Loading .github/workflows/ci.yml +6 −0 Original line number Original line Diff line number Diff line Loading @@ -163,6 +163,12 @@ jobs: - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove_target - verify_output_align_duplicates_remove_target - verify_output_peak_calling_only_peak_calling - verify_output_peak_calling_only_peak_calling - test_bam_scale_none - test_bam_scale_spikein - test_bam_scale_cpm - test_bam_scale_rpkm - test_bam_scale_bpm - test_bam_scale_cpm_iggscale - test_peak_callers - test_peak_callers - test_conseneus_peaks_group - test_conseneus_peaks_group - test_conseneus_peaks_all - test_conseneus_peaks_all Loading tests/test_bam_scaling.yml 0 → 100644 +62 −0 Original line number Original line Diff line number Diff line - name: test_bam_scale_none command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode None -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_none files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1" - name: test_bam_scale_spikein command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode Spikein -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_spikein files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 10000" - name: test_bam_scale_cpm command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode CPM -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_cpm files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1607.72" - name: test_bam_scale_rpkm command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode RPKM -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_rpkm files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1.60772e+06" - name: test_bam_scale_bpm command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode RPKM -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_bpm files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1607.72" - name: test_bam_scale_cpm_iggscale command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode CPM --igg_scale_factor 0.1 -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_cpm_iggscale files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1607.72" - path: results/03_peak_calling/01_bam_to_bedgraph/igg_R1.sorted.bedGraph contains: - "chr20 606391 606415 285.714" Loading
.github/workflows/ci.yml +6 −0 Original line number Original line Diff line number Diff line Loading @@ -163,6 +163,12 @@ jobs: - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove - verify_output_align_duplicates_remove_target - verify_output_align_duplicates_remove_target - verify_output_peak_calling_only_peak_calling - verify_output_peak_calling_only_peak_calling - test_bam_scale_none - test_bam_scale_spikein - test_bam_scale_cpm - test_bam_scale_rpkm - test_bam_scale_bpm - test_bam_scale_cpm_iggscale - test_peak_callers - test_peak_callers - test_conseneus_peaks_group - test_conseneus_peaks_group - test_conseneus_peaks_all - test_conseneus_peaks_all Loading
tests/test_bam_scaling.yml 0 → 100644 +62 −0 Original line number Original line Diff line number Diff line - name: test_bam_scale_none command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode None -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_none files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1" - name: test_bam_scale_spikein command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode Spikein -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_spikein files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 10000" - name: test_bam_scale_cpm command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode CPM -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_cpm files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1607.72" - name: test_bam_scale_rpkm command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode RPKM -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_rpkm files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1.60772e+06" - name: test_bam_scale_bpm command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode RPKM -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_bpm files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1607.72" - name: test_bam_scale_cpm_iggscale command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --normalisation_mode CPM --igg_scale_factor 0.1 -c tests/config/nextflow.config tags: - test_bam_scale - test_bam_scale_cpm_iggscale files: - path: results/03_peak_calling/01_bam_to_bedgraph/h3k27me3_R1.sorted.bedGraph contains: - "chr20 171984 172009 1607.72" - path: results/03_peak_calling/01_bam_to_bedgraph/igg_R1.sorted.bedGraph contains: - "chr20 606391 606415 285.714"
