Loading .github/workflows/ci.yml +3 −0 Original line number Diff line number Diff line Loading @@ -164,6 +164,9 @@ jobs: - verify_output_align_duplicates_remove_target - verify_output_peak_calling_only_peak_calling - test_peak_callers - test_conseneus_peaks_group - test_conseneus_peaks_all - test_conseneus_peaks_invalid - verify_output_reporting steps: - uses: actions/checkout@v2 Loading tests/test_consenseus_peaks.yml 0 → 100644 +25 −0 Original line number Diff line number Diff line - name: test_conseneus_peaks_group command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode group -c tests/config/nextflow.config tags: - test_conseneus_peaks - test_conseneus_peaks_group files: - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.bed - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.filtered.awk.bed - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.bed - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.filtered.awk.bed - name: test_conseneus_peaks_all command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode all -c tests/config/nextflow.config tags: - test_conseneus_peaks - test_conseneus_peaks_all files: - path: results/03_peak_calling/05_consensus_peaks/all_samples.awk.bed - path: results/03_peak_calling/05_consensus_peaks/all_samples.consensus.peaks.bed - name: test_conseneus_peaks_invalid command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode test -c tests/config/nextflow.config - test_conseneus_peaks - test_conseneus_peaks_invalid exit_code: 1 No newline at end of file workflows/cutandrun.nf +5 −0 Original line number Diff line number Diff line Loading @@ -76,6 +76,11 @@ if ((caller_list + callers).unique().size() != caller_list.size()) { exit 1, "Invalid variant calller option: ${params.peakcaller}. Valid options: ${caller_list.join(', ')}" } conseneus_mode_list = ['group', 'all'] if (!(params.consensus_peak_mode in conseneus_mode_list)) { exit 1, "Invalid conseneus mode option: ${params.consensus_peak_mode}. Valid options: ${conseneus_mode_list.join(', ')}" } /* ======================================================================================== IMPORT LOCAL MODULES/SUBWORKFLOWS Loading Loading
.github/workflows/ci.yml +3 −0 Original line number Diff line number Diff line Loading @@ -164,6 +164,9 @@ jobs: - verify_output_align_duplicates_remove_target - verify_output_peak_calling_only_peak_calling - test_peak_callers - test_conseneus_peaks_group - test_conseneus_peaks_all - test_conseneus_peaks_invalid - verify_output_reporting steps: - uses: actions/checkout@v2 Loading
tests/test_consenseus_peaks.yml 0 → 100644 +25 −0 Original line number Diff line number Diff line - name: test_conseneus_peaks_group command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode group -c tests/config/nextflow.config tags: - test_conseneus_peaks - test_conseneus_peaks_group files: - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.bed - path: results/03_peak_calling/05_consensus_peaks/h3k4me3.consensus.peaks.filtered.awk.bed - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.bed - path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.filtered.awk.bed - name: test_conseneus_peaks_all command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode all -c tests/config/nextflow.config tags: - test_conseneus_peaks - test_conseneus_peaks_all files: - path: results/03_peak_calling/05_consensus_peaks/all_samples.awk.bed - path: results/03_peak_calling/05_consensus_peaks/all_samples.consensus.peaks.bed - name: test_conseneus_peaks_invalid command: nextflow run main.nf -profile docker,test_full_small --only_peak_calling true --skip_fastqc true --consensus_peak_mode test -c tests/config/nextflow.config - test_conseneus_peaks - test_conseneus_peaks_invalid exit_code: 1 No newline at end of file
workflows/cutandrun.nf +5 −0 Original line number Diff line number Diff line Loading @@ -76,6 +76,11 @@ if ((caller_list + callers).unique().size() != caller_list.size()) { exit 1, "Invalid variant calller option: ${params.peakcaller}. Valid options: ${caller_list.join(', ')}" } conseneus_mode_list = ['group', 'all'] if (!(params.consensus_peak_mode in conseneus_mode_list)) { exit 1, "Invalid conseneus mode option: ${params.consensus_peak_mode}. Valid options: ${conseneus_mode_list.join(', ')}" } /* ======================================================================================== IMPORT LOCAL MODULES/SUBWORKFLOWS Loading
