Loading .github/workflows/ci.yml +1 −0 Original line number Diff line number Diff line Loading @@ -189,6 +189,7 @@ jobs: - verify_output_reporting_skip_igv - verify_output_reporting_skip_heatmaps - verify_output_reporting_skip_multiqc - verify_output_skip_frip steps: - name: Checkout Code uses: actions/checkout@v2 Loading nextflow.config +1 −0 Original line number Diff line number Diff line Loading @@ -85,6 +85,7 @@ params { skip_igv = false skip_heatmaps = false skip_multiqc = false skip_frip = false // Boilerplate options outdir = "./results" Loading tests/test_verify_output_skip_frip.yml 0 → 100644 +17 −0 Original line number Diff line number Diff line - name: test_verify_output_skip_frip_true command: nextflow run main.nf -profile docker,test --skip_frip true -c tests/config/nextflow.config tags: - verify_output_skip_frip files: - path: results/04_reporting/qc/06_04_frags_in_peaks.csv should_exist: false - path: results/04_reporting/qc/06_04_frags_in_peaks.png should_exist: false - name: test_verify_output_skip_frip_false command: nextflow run main.nf -profile docker,test --skip_frip false -c tests/config/nextflow.config tags: - verify_output_skip_frip files: - path: results/04_reporting/qc/06_04_frags_in_peaks.csv - path: results/04_reporting/qc/06_04_frags_in_peaks.png workflows/cutandrun.nf +21 −19 Original line number Diff line number Diff line Loading @@ -800,6 +800,8 @@ workflow CUTANDRUN { // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, BED] //ch_bam_bai_bed | view ch_samtools_bam_ctrl = ch_samtools_bam if(!params.skip_frip) { /* * MODULE: Calculate Frip scores for samples */ Loading @@ -817,9 +819,9 @@ workflow CUTANDRUN { "", "" ) ch_samtools_bam_ctrl = ch_samtools_bam ch_samtools_bam = ANNOTATE_FRIP_META.out.output //ch_samtools_bam | view } /* * MODULE: Trim unwanted columns for downstream reporting Loading Loading
.github/workflows/ci.yml +1 −0 Original line number Diff line number Diff line Loading @@ -189,6 +189,7 @@ jobs: - verify_output_reporting_skip_igv - verify_output_reporting_skip_heatmaps - verify_output_reporting_skip_multiqc - verify_output_skip_frip steps: - name: Checkout Code uses: actions/checkout@v2 Loading
nextflow.config +1 −0 Original line number Diff line number Diff line Loading @@ -85,6 +85,7 @@ params { skip_igv = false skip_heatmaps = false skip_multiqc = false skip_frip = false // Boilerplate options outdir = "./results" Loading
tests/test_verify_output_skip_frip.yml 0 → 100644 +17 −0 Original line number Diff line number Diff line - name: test_verify_output_skip_frip_true command: nextflow run main.nf -profile docker,test --skip_frip true -c tests/config/nextflow.config tags: - verify_output_skip_frip files: - path: results/04_reporting/qc/06_04_frags_in_peaks.csv should_exist: false - path: results/04_reporting/qc/06_04_frags_in_peaks.png should_exist: false - name: test_verify_output_skip_frip_false command: nextflow run main.nf -profile docker,test --skip_frip false -c tests/config/nextflow.config tags: - verify_output_skip_frip files: - path: results/04_reporting/qc/06_04_frags_in_peaks.csv - path: results/04_reporting/qc/06_04_frags_in_peaks.png
workflows/cutandrun.nf +21 −19 Original line number Diff line number Diff line Loading @@ -800,6 +800,8 @@ workflow CUTANDRUN { // EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, BED] //ch_bam_bai_bed | view ch_samtools_bam_ctrl = ch_samtools_bam if(!params.skip_frip) { /* * MODULE: Calculate Frip scores for samples */ Loading @@ -817,9 +819,9 @@ workflow CUTANDRUN { "", "" ) ch_samtools_bam_ctrl = ch_samtools_bam ch_samtools_bam = ANNOTATE_FRIP_META.out.output //ch_samtools_bam | view } /* * MODULE: Trim unwanted columns for downstream reporting Loading
