").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/picard_metrics/").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/samtools_stats/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert snapshot(path("$outputDir/genome").list()).match("genome") }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } ) } diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap new file mode 100644 index 00000000..99c31a0f --- /dev/null +++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap @@ -0,0 +1,28 @@ +{ + "genome": { + "content": [ + "genome.fa:md5,4bad9f4b18056156a81f7f952abbe125", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" + ], + "timestamp": "2023-06-23T13:56:40+0000" + }, + "software_versions": { + "content": [ + "{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=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + ], + "timestamp": "2023-06-23T13:56:40+0000" + }, + "bwa/mergedLibrary/": { + "content": [ + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,6052d838940368af809a0c81df241dd4", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,f3ecec0228ecb264cb7d8f8f4d4e70fb", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,dcc595a4bdeaeb6b2e61f188ae359148", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,5f9d38d4b2972f25314ed6d712a53a40", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,cb069d548dfb4c75d6bcd76ddb08a42c", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,0f4504a16448f5355111985e04d2a4bb" + ], + "timestamp": "2023-06-23T13:56:40+0000" + } +} \ No newline at end of file diff --git a/tests/pipeline/test_aligner_chromap.nf.test b/tests/pipeline/test_aligner_chromap.nf.test index 678a1929..f433943a 100644 --- a/tests/pipeline/test_aligner_chromap.nf.test +++ b/tests/pipeline/test_aligner_chromap.nf.test @@ -9,14 +9,33 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" aligner = "chromap" } } then { assertAll( - { assert workflow.success } + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert snapshot(path("$outputDir/chromap/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), + path("$outputDir/chromap/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), + path("$outputDir/chromap/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), + path("$outputDir/chromap/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), + path("$outputDir/chromap/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), + path("$outputDir/chromap/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/chromap/mergedLibrary/bigwig/").exists() }, + { assert new File("$outputDir/chromap/mergedLibrary/deepTools/").exists() }, + { assert new File("$outputDir/chromap/mergedLibrary/macs2/").exists() }, + { assert new File("$outputDir/chromap/mergedLibrary/phantompeakqualtools/").exists() }, + { assert new File("$outputDir/chromap/mergedLibrary/picard_metrics/").exists() }, + { assert new File("$outputDir/chromap/mergedLibrary/samtools_stats/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert snapshot(path("$outputDir/genome").list()).match("genome") }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } ) } diff --git a/tests/pipeline/test_aligner_chromap.nf.test.snap b/tests/pipeline/test_aligner_chromap.nf.test.snap new file mode 100644 index 00000000..3bf9d3ae --- /dev/null +++ b/tests/pipeline/test_aligner_chromap.nf.test.snap @@ -0,0 +1,28 @@ +{ + "genome": { + "content": [ + "genome.fa:md5,4bad9f4b18056156a81f7f952abbe125", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" + ], + "timestamp": "2023-06-23T14:32:52+0000" + }, + "software_versions": { + "content": [ + "{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}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.16.1}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + ], + "timestamp": "2023-06-23T14:32:52+0000" + }, + "bwa/mergedLibrary/": { + "content": [ + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,09c827aea06dfb2aaf784a7163e9cb40", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,8af1f829f6e10e4580b430abb1dc917d", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,81997090a4be675fd6551db04362906a", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,27937f594fb0d276302b6a162371a909", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,e6bec7c541bcba089a71070bff098d9c", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,ec970977f6de00d52f3624e8b6c18540" + ], + "timestamp": "2023-06-23T14:32:52+0000" + } +} \ No newline at end of file diff --git a/tests/pipeline/test_aligner_star.nf.test b/tests/pipeline/test_aligner_star.nf.test index 250e5697..8c5a1d81 100644 --- a/tests/pipeline/test_aligner_star.nf.test +++ b/tests/pipeline/test_aligner_star.nf.test @@ -16,7 +16,26 @@ nextflow_pipeline { then { assertAll( - { assert workflow.success } + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert snapshot(path("$outputDir/star/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), + path("$outputDir/star/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), + path("$outputDir/star/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), + path("$outputDir/star/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), + path("$outputDir/star/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), + path("$outputDir/star/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/star/mergedLibrary/bigwig/").exists() }, + { assert new File("$outputDir/star/mergedLibrary/deepTools/").exists() }, + { assert new File("$outputDir/star/mergedLibrary/macs2/").exists() }, + { assert new File("$outputDir/star/mergedLibrary/phantompeakqualtools/").exists() }, + { assert new File("$outputDir/star/mergedLibrary/picard_metrics/").exists() }, + { assert new File("$outputDir/star/mergedLibrary/samtools_stats/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert snapshot(path("$outputDir/genome").list()).match("genome") }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } ) } diff --git a/tests/pipeline/test_aligner_star.nf.test.snap b/tests/pipeline/test_aligner_star.nf.test.snap new file mode 100644 index 00000000..c3efc510 --- /dev/null +++ b/tests/pipeline/test_aligner_star.nf.test.snap @@ -0,0 +1,28 @@ +{ + "genome": { + "content": [ + "genome.fa:md5,4bad9f4b18056156a81f7f952abbe125", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" + ], + "timestamp": "2023-06-23T14:22:15+0000" + }, + "software_versions": { + "content": [ + "{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_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, 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=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + ], + "timestamp": "2023-06-23T14:22:15+0000" + }, + "bwa/mergedLibrary/": { + "content": [ + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,8daf8d3b4adf6ad8e93d3bacf4efe059", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,db261844fe9e5f20b250f32a99dbf88a", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,737fa3fdd38998777f1c73f4d1c3eaf7", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,fb54e9065fe338091c2880640f9d202a", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,eb89b7f87024ec83066f2fe4bee106ce", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,80fac2e96d44fe0f33a2bdd98b7a08a4" + ], + "timestamp": "2023-06-23T14:22:15+0000" + } +} \ No newline at end of file diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test b/tests/pipeline/test_skip_consensus_peaks.nf.test index 1da44bb5..39722132 100644 --- a/tests/pipeline/test_skip_consensus_peaks.nf.test +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test @@ -16,7 +16,26 @@ nextflow_pipeline { then { assertAll( - { assert workflow.success } + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert snapshot(path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/bwa/mergedLibrary/bigwig/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/deepTools/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/macs2/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/phantompeakqualtools/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/picard_metrics/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/samtools_stats/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert snapshot(path("$outputDir/genome").list()).match("genome") }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert new File("$outputDir/trimgalore/").exists() } ) } diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap new file mode 100644 index 00000000..f9b22758 --- /dev/null +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap @@ -0,0 +1,28 @@ +{ + "genome": { + "content": [ + "genome.fa:md5,4bad9f4b18056156a81f7f952abbe125", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" + ], + "timestamp": "2023-06-23T14:47:53+0000" + }, + "software_versions": { + "content": [ + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + ], + "timestamp": "2023-06-23T14:47:53+0000" + }, + "bwa/mergedLibrary/": { + "content": [ + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,cfe3ca6d25ea7e6bc2aaa7722da41788", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,89419543b9259872c37c13bd98d50618", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,81cdda5b11aaa901a788cc7b1bbde5c3", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,0a31e5e50e3a27775d50c76c699cd1bd", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,e532ef8339f6c927752860b1a963b52e", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,2d7e47d3384b2b349d63d57849628e72" + ], + "timestamp": "2023-06-23T14:47:53+0000" + } +} \ No newline at end of file diff --git a/tests/pipeline/test_skip_trimming.nf.test b/tests/pipeline/test_skip_trimming.nf.test index 43b25c7a..554e631b 100644 --- a/tests/pipeline/test_skip_trimming.nf.test +++ b/tests/pipeline/test_skip_trimming.nf.test @@ -16,7 +16,26 @@ nextflow_pipeline { then { assertAll( - { assert workflow.success } + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert snapshot(path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), + path("$outputDir/bwa/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/bwa/mergedLibrary/bigwig/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/deepTools/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/macs2/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/phantompeakqualtools/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/picard_metrics/").exists() }, + { assert new File("$outputDir/bwa/mergedLibrary/samtools_stats/").exists() }, + { assert new File("$outputDir/fastqc/").exists() }, + { assert snapshot(path("$outputDir/genome").list()).match("genome") }, + { assert new File("$outputDir/igv/").exists() }, + { assert new File("$outputDir/multiqc/").exists() }, + { assert new File("$outputDir/pipeline_info/").exists() }, + { assert !new File("$outputDir/trimgalore/").exists() } ) } diff --git a/tests/pipeline/test_skip_trimming.nf.test.snap b/tests/pipeline/test_skip_trimming.nf.test.snap new file mode 100644 index 00000000..6f06afee --- /dev/null +++ b/tests/pipeline/test_skip_trimming.nf.test.snap @@ -0,0 +1,28 @@ +{ + "genome": { + "content": [ + "genome.fa:md5,4bad9f4b18056156a81f7f952abbe125", + "genome.fa.fai:md5,6f4c0ce5258e6948135ad006e1f9ee1b", + "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", + "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" + ], + "timestamp": "2023-06-23T15:06:21+0000" + }, + "software_versions": { + "content": [ + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + ], + "timestamp": "2023-06-23T03:10:19+0000" + }, + "bwa/mergedLibrary/": { + "content": [ + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,3784f0f45f705e76b7a11133e811bc13", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,473f9ff8b34a6968de047a1c3a6c379a", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,384b136e3faffebd240d132db48d8813", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,ceef2717e4f89e22671e6d71409c489b", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,63e4289ef16e109345ff970edb456a92", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,58a7ba9229e6c5ee06f73bcbfeecdbef" + ], + "timestamp": "2023-06-23T15:06:21+0000" + } +} From 05399b726a492dfeeb356ac50abd0033a4103569 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Fri, 23 Jun 2023 14:50:04 -0400 Subject: [PATCH 5/9] update snapshots --- tests/pipeline/test_aligner_bowtie2.nf.test.snap | 16 ++++++++-------- tests/pipeline/test_skip_trimming.nf.test.snap | 10 +++++----- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap index 99c31a0f..033fcd05 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test.snap +++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T13:56:40+0000" + "timestamp": "2023-06-23T16:33:44+0000" }, "software_versions": { "content": [ "{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=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T13:56:40+0000" + "timestamp": "2023-06-23T16:33:44+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,6052d838940368af809a0c81df241dd4", + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,4afe18929f1525a083851d7f0ad6080b", "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,f3ecec0228ecb264cb7d8f8f4d4e70fb", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,dcc595a4bdeaeb6b2e61f188ae359148", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,5f9d38d4b2972f25314ed6d712a53a40", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,cb069d548dfb4c75d6bcd76ddb08a42c", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,0f4504a16448f5355111985e04d2a4bb" + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,f3de46b851e40c3ed594bd4b026a01c3", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,5f2e28b9e2beaa762d0854d85a3fdd29", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,94b1bdfbd2a2c126557c9b2e960c5899", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,609a3dcaf181ed44abb30ea0c58b042d" ], - "timestamp": "2023-06-23T13:56:40+0000" + "timestamp": "2023-06-23T16:33:44+0000" } } \ No newline at end of file diff --git a/tests/pipeline/test_skip_trimming.nf.test.snap b/tests/pipeline/test_skip_trimming.nf.test.snap index 6f06afee..8a17514f 100644 --- a/tests/pipeline/test_skip_trimming.nf.test.snap +++ b/tests/pipeline/test_skip_trimming.nf.test.snap @@ -6,13 +6,13 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T15:06:21+0000" + "timestamp": "2023-06-23T17:20:02+0000" }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T03:10:19+0000" + "timestamp": "2023-06-23T17:20:02+0000" }, "bwa/mergedLibrary/": { "content": [ @@ -23,6 +23,6 @@ "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,63e4289ef16e109345ff970edb456a92", "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,58a7ba9229e6c5ee06f73bcbfeecdbef" ], - "timestamp": "2023-06-23T15:06:21+0000" + "timestamp": "2023-06-23T17:20:02+0000" } -} +} \ No newline at end of file From 0fc7920fa2057d97e32143aef035470e31b88737 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Sun, 25 Jun 2023 14:48:43 -0400 Subject: [PATCH 6/9] update snapshots after rebase --- tests/pipeline/test.nf.test.snap | 2 +- tests/pipeline/test_aligner_bowtie2.nf.test.snap | 2 +- tests/pipeline/test_aligner_chromap.nf.test.snap | 2 +- tests/pipeline/test_aligner_star.nf.test.snap | 2 +- tests/pipeline/test_skip_consensus_peaks.nf.test.snap | 2 +- tests/pipeline/test_skip_trimming.nf.test.snap | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index 8bc0edbf..32582165 100644 --- a/tests/pipeline/test.nf.test.snap +++ b/tests/pipeline/test.nf.test.snap @@ -10,7 +10,7 @@ }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-23T03:10:19+0000" }, diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap index 033fcd05..2e417fca 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test.snap +++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap @@ -10,7 +10,7 @@ }, "software_versions": { "content": [ - "{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=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=2.4.4, pigz=2.6, samtools=1.17}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-23T16:33:44+0000" }, diff --git a/tests/pipeline/test_aligner_chromap.nf.test.snap b/tests/pipeline/test_aligner_chromap.nf.test.snap index 3bf9d3ae..36ca994a 100644 --- a/tests/pipeline/test_aligner_chromap.nf.test.snap +++ b/tests/pipeline/test_aligner_chromap.nf.test.snap @@ -10,7 +10,7 @@ }, "software_versions": { "content": [ - "{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}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.16.1}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.17}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-23T14:32:52+0000" }, diff --git a/tests/pipeline/test_aligner_star.nf.test.snap b/tests/pipeline/test_aligner_star.nf.test.snap index c3efc510..964dbaab 100644 --- a/tests/pipeline/test_aligner_star.nf.test.snap +++ b/tests/pipeline/test_aligner_star.nf.test.snap @@ -10,7 +10,7 @@ }, "software_versions": { "content": [ - "{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_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, 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=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, 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=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-23T14:22:15+0000" }, diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap index f9b22758..9e90f1e1 100644 --- a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap @@ -10,7 +10,7 @@ }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-23T14:47:53+0000" }, diff --git a/tests/pipeline/test_skip_trimming.nf.test.snap b/tests/pipeline/test_skip_trimming.nf.test.snap index 8a17514f..9c04b88a 100644 --- a/tests/pipeline/test_skip_trimming.nf.test.snap +++ b/tests/pipeline/test_skip_trimming.nf.test.snap @@ -10,7 +10,7 @@ }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-23T17:20:02+0000" }, From 99f3098b49f4c4dde7962114c5254262a89bae66 Mon Sep 17 00:00:00 2001 From: Sateesh Date: Sun, 25 Jun 2023 23:56:15 +0000 Subject: [PATCH 7/9] update snapshots --- tests/pipeline/test.nf.test.snap | 20 +++++++++---------- .../test_aligner_bowtie2.nf.test.snap | 20 +++++++++---------- .../test_aligner_chromap.nf.test.snap | 20 +++++++++---------- tests/pipeline/test_aligner_star.nf.test.snap | 18 ++++++++--------- .../test_skip_consensus_peaks.nf.test.snap | 20 +++++++++---------- .../pipeline/test_skip_trimming.nf.test.snap | 20 +++++++++---------- 6 files changed, 59 insertions(+), 59 deletions(-) diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap index 32582165..a3897eba 100644 --- a/tests/pipeline/test.nf.test.snap +++ b/tests/pipeline/test.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T03:10:19+0000" + "timestamp": "2023-06-25T23:19:20+0000" }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T03:10:19+0000" + "timestamp": "2023-06-25T23:19:20+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,cfe3ca6d25ea7e6bc2aaa7722da41788", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,89419543b9259872c37c13bd98d50618", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,81cdda5b11aaa901a788cc7b1bbde5c3", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,0a31e5e50e3a27775d50c76c699cd1bd", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,e532ef8339f6c927752860b1a963b52e", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,2d7e47d3384b2b349d63d57849628e72" + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,d7bee922bf952cf61386fc16ca4caa97", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,77546d38f90715f72970ee79115867e8", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,9e08abe685744dfbc007b98f75e35a6b", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,7a633fa29c9dd0572c20f71c10f3b0e7", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,dbfc6b58eee6d28dc56aac5fa38703b1", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,b61cb600c3866477c0c3957b779bf5f0" ], - "timestamp": "2023-06-23T03:10:19+0000" + "timestamp": "2023-06-25T23:19:21+0000" } } \ No newline at end of file diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap index 2e417fca..1666c87e 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test.snap +++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T16:33:44+0000" + "timestamp": "2023-06-25T22:21:30+0000" }, "software_versions": { "content": [ - "{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=2.4.4, pigz=2.6, samtools=1.17}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T16:33:44+0000" + "timestamp": "2023-06-25T22:21:30+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,4afe18929f1525a083851d7f0ad6080b", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,f3ecec0228ecb264cb7d8f8f4d4e70fb", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,f3de46b851e40c3ed594bd4b026a01c3", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,5f2e28b9e2beaa762d0854d85a3fdd29", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,94b1bdfbd2a2c126557c9b2e960c5899", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,609a3dcaf181ed44abb30ea0c58b042d" + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,10997bfdf2b0fa2804cac74c200bcbe9", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,c17d27a4acab11f22984900d0bd4a11e", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,928396e96edc025e5a22a0f0c12dcae2", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,5d2cd614dbcf73780a030a703e80440d", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,33e29b69167e52744e3ea5c2e4321557", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,93b3219da8a268fe090ad604c2e42fae" ], - "timestamp": "2023-06-23T16:33:44+0000" + "timestamp": "2023-06-25T22:21:30+0000" } } \ No newline at end of file diff --git a/tests/pipeline/test_aligner_chromap.nf.test.snap b/tests/pipeline/test_aligner_chromap.nf.test.snap index 36ca994a..a7f4e53f 100644 --- a/tests/pipeline/test_aligner_chromap.nf.test.snap +++ b/tests/pipeline/test_aligner_chromap.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T14:32:52+0000" + "timestamp": "2023-06-25T22:30:14+0000" }, "software_versions": { "content": [ - "{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}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.17}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.16.1}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T14:32:52+0000" + "timestamp": "2023-06-25T22:30:14+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,09c827aea06dfb2aaf784a7163e9cb40", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,8af1f829f6e10e4580b430abb1dc917d", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,81997090a4be675fd6551db04362906a", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,27937f594fb0d276302b6a162371a909", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,e6bec7c541bcba089a71070bff098d9c", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,ec970977f6de00d52f3624e8b6c18540" + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,aaf444d7627fe5e0d2856e3e8a416cb5", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,0fee8fec43ad772baa865e38d9d37a6a", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,7ae794cae2dd2b94c90cd1b6d49e0bb7", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,59c588edd52f6545f0ae9dc22f3f7b99", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,1413130a432d2c4a9c5304f1cb375237", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,9d5d34267094cc2c306237e4794316cc" ], - "timestamp": "2023-06-23T14:32:52+0000" + "timestamp": "2023-06-25T22:30:14+0000" } } \ No newline at end of file diff --git a/tests/pipeline/test_aligner_star.nf.test.snap b/tests/pipeline/test_aligner_star.nf.test.snap index 964dbaab..ec5035f6 100644 --- a/tests/pipeline/test_aligner_star.nf.test.snap +++ b/tests/pipeline/test_aligner_star.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T14:22:15+0000" + "timestamp": "2023-06-25T22:33:07+0000" }, "software_versions": { "content": [ "{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_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, 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=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T14:22:15+0000" + "timestamp": "2023-06-25T22:33:07+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,8daf8d3b4adf6ad8e93d3bacf4efe059", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,db261844fe9e5f20b250f32a99dbf88a", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,737fa3fdd38998777f1c73f4d1c3eaf7", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,fb54e9065fe338091c2880640f9d202a", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,eb89b7f87024ec83066f2fe4bee106ce", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,80fac2e96d44fe0f33a2bdd98b7a08a4" + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,1d6e8880d67e495dd1376d2194cec8a4", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,ad0da738b20b9391a25285dffd427cb6", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,39663f6613376984f7ed06f25bf7cedd", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,69401828a817dbbfacadbdb20c3e8371", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,469c1e4c6d15c4b6591a9ca36017f285", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,6cb89042d5a81b79c797e06177a04f41" ], - "timestamp": "2023-06-23T14:22:15+0000" + "timestamp": "2023-06-25T22:33:07+0000" } } \ No newline at end of file diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap index 9e90f1e1..217024df 100644 --- a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap +++ b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T14:47:53+0000" + "timestamp": "2023-06-25T23:42:37+0000" }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T14:47:53+0000" + "timestamp": "2023-06-25T23:42:37+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,cfe3ca6d25ea7e6bc2aaa7722da41788", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,89419543b9259872c37c13bd98d50618", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,81cdda5b11aaa901a788cc7b1bbde5c3", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,0a31e5e50e3a27775d50c76c699cd1bd", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,e532ef8339f6c927752860b1a963b52e", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,2d7e47d3384b2b349d63d57849628e72" + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,d7bee922bf952cf61386fc16ca4caa97", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,77546d38f90715f72970ee79115867e8", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,9e08abe685744dfbc007b98f75e35a6b", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,7a633fa29c9dd0572c20f71c10f3b0e7", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,dbfc6b58eee6d28dc56aac5fa38703b1", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,b61cb600c3866477c0c3957b779bf5f0" ], - "timestamp": "2023-06-23T14:47:53+0000" + "timestamp": "2023-06-25T23:42:37+0000" } } \ No newline at end of file diff --git a/tests/pipeline/test_skip_trimming.nf.test.snap b/tests/pipeline/test_skip_trimming.nf.test.snap index 9c04b88a..4ab62e11 100644 --- a/tests/pipeline/test_skip_trimming.nf.test.snap +++ b/tests/pipeline/test_skip_trimming.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-23T17:20:02+0000" + "timestamp": "2023-06-25T23:55:28+0000" }, "software_versions": { "content": [ - "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" + "{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=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-23T17:20:02+0000" + "timestamp": "2023-06-25T23:55:28+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,3784f0f45f705e76b7a11133e811bc13", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,473f9ff8b34a6968de047a1c3a6c379a", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,384b136e3faffebd240d132db48d8813", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,ceef2717e4f89e22671e6d71409c489b", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,63e4289ef16e109345ff970edb456a92", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,58a7ba9229e6c5ee06f73bcbfeecdbef" + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,78d3f645ed745f164ca42cce6942086c", + "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,f584d049da692581f0cafa75c6adf469", + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,927de7ba2cb30ee8235f273b3c4a86fc", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,9e80eaea382f9fbfd8ce000d1130785f", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,0899b798da9eb097a5b3fe29f3e5a056", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,25707d4184d1a4a9c11bc52f65f1ce03" ], - "timestamp": "2023-06-23T17:20:02+0000" + "timestamp": "2023-06-25T23:55:28+0000" } } \ No newline at end of file From 63d822acd22315bb6d62b39a23b8ac6a8e38a62e Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Sun, 25 Jun 2023 20:54:54 -0400 Subject: [PATCH 8/9] fix failing bowtie2 snap --- tests/pipeline/test_aligner_bowtie2.nf.test.snap | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap index 1666c87e..c8e51b80 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test.snap +++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap @@ -6,23 +6,23 @@ "genome.fa.sizes:md5,e122f8021a5ef14104c32785cb9b7adc", "genome.include_regions.bed:md5,58b27f8faf81d116a596c37be421ce01" ], - "timestamp": "2023-06-25T22:21:30+0000" + "timestamp": "2023-06-26T00:54:15+0000" }, "software_versions": { "content": [ "{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=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], - "timestamp": "2023-06-25T22:21:30+0000" + "timestamp": "2023-06-26T00:54:15+0000" }, "bwa/mergedLibrary/": { "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,10997bfdf2b0fa2804cac74c200bcbe9", + "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,3b4bc24c4aa0712bef42558de52c6a7b", "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,c17d27a4acab11f22984900d0bd4a11e", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,928396e96edc025e5a22a0f0c12dcae2", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,5d2cd614dbcf73780a030a703e80440d", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,33e29b69167e52744e3ea5c2e4321557", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,93b3219da8a268fe090ad604c2e42fae" + "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,b291fad2f1f5a310771d968584ae92e0", + "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,0e30d0dcdf94b8c6a25b1e1be7360ec9", + "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,398c07c2ecc30ca3a93d065af2a7003c", + "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,df9b770a1278f90e08fb3ef889e8ae35" ], - "timestamp": "2023-06-25T22:21:30+0000" + "timestamp": "2023-06-26T00:54:15+0000" } } \ No newline at end of file From b764ac4a25270b71d9b230ffd068baf07f0b00e7 Mon Sep 17 00:00:00 2001 From: Sateesh Peri Date: Mon, 26 Jun 2023 11:20:05 -0400 Subject: [PATCH 9/9] update bowtie2 snap --- tests/pipeline/test_aligner_bowtie2.nf.test | 12 ++++++------ tests/pipeline/test_aligner_bowtie2.nf.test.snap | 11 ----------- 2 files changed, 6 insertions(+), 17 deletions(-) diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test b/tests/pipeline/test_aligner_bowtie2.nf.test index 860d78ef..0637717f 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test +++ b/tests/pipeline/test_aligner_bowtie2.nf.test @@ -18,12 +18,12 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert snapshot(path("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam"), - path("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam"), - path("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam"), - path("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam"), - path("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam"), - path("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam")).match("bwa/mergedLibrary/") }, + { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP1.mLb.clN.sorted.bam").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_INPUT_REP2.mLb.clN.sorted.bam").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP1.mLb.clN.sorted.bam").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T0_REP2.mLb.clN.sorted.bam").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP1.mLb.clN.sorted.bam").exists() }, + { assert new File("$outputDir/bowtie2/mergedLibrary/SPT5_T15_REP2.mLb.clN.sorted.bam").exists() }, { assert new File("$outputDir/bowtie2/mergedLibrary/bigwig/").exists() }, { assert new File("$outputDir/bowtie2/mergedLibrary/deepTools/").exists() }, { assert new File("$outputDir/bowtie2/mergedLibrary/macs2/").exists() }, diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap index c8e51b80..fc7d34be 100644 --- a/tests/pipeline/test_aligner_bowtie2.nf.test.snap +++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap @@ -13,16 +13,5 @@ "{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=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}" ], "timestamp": "2023-06-26T00:54:15+0000" - }, - "bwa/mergedLibrary/": { - "content": [ - "SPT5_INPUT_REP1.mLb.clN.sorted.bam:md5,3b4bc24c4aa0712bef42558de52c6a7b", - "SPT5_INPUT_REP2.mLb.clN.sorted.bam:md5,c17d27a4acab11f22984900d0bd4a11e", - "SPT5_T0_REP1.mLb.clN.sorted.bam:md5,b291fad2f1f5a310771d968584ae92e0", - "SPT5_T0_REP2.mLb.clN.sorted.bam:md5,0e30d0dcdf94b8c6a25b1e1be7360ec9", - "SPT5_T15_REP1.mLb.clN.sorted.bam:md5,398c07c2ecc30ca3a93d065af2a7003c", - "SPT5_T15_REP2.mLb.clN.sorted.bam:md5,df9b770a1278f90e08fb3ef889e8ae35" - ], - "timestamp": "2023-06-26T00:54:15+0000" } } \ No newline at end of file