From f64efd0945922415d64c7b58dfc1776dd1773d5b Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 20 Aug 2024 19:55:36 +0000 Subject: [PATCH] Minimal profiles for testing ci settings --- .github/workflows/ci.yml | 85 ++---- tests/test.nf.test | 274 +------------------ tests/test.nf.test.snap | 319 ---------------------- tests/test_index.nf.test | 241 +--------------- tests/test_index.nf.test.snap | 292 -------------------- tests/test_mirgenedb.nf.test | 27 ++ tests/test_no_genome.nf.test | 272 +----------------- tests/test_no_genome.nf.test.snap | 311 --------------------- tests/test_technical_repeats.nf.test | 120 +------- tests/test_technical_repeats.nf.test.snap | 153 ----------- tests/test_umi.nf.test | 166 +---------- tests/test_umi.nf.test.snap | 217 --------------- 12 files changed, 51 insertions(+), 2426 deletions(-) delete mode 100644 tests/test.nf.test.snap delete mode 100644 tests/test_index.nf.test.snap create mode 100644 tests/test_mirgenedb.nf.test delete mode 100644 tests/test_no_genome.nf.test.snap delete mode 100644 tests/test_technical_repeats.nf.test.snap delete mode 100644 tests/test_umi.nf.test.snap diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c798356f..41843f15 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,53 +1,34 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: + push: + branches: + - dev pull_request: + release: + types: [published] env: NXF_ANSI_LOG: false - NFT_VER: "0.8.4" - NFT_WORKDIR: "~" - NFT_DIFF: "pdiff" - NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" + CAPSULE_LOG: none + NFTEST_VER: "0.8.4" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true -jobs: - nf-test-changes: - name: Check for changes - runs-on: ubuntu-latest - outputs: - nf_test_files: ${{ steps.list.outputs.components }} - steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: List nf-test files - id: list - uses: adamrtalbot/detect-nf-test-changes@v0.0.2 - with: - head: ${{ github.sha }} - base: origin/${{ github.base_ref }} - include: .github/include.yaml - - - name: print list of nf-test files - run: | - echo ${{ steps.list.outputs.components }} +jobs: test: - name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} - needs: [nf-test-changes] - if: needs.nf-test-changes.outputs.nf_test_files != '[]' + name: Run pipeline with test data + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}" runs-on: ubuntu-latest strategy: fail-fast: false matrix: NXF_VER: + - "23.04.0" - "latest-everything" - - "23.04" - nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - "test" - "test_no_genome" @@ -64,53 +45,25 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - architecture: "x64" + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Install pdiff to see diff between nf-test snapshots + - name: Install nf-test run: | - python -m pip install --upgrade pip - pip install pdiff - - - uses: nf-core/setup-nf-test@v1 + wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + sudo mv nf-test /usr/local/bin/ - name: Run nf-test - run: | - nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap - - - uses: pcolby/tap-summary@v1 - with: - path: >- - test.tap + run: nf-test test tests/${{ matrix.profile }}.nf.test --profile +docker --junitxml=test.xml - name: Output log on failure if: failure() run: | sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log + batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml - name: Publish Test Report uses: mikepenz/action-junit-report@v3 if: always() # always run even if the previous step fails with: report_paths: test.xml - - confirm-pass: - runs-on: ubuntu-latest - needs: [test] - if: always() - steps: - - name: All tests ok - if: ${{ !contains(needs.*.result, 'failure') }} - run: exit 0 - - name: One or more tests failed - if: ${{ contains(needs.*.result, 'failure') }} - run: exit 1 - - - name: debug-print - if: always() - run: | - echo "toJSON(needs) = ${{ toJSON(needs) }}" - echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/tests/test.nf.test b/tests/test.nf.test index 098e74d5..3d766b2b 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -18,279 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 196 }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 196 } ) } diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap deleted file mode 100644 index b26b2a15..00000000 --- a/tests/test.nf.test.snap +++ /dev/null @@ -1,319 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:11.173010609" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:41.566106027" - }, - "genome_quant": { - "content": [ - "Clone9_N2_mature_hairpin_genome.sorted.flagstat:md5,b8fbbdaca0458b19732312dea2997be8", - "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,18f0028f1cfc137ef8f089e465fe20f5", - "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", - "Control_N3_mature_hairpin_genome.sorted.stats:md5,53e8fca566dd5dd8553b25c38e961f6b", - "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,fb089da3351a3f8c0bc742f3f4533349", - "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,8ec73033ee0e2ad16fdc497b209adb50", - "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,dbe38679a68d55b8a182831e336eebb1", - "Clone9_N1_mature_hairpin_genome.sorted.bam:md5,7acf27a7533fbec27aa270637a919bed", - "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,4d552770e6d3b06775b6f484684f7a77", - "Control_N2_mature_hairpin_genome.sorted.stats:md5,f105861208044e44644c74449d0c6142", - "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", - "Clone1_N1_mature_hairpin_genome.sorted.bam:md5,1a438500002e75f6bf8cca6fe191b580", - "Control_N2_mature_hairpin_genome.sorted.bam.bai:md5,9b5d9073c4ffad7f128249ba2fef8b5c", - "Clone1_N1_mature_hairpin_genome.sorted.bam.bai:md5,0dfb96ad1d7201c0684c92b6caf4883e", - "Clone1_N3_mature_hairpin_genome.sorted.idxstats:md5,d680e48370d319f1891cdd61b8754644", - "Clone9_N3_mature_hairpin_genome.sorted.bam:md5,0427bf26d0a19a9f67c849ced65d7236", - "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,64b19984a4c2fa55e69a28fe7c138d7c", - "Control_N3_mature_hairpin_genome.sorted.bam.bai:md5,aab8b4709b5bcab35fe8b4b68a2f8550", - "Clone9_N2_mature_hairpin_genome.sorted.bam:md5,85456566c2745be254fee1bc633c503b", - "Control_N1_mature_hairpin_genome.sorted.bam:md5,c6ab347e1b3bba44b66da20fda537fe3", - "Control_N3_mature_hairpin_genome.sorted.flagstat:md5,ae834e3dbaa18aa9bce66c3b0034c430", - "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,a199f8999ba915a81acfc450e0db8393", - "Control_N3_mature_hairpin_genome.sorted.bam:md5,68be42f8696b4ef53d917706fa73b183", - "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,fe01b41ed88612c28b667817c4a8fcc1", - "Clone1_N3_mature_hairpin_genome.sorted.bam:md5,fee1f04d814e3b20a33322487a2165e6", - "Clone9_N1_mature_hairpin_genome.sorted.bam.bai:md5,73e9d2c87726c85b18bb622e43b9d716", - "Clone1_N3_mature_hairpin_genome.sorted.flagstat:md5,9dee041c82ad3b2d2ab4f8986822f2ce", - "Control_N2_mature_hairpin_genome.sorted.bam:md5,b1a91d8754d5a480ec9d05f93d9f3025", - "Control_N1_mature_hairpin_genome.sorted.stats:md5,b2afcfcb9e785a71bb5fce25b87fd67a", - "Clone9_N2_mature_hairpin_genome.sorted.bam.bai:md5,a66453d898f5cb49fc945b0f8cfe5ff3", - "Control_N3_mature_hairpin_genome.sorted.idxstats:md5,94d53c9ad335779a1ea25fd5b4b08069", - "Control_N1_mature_hairpin_genome.sorted.bam.bai:md5,915c6a1d11d7f69ef575f79dc3a08aa0", - "Clone9_N2_mature_hairpin_genome.sorted.stats:md5,6db5d451fa95a77247d38c4a263cf05d", - "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,f819db926f570a9bb1cf9b6adff7d758", - "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,0a227abfa6aa10023219bce7b2795b67", - "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,2fd8cd41edde2292f857528658c3e0a1", - "Clone9_N2_mature_hairpin_genome.sorted.idxstats:md5,61c4821cba66c91272e62547617db2c9", - "Clone1_N3_mature_hairpin_genome.sorted.bam.bai:md5,667b65be13c5b4984f15f402e84d2949", - "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,169a196ee2da6945392f6a361164ffc5", - "Clone9_N3_mature_hairpin_genome.sorted.bam.bai:md5,c8b6df11a72663b9ca445847b6ae7112" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:11.797960575" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:11.154500508" - }, - "fastqc": { - "content": [ - "Control_N1.raw_fastqc.zip:md5,4945e02703cd784c0ba587f371bd6f67", - "Clone9_N3.raw_fastqc.zip:md5,c6713743bb347f82dacabadfe9b1852e", - "Clone9_N1.raw_fastqc.zip:md5,f73e5b9915222ed05297bedbb51221e3", - "Control_N3.raw_fastqc.zip:md5,cbf237bc37344817bc720c840ed64c17", - "Clone1_N3.raw_fastqc.zip:md5,d58dce4bd438620a01bbb6a101ed2d5d", - "Control_N2.raw_fastqc.zip:md5,2a470a5c426dfdd8fcc869e243d77267", - "Clone9_N2.raw_fastqc.zip:md5,334b6c0a58619499cc4bcbc1421cd929", - "Clone1_N1.raw_fastqc.zip:md5,ee48e5fd1f87377d1d69b8a7f1cd23cc", - "Control_N3.trim_fastqc.zip:md5,b30a77afece684d59a16711cbd20744f", - "Clone9_N3.trim_fastqc.zip:md5,904abad8ce0fdaf6160f0f1fd7a66726", - "Clone9_N2.trim_fastqc.zip:md5,649b56c3dd1310e8a8fceaf8e3382c35", - "Clone9_N1.trim_fastqc.zip:md5,982945e7e8e052394772ad894fdcb402", - "Clone1_N1.trim_fastqc.zip:md5,d0d0f3d0c7bea925a9e7f4169ed4f44e", - "Control_N2.trim_fastqc.zip:md5,2e8dcbe9c8d87a533268cc40aa8ce6c7", - "Control_N1.trim_fastqc.zip:md5,628ac81e0ad2b4852a2a0048fcc7c268", - "Clone1_N3.trim_fastqc.zip:md5,1275f55e2d3c20b04d2a37bd36184d00" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:28.698286359" - }, - "multiqc": { - "content": [ - "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", - "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", - "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,f214e5c6c2e16e9fc0721e3299aa6af7", - "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", - "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", - "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,61a77aab820a3eba21a51e32168b45e3", - "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", - "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", - "multiqc_general_stats.txt:md5,b4693299615f59864df56a7279bf1bc5", - "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", - "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", - "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", - "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", - "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", - "fastqc_top_overrepresented_sequences_table.txt:md5,9acec391e0a46858e110f5baa65fb0a9", - "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", - "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", - "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", - "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", - "samtools_alignment_plot.txt:md5,f87f3d2101f70e840c57df850bd1e3be", - "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", - "mirtop_read_count_plot.txt:md5,29cce56b45edc10ff63badfa49eaf6b9", - "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "mirtop_unique_read_count_plot.txt:md5,b540743844ef0cdb81390b9db1d23afe", - "mirtop_mean_read_count_plot.txt:md5,837e240c5ecd10b95257e65fcd9f8393", - "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", - "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", - "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", - "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", - "multiqc_sources.txt:md5,ff2a4d4e1142cf341d6d14ae56dca6e8", - "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:11.501195707" - }, - "mirna_quant": { - "content": [ - "Control_N1_mature_hairpin.sorted.stats:md5,feb69ad2f8bbc527e39502a297f08abd", - "Control_N1_mature_hairpin.sorted.idxstats:md5,e1f455195f1cb42a1d1e58770aaeb2b4", - "Clone1_N3_mature_hairpin.sorted.flagstat:md5,6f14ec4cd502c0eb213b1905b4568a76", - "Clone9_N2_mature_hairpin.sorted.stats:md5,7bb8654d44dac245aec6aa045250628a", - "Clone9_N3_mature_hairpin.sorted.flagstat:md5,efc65cb620ca139b19967e12f13ba007", - "Control_N1_mature_hairpin.sorted.bam.bai:md5,38248e27a6928359b3ffb2cd38accfeb", - "Control_N3_mature_hairpin.sorted.bam.bai:md5,2517024b6a616d267528e3ca9d1fc48d", - "Control_N1_mature_hairpin.sorted.flagstat:md5,41769a400a176ea78432749f07f80fda", - "Control_N1_mature_hairpin.sorted.bam:md5,0eab30f74fc0bd6d14ccd70a277a9746", - "Clone9_N1_mature_hairpin.sorted.stats:md5,155f327a9be0afa9584ec426826b5457", - "Clone1_N3_mature_hairpin.sorted.bam:md5,b6db05f1752865f1f41a87b42b1344e1", - "Control_N2_mature_hairpin.sorted.stats:md5,1195dd51f77e338db83dc66476ac7c5f", - "Clone9_N1_mature_hairpin.sorted.bam.bai:md5,c8e5fd0e315417c7bfc741fb3f9482e0", - "Control_N3_mature_hairpin.sorted.idxstats:md5,2c44710ce63bdebb12d64c729ef338b0", - "Control_N2_mature_hairpin.sorted.bam.bai:md5,fc6c5ea2d38928afad19a85ea7b51b47", - "Clone1_N3_mature_hairpin.sorted.bam.bai:md5,d1114e75e59ba3a957612b3d59b77675", - "Clone1_N1_mature_hairpin.sorted.idxstats:md5,0bca2d01f734128f3c11cf2697433048", - "Clone9_N3_mature_hairpin.sorted.idxstats:md5,9523d29d411c2efb0a1756355230fa98", - "Control_N2_mature_hairpin.sorted.idxstats:md5,8859b6e432cef8b24d5fb258a06aaabe", - "Clone9_N2_mature_hairpin.sorted.flagstat:md5,663ae0bb8b29d1e1c3d75ef5df1015a4", - "Clone9_N1_mature_hairpin.sorted.flagstat:md5,3e4b295b54df05c438603edaa53123b1", - "Control_N3_mature_hairpin.sorted.flagstat:md5,f3df866b94dc6ef355b01f22047aaf4f", - "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,5ee1751e41db25b7f2f110f58bbf7265", - "Clone1_N1_mature_hairpin.sorted.bam:md5,90241892e182624a3a9723f1067d62bd", - "Control_N3_mature_hairpin.sorted.bam:md5,c57b368d688cf84a120a111652fe21a6", - "Clone9_N3_mature_hairpin.sorted.stats:md5,9f61c028bb1c92667e31093156ada662", - "Clone1_N1_mature_hairpin.sorted.stats:md5,bd02cb15e666054edecc89d392d72902", - "Clone9_N2_mature_hairpin.sorted.idxstats:md5,04b1c0ea4f133b5ee9086eec1f4077e7", - "Clone1_N3_mature_hairpin.sorted.stats:md5,471db325d8ccd1fe787b5dd91dccf487", - "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,b10a95e003f8af2a0926ab38b0bcef61", - "Control_N2_mature_hairpin.sorted.flagstat:md5,2605548b5ab1e6ad6b5cf88ea0030909", - "Clone9_N1_mature_hairpin.sorted.idxstats:md5,238b462a2418d545418c0b3a28029bdf", - "Clone9_N2_mature_hairpin.sorted.bam.bai:md5,3566fc7328df89c8a2ed3b6dfcc60347", - "Control_N3_mature_hairpin.sorted.stats:md5,2f2249c537451d1f72dfe298f16093ac", - "Clone9_N1_mature_hairpin.sorted.bam:md5,4a8d7da1400e517fa08e196ac1967ecd", - "Clone9_N2_mature_hairpin.sorted.bam:md5,54c118f5f09e088de202bb633ede528b", - "Clone1_N1_mature_hairpin.sorted.flagstat:md5,8d0c785fec7b300200863c68b158444c", - "Control_N2_mature_hairpin.sorted.bam:md5,b03472ce507546b4f703d95a102a3ba4", - "Clone9_N3_mature_hairpin.sorted.bam:md5,0702924e1eef55817b1542e031c66e4d", - "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", - "Control_N1_mature.sorted.bam.bai:md5,9ad0d0c840f6335ae7227cfdf03f714a", - "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", - "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", - "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", - "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", - "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", - "Clone9_N3_mature.sorted.bam:md5,326a16bafc12f91277d43718612784a7", - "Clone9_N1_mature.sorted.bam.bai:md5,0d1a7dbe6e97f7fa4811790e6640c978", - "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", - "Clone1_N1_mature.sorted.bam:md5,216cd7ea3aef9cdb3dc58f5a273ac995", - "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", - "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", - "Control_N1_mature.sorted.bam:md5,dde5afbe3b7b28da315eefafe279a9b8", - "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", - "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", - "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", - "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", - "Control_N2_mature.sorted.bam.bai:md5,01e9905b9d121d3c0341488bade69180", - "Control_N2_mature.sorted.bam:md5,52b89aab08865d6639269583fc1a42ac", - "Clone9_N2_mature.sorted.bam.bai:md5,a68809526ec55ae96f6eb62a170ac5ca", - "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", - "Control_N3_mature.sorted.bam.bai:md5,720f79c56ab38ba1ebafeb9c0fe5cf45", - "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", - "Clone9_N2_mature.sorted.bam:md5,8250cb44af17d1ccee889f14b41e5da1", - "Clone1_N3_mature.sorted.bam.bai:md5,567e08c765069502219a2bf080a84600", - "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", - "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", - "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", - "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", - "Clone9_N3_mature.sorted.bam.bai:md5,b1ac22e2ceb13f78bcede9cef82d2989", - "Clone1_N1_mature.sorted.bam.bai:md5,6b5783e42dca72415ed9cc25cd94b6cb", - "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", - "Control_N3_mature.sorted.bam:md5,9016fcda58013dedb5dea875cc718bd8", - "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", - "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", - "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", - "Clone1_N3_mature.sorted.bam:md5,ffa1485c08ac5f4a2edebb88c892a7d6", - "Clone9_N1_mature.sorted.bam:md5,9fc8f4311a10f8ed65151017d861ab7f", - "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", - "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", - "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", - "mirtop.tsv:md5,671628c0cf82376f674562ba1a6f6790", - "mirtop.gff:md5,598d14684b224dc897e3324448da2a7d", - "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", - "mirtop_stats.txt:md5,8b1ce9988d872c72ab3b23ed43000f7c", - "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", - "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", - "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", - "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", - "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", - "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,5673c4e9f6715d7ae7e137035e7e080e", - "mature_normalized_CPM.txt:md5,f6d11da1bb701b19780093094421c10e", - "hairpin_logtpm.csv:md5,923c8fff7480c89bcb18acfa2b398b4a", - "mature_logtpm.txt:md5,8851354ac087c8547aa9710eb49bc1d5", - "mature_edgeR_MDS_plot_coordinates.txt:md5,dfca9dca59af62be59bf43a10c9ee27e", - "hairpin_unmapped_read_counts.txt:md5,432fb18356e27c15569b62140f482435", - "mature_edgeR_MDS_distance_matrix.txt:md5,d386896da5ba156a76052895253f41c5", - "mature_log2CPM_sample_distances.txt:md5,bea4b11907cd6badbc68e9b505a48bb8", - "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,71074c2cb4661feaf822929250c8d3a9", - "hairpin_logtpm.txt:md5,d474bafadfed004173d15094ff6d4e25", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,666f384ea6cdd06a6140b8b9c8e2bb66", - "mature_logtpm.csv:md5,2ecf0babb4dfed8f25be9a40b953855d", - "hairpin_normalized_CPM.txt:md5,1c1104bda88b19465e890e8f7fdbac86", - "mature_counts.csv:md5,c006871cb0a4b01c47de2c0d8955fd0a", - "hairpin_counts.csv:md5,64d35f8b6fa3dfac237d944c1463cd03" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:15.071197394" - } -} \ No newline at end of file diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 86e6b2f9..6996ff69 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -18,246 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 161 }, - - { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), - path("$outputDir/untar/bowtie_index/genome.2.ebwt"), - path("$outputDir/untar/bowtie_index/genome.1.ebwt"), - path("$outputDir/untar/bowtie_index/genome.3.ebwt"), - path("$outputDir/untar/bowtie_index/genome.4.ebwt"), - path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt") - ).match("untar") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 161 } ) } diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap deleted file mode 100644 index f9fb5e9f..00000000 --- a/tests/test_index.nf.test.snap +++ /dev/null @@ -1,292 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.023826353" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - 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"Control_N2_mature_hairpin.sorted.bam:md5,79a584d7c68f57697257cda41e6b6ccf", - "Clone9_N3_mature_hairpin.sorted.bam:md5,946f27f50f1658c64c2c222c2f37d2b8", - "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", - "Control_N1_mature.sorted.bam.bai:md5,9ad0d0c840f6335ae7227cfdf03f714a", - "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", - "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", - "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", - "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", - "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", - "Clone9_N3_mature.sorted.bam:md5,6a20122570543da6042a94fade945407", - "Clone9_N1_mature.sorted.bam.bai:md5,0d1a7dbe6e97f7fa4811790e6640c978", - "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", - "Clone1_N1_mature.sorted.bam:md5,dc305cfe5c54b93e5b91b00dba676780", - "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", - "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", - "Control_N1_mature.sorted.bam:md5,1c6e2e02df78ae15c535726b448e3704", - "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", - "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", - "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", - "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", - "Control_N2_mature.sorted.bam.bai:md5,01e9905b9d121d3c0341488bade69180", - "Control_N2_mature.sorted.bam:md5,57f6e91f83799f8b9cbc739a1a28ab78", - "Clone9_N2_mature.sorted.bam.bai:md5,a68809526ec55ae96f6eb62a170ac5ca", - "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", - "Control_N3_mature.sorted.bam.bai:md5,720f79c56ab38ba1ebafeb9c0fe5cf45", - "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", - "Clone9_N2_mature.sorted.bam:md5,d96c5b1d9f1111936037a605043becdf", - "Clone1_N3_mature.sorted.bam.bai:md5,567e08c765069502219a2bf080a84600", - "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", - "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", - "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", - "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", - "Clone9_N3_mature.sorted.bam.bai:md5,b1ac22e2ceb13f78bcede9cef82d2989", - "Clone1_N1_mature.sorted.bam.bai:md5,6b5783e42dca72415ed9cc25cd94b6cb", - "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", - "Control_N3_mature.sorted.bam:md5,19a7b1b8801094562492576c28ec33c7", - "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", - "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", - "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", - "Clone1_N3_mature.sorted.bam:md5,6176d098a0384709aa5d3589258c701d", - "Clone9_N1_mature.sorted.bam:md5,7a1024fc323335f31ebc8297dd789fc2", - "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", - "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", - "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", - "mirtop.tsv:md5,8401bbe98e85a6d8b1ab7466d2e178ac", - "mirtop.gff:md5,57cc78c6e20626b41ec833dda81c40d1", - "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", - "mirtop_stats.txt:md5,8b1ce9988d872c72ab3b23ed43000f7c", - "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", - "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", - "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", - "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", - "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", - "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,41348458c2a8874dcb8a82a30c3f0e43", - "mature_normalized_CPM.txt:md5,88c481df2e8b073ebfaf440620a2cd2a", - "hairpin_logtpm.csv:md5,87f2d92a9ca3ed5390b4cc903776fde4", - "mature_logtpm.txt:md5,c5cd8a9a2176af9d0f7759f92233929d", - "mature_edgeR_MDS_plot_coordinates.txt:md5,29584c2e2e2378a91e891a628f63a892", - "hairpin_unmapped_read_counts.txt:md5,7618d6bdc018e5712343bf4eb8d94fa4", - "mature_edgeR_MDS_distance_matrix.txt:md5,974273c499e26854e27c2cdbe9fa5f2c", - "mature_log2CPM_sample_distances.txt:md5,bea4b11907cd6badbc68e9b505a48bb8", - "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,c8377298e59143e17f9d0822c83059c3", - "hairpin_logtpm.txt:md5,96d146b5de6066b609b56a2344dfde67", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,dedaa69ffc330ce3b61593f2c58054e3", - "mature_logtpm.csv:md5,1a22f980708232227336118a8212fa32", - "hairpin_normalized_CPM.txt:md5,02e3803d5a9b0e2f4be94fac0cb94429", - "mature_counts.csv:md5,4d9f320ae04949cc0111bd90e2a2587d", - "hairpin_counts.csv:md5,fd30079c785a28327226d7c51b68b9cc" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.931370818" - } -} \ No newline at end of file diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test new file mode 100644 index 00000000..19636057 --- /dev/null +++ b/tests/test_mirgenedb.nf.test @@ -0,0 +1,27 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - test_mirgenedb" + script "main.nf" + profile "test_mirgenedb" + tag "test_mirgenedb" + tag "pipeline" + + test("test_mirgenedb") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 193 } + ) + } + + } + +} diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index 3b502706..2805ce3c 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -18,277 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 147 }, - - { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N2_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 147 } ) } diff --git a/tests/test_no_genome.nf.test.snap b/tests/test_no_genome.nf.test.snap deleted file mode 100644 index 2e8a572d..00000000 --- a/tests/test_no_genome.nf.test.snap +++ /dev/null @@ -1,311 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "fasta_bidx.3.ebwt:md5,cccaad86d0d5e5f3c1d4ca3a700ee980", - "fasta_bidx.1.ebwt:md5,9935201150ff358248380e07219fe093", - "fasta_bidx.rev.1.ebwt:md5,5e75ec9fb284ba316b3982a93f4ded49", - "fasta_bidx.rev.2.ebwt:md5,ba8e745f11b3d28240a78efd5bf2a7b0", - "fasta_bidx.4.ebwt:md5,96e2e8ec9f02d324d845e0708ff4b552", - "fasta_bidx.2.ebwt:md5,9cf18dd788535404d7fd6a62450d2ce0", - "fasta_bidx.3.ebwt:md5,a6d3abdddbf80cb9b2c97bbd7bc1f084", - "fasta_bidx.1.ebwt:md5,a2162fb747e95535ea5a67023b8961cf", - "fasta_bidx.rev.1.ebwt:md5,27578696198a61b0a3f783802823337e", - "fasta_bidx.rev.2.ebwt:md5,726c60d9a0108739ba9b61774bc39633", - "fasta_bidx.4.ebwt:md5,62e35549f28a1a85ccaf35858b1726aa", - "fasta_bidx.2.ebwt:md5,876ebed9375cda6f248dfc940308fa5e" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:10.78656165" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:26:58.977826663" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:10.784750713" - }, - "fastqc": { - "content": [ - "Control_N1.raw_fastqc.zip:md5,af5b899930327b5cd9cca384a6e00f27", - 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"mirtop.gff:md5,f6220d75e81e67be3fbbd0251ce2947b", - "mirtop_rawData.tsv:md5,98c46ade3ba0b141f1306c1dbc9a3ff1", - "mirtop_stats.txt:md5,b28c2f920f1e73f827f32fdd31654cbd", - "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", - "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", - "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", - "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", - "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", - "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", - "hairpin.fa_igenome.fa_idx.fa:md5,f7ee61ca4537300386fdb85c7dec24d2", - "mature.fa_igenome.fa_idx.fa:md5,48215f56ca0bfbdbb1a28482457283e3", - "hairpin.fa_igenome.fa:md5,cddcc379892cb43e807ff54feafafbc1", - "mature.fa_igenome.fa:md5,48215f56ca0bfbdbb1a28482457283e3", - "mature_unmapped_read_counts.txt:md5,edc81b30c58368abb964fe13310f9c04", - "mature_normalized_CPM.txt:md5,d8d8712785f930456e8e739c4081ccbb", - "hairpin_logtpm.csv:md5,2d1c128288f7d8aa8ea870d488fb0586", - "mature_logtpm.txt:md5,b47a967bbd764361beffe188ae31d278", - "mature_edgeR_MDS_plot_coordinates.txt:md5,af754c03339430a71c0998d8f0580e68", - "hairpin_unmapped_read_counts.txt:md5,b81d5b91da9af7eb747ab8b6a9243e26", - "mature_edgeR_MDS_distance_matrix.txt:md5,18533a2afb0a6fad6be1d879690111f7", - "mature_log2CPM_sample_distances.txt:md5,980bba51cd88ae0c8ac418fe653492af", - "hairpin_log2CPM_sample_distances.txt:md5,7cca5268281ff6e24f849526589b9e48", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,fcd5a68b940856b28eac2ea029f61967", - "hairpin_logtpm.txt:md5,912a1604f482d5b4bb54199b0f07c6eb", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,cbef839bb66d6e832243df2bd46d4ebd", - "mature_logtpm.csv:md5,120c6af7180855ba68098685ca81c392", - "hairpin_normalized_CPM.txt:md5,47a03cbecaf025fdcebdb17148ace558", - "mature_counts.csv:md5,2ffb977afc7b61a79056c2868cd53222", - "hairpin_counts.csv:md5,118236c7fa7b56fa78e495582eaf285d" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:11.083677532" - } -} \ No newline at end of file diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index 22f5accf..f01233aa 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -18,125 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 75 }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 75 } ) } diff --git a/tests/test_technical_repeats.nf.test.snap b/tests/test_technical_repeats.nf.test.snap deleted file mode 100644 index f18a5b4c..00000000 --- a/tests/test_technical_repeats.nf.test.snap +++ /dev/null @@ -1,153 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:09.347754579" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,2843855add34a73acd332a112bd80a34", - "mirtrace-stats-length.tsv:md5,71591c754eed9db419b91fb499f8e2ab", - "mirtrace-stats-contamination_detailed.tsv:md5,c16e27cc433dacdd5bfff09a9aaab736", - "mirtrace-stats-qcstatus.tsv:md5,37465e5d4d756792b95f187e6406fc6b", - "mirtrace-stats-contamination_basic.tsv:md5,ca3f99b1b89d2674864b62bbf9c41592", - "mirtrace-stats-phred.tsv:md5,1ac6fdae848cc4e39904edc361f75d1f", - "mirtrace-stats-mirna-complexity.tsv:md5,c69c4762a887a8e792c896dc5d3866b8", - "Clone1_N1.fastp.fasta:md5,7630d5d8f047d2f7e9492598e6f97c84", - "Control_N1.fastp.fasta:md5,534de89c8354a874458497804dcb7785", - "Clone9_N3.fastp.fasta:md5,0f2ef6c209a0b591d4eff5d77b713957", - "Clone1_N1.fastp.fasta:md5,f49d63f3d05aeb349f58f2bb95552332", - "Control_N1.fastp.fasta:md5,b34c20e0736351db5d0d1d3236de18ec", - "Clone9_N3.fastp.fasta:md5,726d1d14a88d7b816bb97bab9f006c45" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:17.175802364" - }, - "genome_quant": { - "content": [ - "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,41e0b4dc62f9b8779534d67630ea6ab6", - "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,872a90aca4d070f9403ae86b42666e2c", - "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,50eb08817350b22dbe99bcc3dc7f2a38", - "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,1d56901f0754350ee0925cff76bee6d1", - "Clone1_N1_mature_hairpin_genome.sorted.bam:md5,aee26f20d3188c9e0c17c8b19ee01068", - "Clone1_N1_mature_hairpin_genome.sorted.bam.bai:md5,bf5167b68a29df979ea14a3cb148c4ac", - "Clone9_N3_mature_hairpin_genome.sorted.bam:md5,b80e7a38ab0f940047d39cd8ef3e1905", - "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,964b1ec118f45c5cb9443efc996b4b3e", - "Control_N1_mature_hairpin_genome.sorted.bam:md5,d153cfca67b7fd8fee388b22302c20c7", - "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,6f43b2104f522103671ce78dc7d75b6d", - "Control_N1_mature_hairpin_genome.sorted.stats:md5,97f2c3ceb62b98d9169b226e954a1150", - "Control_N1_mature_hairpin_genome.sorted.bam.bai:md5,dc7706620275f5a43b52066970c1474d", - "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,6561bdbc8589548d965823d7f43dee39", - "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,f6408e25770f9a8530126900c314332f", - "Clone9_N3_mature_hairpin_genome.sorted.bam.bai:md5,5fa626110a289ede3549c4c73b53d714" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:09.615825899" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:09.345801293" - }, - "mirna_quant": { - "content": [ - "Control_N1_mature_hairpin.sorted.stats:md5,41ed031d9ee3d775fab782beea7c2c5e", - "Control_N1_mature_hairpin.sorted.idxstats:md5,2bb41d5a20116c7457ef45c1b294d22d", - "Clone9_N3_mature_hairpin.sorted.flagstat:md5,79f3d50c45d9aa0d2525f5f1411e8dd5", - "Control_N1_mature_hairpin.sorted.bam.bai:md5,b901e66cbdd91b38b32c49671c2b0538", - "Control_N1_mature_hairpin.sorted.flagstat:md5,e727c4751070cf76ebfd484c0e37d990", - "Control_N1_mature_hairpin.sorted.bam:md5,579a1e43d1a6205ac2c118c1b39bbdae", - "Clone1_N1_mature_hairpin.sorted.idxstats:md5,f2a16cf301d8cfd5f9f99edb610705c7", - "Clone9_N3_mature_hairpin.sorted.idxstats:md5,98db6ef38c05a65ee7ef5a7520f4f51c", - "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,4bd9a2f4353cdc65a1db6edbdbab7a82", - "Clone1_N1_mature_hairpin.sorted.bam:md5,9557cc47f4e70261cc583b81fd3c55dd", - "Clone9_N3_mature_hairpin.sorted.stats:md5,52d607b29c6fae0a72cb55b83a5d550f", - "Clone1_N1_mature_hairpin.sorted.stats:md5,3fc6353abadc1c6e2687bc7a081f93a2", - "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,75f78a876d94179713ce913a1dc43a79", - "Clone1_N1_mature_hairpin.sorted.flagstat:md5,f6d7848cf9c70cd3469ce1944d17be3c", - "Clone9_N3_mature_hairpin.sorted.bam:md5,d04faf5b2a33091861b1687e78ad23c7", - "Control_N1_mature.sorted.bam.bai:md5,01b52ea90bacac2ed44b4b165b03fe1f", - "Clone1_N1_mature.sorted.stats:md5,edfa6dab3271e66f743da2aca3ea7663", - "Clone9_N3_mature.sorted.bam:md5,d0fcf12036df675761eddb6e03eee657", - "Clone9_N3_mature.sorted.stats:md5,4fe47f64e7bdd0e1efeaa8271e92000a", - "Clone1_N1_mature.sorted.bam:md5,09f0d3c5b4e216d300904235fbb82494", - "Control_N1_mature.sorted.bam:md5,b2947881dd6b9631d701e175b7ac77e4", - "Control_N1_mature.sorted.stats:md5,9abec7b88211f78d0e743dbedb1e1125", - "Control_N1_mature.sorted.idxstats:md5,8e96945e95b03c3c33867c98dece1e4e", - "Clone9_N3_mature.sorted.idxstats:md5,f92b6bdb8bf206757d8e2733f60f3c1b", - "Clone9_N3_mature.sorted.flagstat:md5,bbb6bc880f6fc9424fc16b095af752b9", - "Clone9_N3_mature.sorted.bam.bai:md5,2504e62544b9f89fdbe2e8ad20b7e727", - "Clone1_N1_mature.sorted.bam.bai:md5,97c3b9ace9b0451ca7f6b9230e64bbfa", - "Clone1_N1_mature.sorted.idxstats:md5,f80f8349d8a814e8f67ef4c30e2f6a53", - "Clone1_N1_mature.sorted.flagstat:md5,e6adf8d4926033f9ae6a0d5ab42bd267", - "Control_N1_mature.sorted.flagstat:md5,f10e74138d682fed95c076112b7f9236", - "mirna.tsv:md5,b884a1dadb2a803fc3838f124695c68c", - "mirtop.tsv:md5,e82e7e158ad6541f7240d370c998b162", - "mirtop.gff:md5,e421a0dd1676ebdd331d4463fd7ec202", - "mirtop_rawData.tsv:md5,edae282cde52e6b60d42962479866cb3", - "mirtop_stats.txt:md5,3e59e311a62e873c7ec780d537d5e6a9", - "Control_N1.fastp_trimmed.fastq.gz:md5,8d0676323aa9e84556cdf209db92b6ed", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,1ce9b5ab0591aa067c0bcfbc4852cd19", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,abb626ba9f41ef35a3684d2b5b4f2c4f", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,6f07c6c8054b843783c2b52888c12072", - "mature_normalized_CPM.txt:md5,025ac0731eb3817362983dcf6f3b4f79", - "hairpin_logtpm.csv:md5,4ac659c6e352ecd45970659eef009d33", - "mature_logtpm.txt:md5,9d0d4718cb7f72abbb26380745f42bc4", - "mature_edgeR_MDS_plot_coordinates.txt:md5,ef1fcf3b375b65c0611e32f1fa527759", - "hairpin_unmapped_read_counts.txt:md5,64a71970c8ebb5a7326f487c20685cee", - "mature_edgeR_MDS_distance_matrix.txt:md5,9b2553e2af74f3093386c88945d16514", - "mature_log2CPM_sample_distances.txt:md5,3e65534b731a92efdfe0373ff0b963ff", - "hairpin_log2CPM_sample_distances.txt:md5,2d89f929eff72230c1a6e8bffc8fa17a", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,5001dc46960da9b83f7c528ad8116ddd", - "hairpin_logtpm.txt:md5,2bfc416b0011b131a5d2b8a4b8d3d7b5", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,f3ff4a57f6c4e8c9a3065c5fde85438b", - "mature_logtpm.csv:md5,2729c7b78855871f8b07804ab36ba8dd", - "hairpin_normalized_CPM.txt:md5,89c4abe13c09cd3e58b67a1e46e8e6e3", - "mature_counts.csv:md5,7714ee131dca993a1de82f22768db77d", - "hairpin_counts.csv:md5,55b0389a0a101bbf09a4718532f64514" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:11.127160605" - } -} \ No newline at end of file diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index 1901837d..b905c55c 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -18,171 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 64 }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_contamination_check_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") - ).match("umi_dedup") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195117_SRR11631013.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 64 } ) } diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap deleted file mode 100644 index 2becd637..00000000 --- a/tests/test_umi.nf.test.snap +++ /dev/null @@ -1,217 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:19.829287378" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,00e584439bec82f5de8d6485a73dec37", - "mirtrace-stats-length.tsv:md5,3edbc31452dba97f8b829e3f8f635955", - "mirtrace-stats-contamination_detailed.tsv:md5,428d2fd6ea0a6f2af1018a557e89bece", - "mirtrace-stats-qcstatus.tsv:md5,de4f8a670b736bedf348d358cfdfb9fc", - "mirtrace-stats-contamination_basic.tsv:md5,3d54b37ab3206e9fec909fe3ea1a4777", - "mirtrace-stats-phred.tsv:md5,8cf9fc2223b9aeb50f92c8845edbf535", - "mirtrace-stats-mirna-complexity.tsv:md5,cd2f37963adeee159764a89688a4a6a5", - "SRX8195118_SRR11631014.fastp.fasta:md5,99e2ce92ce102bd3fedc3a9d3b926873", - "SRX8195117_SRR11631013.fastp.fasta:md5,e0e31d882568a7853dea75b3c595108f", - "SRX8195118_SRR11631014.fastp.fasta:md5,7db07b8c0b9e2b484eb3d42a04e480d1", - "SRX8195117_SRR11631013.fastp.fasta:md5,eb1ba9fa6f7d956e5d650fdd306d5634" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:46.029580614" - }, - "umi_dedup": { - "content": [ - "SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz:md5,247d78a2d700012064d0b2e28d04b061", - "SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz:md5,af2b98d9bd6d0760a7eb07813d015aee", - "SRX8195118_SRR11631014.umi_extract.fastq.gz:md5,d2928324ae465d3d8eaf65c24418b8cf", - "SRX8195117_SRR11631013.umi_extract.fastq.gz:md5,1aeed318fab39fa646ff790a025bd21d" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:20.579451915" - }, - "genome_quant": { - "content": [ - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai:md5,a2550ac81a655836969f91a4fbf64cf6", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam:md5,b0534300df725919db7e38a8215d22b4", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam:md5,2dbac90f7439b878605b920ea7aa66a9", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat:md5,235383f64a943885f5d899f5b8e03eba", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai:md5,51444acc5b1c67d4bba3809a40e1ffd3", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,053912820064080299710bfbe7baf3c7", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,e19093f62044a7d053a0073092c506f3" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:20.293351627" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:19.827254847" - }, - "fastqc": { - "content": [ - "SRX8195117_SRR11631013.raw_fastqc.zip:md5,26a041b01b10149a90a1a9233cb5cfd8", - "SRX8195118_SRR11631014.raw_fastqc.zip:md5,8a4b0ed8cf615100055caf5eb66afc9f", - "SRX8195117_SRR11631013.trim_fastqc.zip:md5,626143589a7acc028b2ecd01f687f03f", - "SRX8195118_SRR11631014.trim_fastqc.zip:md5,26ab263d79de53ded2eeb0d3a905f82e" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:36.864495018" - }, - "multiqc": { - "content": [ - "fastqc-status-check-heatmap.txt:md5,c1509fdd74b21a718fe099de64514995", - "fastp_filtered_reads_plot.txt:md5,3aaa79e1ede44347971c26100d9e954b", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc_sequence_counts_plot-1.txt:md5,24744e039ce4dbcbacf42edbfd642a8b", - "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", - "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,74808822577fb62efb39811272e6919e", - "fastqc_sequence_length_distribution_plot.txt:md5,8c34b57ec084e2da9d62c254c0a517f4", - "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,b5ae95ecd73055798ed70947dda3747c", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,89adfa92b1cde0ad4e401b430bbc68ce", - "multiqc_general_stats.txt:md5,b56535ef53b3ca4477aac99845712fa5", - "fastqc_per_base_n_content_plot-1.txt:md5,db081d3aa63007e5a78113f0fc26f27d", - "fastqc_per_base_n_content_plot.txt:md5,5b5b8cee3162d092c0bcddffbd000f34", - "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,66a47c7ce00ede2053f8e6eb20ec3417", - "fastqc_per_sequence_quality_scores_plot.txt:md5,3aa99649540afc898d32d2e49a364487", - "mirtrace_qc_plot.txt:md5,b08d11ea51c54e615f9608002644c787", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,4108da6fe352558a652ee2b17d609e07", - "mirtrace_length_plot.txt:md5,440a84ce9bbdb89b736e4e2446382665", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc-status-check-heatmap-1.txt:md5,cb2ea844834808ae4c95c6440269cf2e", - "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", - "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", - "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", - "samtools_alignment_plot.txt:md5,5e828961dbd55a6d6872221c49dfdc59", - "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", - "mirtop_read_count_plot.txt:md5,2603cd59d95e71863e264ca9589591fa", - "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", - "mirtop_unique_read_count_plot.txt:md5,5082d66ba230c780e87b78be589a2c3d", - "mirtop_mean_read_count_plot.txt:md5,5e2897fd0291f6e81a350786620f9b5a", - "mirtrace_contamination_check_plot.txt:md5,7f12917ce506127a729edb733fdda511", - "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", - "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c2f2f9282a50c3eef475664cc969b8ec", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,15d8fa32e0c11ef0d3d10fc28370972c", - "fastqc_adapter_content_plot-1.txt:md5,89cd342fdc6fbba5f67078c9a2f0c684", - "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f832e92fb36db181ed1079be110edb2a", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,488e25de89d18d20f29b86f2580a8df9", - "multiqc_sources.txt:md5,e3350035ab949e3f5093d506077b0fe0", - "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,d673e3b18c40c5af1edccffba386d678" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:20.057500216" - }, - "mirna_quant": { - "content": [ - "SRX8195117_SRR11631013_seqcluster.bam:md5,822cab8f3a85ddb27697cff48c702a2e", - 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], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:27.68981406" - } -} \ No newline at end of file