Loading nextflow.config +0 −1 Original line number Diff line number Diff line Loading @@ -51,7 +51,6 @@ params { minimum_alignment_q_score = 0 // Deduplication //skip_markduplicates = false skip_removeduplicates = false dedup_target_reads = false only_filtering = false Loading tests/test_verify_output_duplicates.yml +3 −3 Original line number Diff line number Diff line - name: test_verify_output_duplicates_mark command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config tags: - verify_output - verify_output_align Loading @@ -15,7 +15,7 @@ - path: results/02_alignment/bowtie2/target/markdup/samtools_stats/igg_R1.target.markdup.bam.flagstat - name: test_verify_output_duplicates_remove command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads false command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --dedup_target_reads false tags: - verify_output - verify_output_align Loading @@ -32,7 +32,7 @@ should_exist: false - name: test_verify_output_duplicates_remove_target command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads true command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --dedup_target_reads true tags: - verify_output - verify_output_align Loading workflows/cutandrun.nf +0 −2 Original line number Diff line number Diff line Loading @@ -74,9 +74,7 @@ def run_multiqc = true def run_peak_plotting = true if(params.minimum_alignment_q_score > 0) { run_q_filter = true } //if(params.skip_markduplicates) { run_mark_dups = false } if(params.skip_removeduplicates || !run_mark_dups) { run_remove_dups = false } //if(params.skip_peak_calling) { run_peak_calling = false } if(!params.gene_bed || params.skip_heatmaps) { run_deep_tools = false } if(params.skip_multiqc) { run_multiqc = false } if(params.skip_upset_plots) { run_peak_plotting = false } Loading Loading
nextflow.config +0 −1 Original line number Diff line number Diff line Loading @@ -51,7 +51,6 @@ params { minimum_alignment_q_score = 0 // Deduplication //skip_markduplicates = false skip_removeduplicates = false dedup_target_reads = false only_filtering = false Loading
tests/test_verify_output_duplicates.yml +3 −3 Original line number Diff line number Diff line - name: test_verify_output_duplicates_mark command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true -c tests/config/nextflow.config tags: - verify_output - verify_output_align Loading @@ -15,7 +15,7 @@ - path: results/02_alignment/bowtie2/target/markdup/samtools_stats/igg_R1.target.markdup.bam.flagstat - name: test_verify_output_duplicates_remove command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads false command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --dedup_target_reads false tags: - verify_output - verify_output_align Loading @@ -32,7 +32,7 @@ should_exist: false - name: test_verify_output_duplicates_remove_target command: nextflow run main.nf -profile docker,test --only_filtering true --skip_fastqc true --dedup_target_reads true command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --dedup_target_reads true tags: - verify_output - verify_output_align Loading
workflows/cutandrun.nf +0 −2 Original line number Diff line number Diff line Loading @@ -74,9 +74,7 @@ def run_multiqc = true def run_peak_plotting = true if(params.minimum_alignment_q_score > 0) { run_q_filter = true } //if(params.skip_markduplicates) { run_mark_dups = false } if(params.skip_removeduplicates || !run_mark_dups) { run_remove_dups = false } //if(params.skip_peak_calling) { run_peak_calling = false } if(!params.gene_bed || params.skip_heatmaps) { run_deep_tools = false } if(params.skip_multiqc) { run_multiqc = false } if(params.skip_upset_plots) { run_peak_plotting = false } Loading
