Loading modules/nf-core/modules/custom/getchromsizes/main.nf +2 −1 Original line number Diff line number Diff line Loading @@ -23,9 +23,10 @@ process CUSTOM_GETCHROMSIZES { """ samtools faidx $fasta cut -f 1,2 ${fasta}.fai > ${fasta}.sizes cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') custom: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } modules/nf-core/modules/fastqc/main.nf +2 −0 Original line number Diff line number Diff line Loading @@ -26,6 +26,7 @@ process FASTQC { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz fastqc $args --threads $task.cpus ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) Loading @@ -36,6 +37,7 @@ process FASTQC { [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) Loading modules/nf-core/modules/gunzip/main.nf +1 −0 Original line number Diff line number Diff line Loading @@ -25,6 +25,7 @@ process GUNZIP { -f \\ $args \\ $archive cat <<-END_VERSIONS > versions.yml "${task.process}": gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') Loading modules/nf-core/modules/macs2/callpeak/main.nf +1 −2 Original line number Diff line number Diff line process MACS2_CALLPEAK { tag "$meta.id" label 'process_medium' Loading Loading @@ -46,6 +44,7 @@ process MACS2_CALLPEAK { --name $prefix \\ --treatment $ipbam \\ $control cat <<-END_VERSIONS > versions.yml "${task.process}": macs2: \$(macs2 --version | sed -e "s/macs2 //g") Loading modules/nf-core/modules/picard/markduplicates/main.nf +3 −3 Original line number Diff line number Diff line Loading @@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES { -Xmx${avail_mem}g \\ MarkDuplicates \\ $args \\ -I $bam \\ -O ${prefix}.bam \\ -M ${prefix}.MarkDuplicates.metrics.txt I=$bam \\ O=${prefix}.bam \\ M=${prefix}.MarkDuplicates.metrics.txt cat <<-END_VERSIONS > versions.yml "${task.process}": Loading Loading
modules/nf-core/modules/custom/getchromsizes/main.nf +2 −1 Original line number Diff line number Diff line Loading @@ -23,9 +23,10 @@ process CUSTOM_GETCHROMSIZES { """ samtools faidx $fasta cut -f 1,2 ${fasta}.fai > ${fasta}.sizes cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') custom: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ }
modules/nf-core/modules/fastqc/main.nf +2 −0 Original line number Diff line number Diff line Loading @@ -26,6 +26,7 @@ process FASTQC { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz fastqc $args --threads $task.cpus ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) Loading @@ -36,6 +37,7 @@ process FASTQC { [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) Loading
modules/nf-core/modules/gunzip/main.nf +1 −0 Original line number Diff line number Diff line Loading @@ -25,6 +25,7 @@ process GUNZIP { -f \\ $args \\ $archive cat <<-END_VERSIONS > versions.yml "${task.process}": gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//') Loading
modules/nf-core/modules/macs2/callpeak/main.nf +1 −2 Original line number Diff line number Diff line process MACS2_CALLPEAK { tag "$meta.id" label 'process_medium' Loading Loading @@ -46,6 +44,7 @@ process MACS2_CALLPEAK { --name $prefix \\ --treatment $ipbam \\ $control cat <<-END_VERSIONS > versions.yml "${task.process}": macs2: \$(macs2 --version | sed -e "s/macs2 //g") Loading
modules/nf-core/modules/picard/markduplicates/main.nf +3 −3 Original line number Diff line number Diff line Loading @@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES { -Xmx${avail_mem}g \\ MarkDuplicates \\ $args \\ -I $bam \\ -O ${prefix}.bam \\ -M ${prefix}.MarkDuplicates.metrics.txt I=$bam \\ O=${prefix}.bam \\ M=${prefix}.MarkDuplicates.metrics.txt cat <<-END_VERSIONS > versions.yml "${task.process}": Loading
