Loading conf/modules.config +1 −1 Original line number Diff line number Diff line Loading @@ -178,7 +178,7 @@ params { suffix = ".awk" publish_dir = "" command = "'/^[^#]/{print}'" command2 = "| head -2 | sed 's/\\t/,/g' - | sed 's/.*/\\L&/g' -" command2 = " > int1.txt && head -2 int1.txt > int2.txt && sed 's/\\t/,/g' int2.txt > int3.txt && sed 's/.*/\\L&/g' int3.txt " publish_files = false } "awk_dt_frag" { Loading modules/local/awk.nf +1 −1 Original line number Diff line number Diff line Loading @@ -33,6 +33,6 @@ process AWK { def ext = options.ext ? "${options.ext}" : "txt" """ awk $options.args $options.command $input $options.command2 > ${prefix}.awk.${ext} echo \$(awk --version 2>&1) | sed 's/^.*version //;' > ${software}.version.txt awk -W version | head -n 1 | egrep -o "([0-9]{1,}\\.)+[0-9]{1,}" > ${software}.version.txt """ } modules/local/awk_script.nf +1 −1 Original line number Diff line number Diff line Loading @@ -30,6 +30,6 @@ process AWK_SCRIPT { def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ awk $options.args -f $script $input > ${prefix}.awk.txt echo \$(awk --version 2>&1) | sed 's/^.*version //;' > ${software}.version.txt awk -W version | head -n 1 | egrep -o "([0-9]{1,}\\.)+[0-9]{1,}" > ${software}.version.txt """ } workflows/cutandrun.nf +4 −1 Original line number Diff line number Diff line Loading @@ -397,7 +397,10 @@ workflow CUTANDRUN { * of reads aligned to the spike-in genome */ ch_samtools_bam .map { row -> [ row[0].id, params.normalisation_c / (row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger()) ] } .map { row -> def denominator = row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger() [ row[0].id, params.normalisation_c / (denominator != 0 ? denominator : 1) ] } .set { ch_scale_factor } // EXAMPLE CHANNEL STRUCT: [id, scale_factor] //ch_scale_factor | view Loading Loading
conf/modules.config +1 −1 Original line number Diff line number Diff line Loading @@ -178,7 +178,7 @@ params { suffix = ".awk" publish_dir = "" command = "'/^[^#]/{print}'" command2 = "| head -2 | sed 's/\\t/,/g' - | sed 's/.*/\\L&/g' -" command2 = " > int1.txt && head -2 int1.txt > int2.txt && sed 's/\\t/,/g' int2.txt > int3.txt && sed 's/.*/\\L&/g' int3.txt " publish_files = false } "awk_dt_frag" { Loading
modules/local/awk.nf +1 −1 Original line number Diff line number Diff line Loading @@ -33,6 +33,6 @@ process AWK { def ext = options.ext ? "${options.ext}" : "txt" """ awk $options.args $options.command $input $options.command2 > ${prefix}.awk.${ext} echo \$(awk --version 2>&1) | sed 's/^.*version //;' > ${software}.version.txt awk -W version | head -n 1 | egrep -o "([0-9]{1,}\\.)+[0-9]{1,}" > ${software}.version.txt """ }
modules/local/awk_script.nf +1 −1 Original line number Diff line number Diff line Loading @@ -30,6 +30,6 @@ process AWK_SCRIPT { def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" """ awk $options.args -f $script $input > ${prefix}.awk.txt echo \$(awk --version 2>&1) | sed 's/^.*version //;' > ${software}.version.txt awk -W version | head -n 1 | egrep -o "([0-9]{1,}\\.)+[0-9]{1,}" > ${software}.version.txt """ }
workflows/cutandrun.nf +4 −1 Original line number Diff line number Diff line Loading @@ -397,7 +397,10 @@ workflow CUTANDRUN { * of reads aligned to the spike-in genome */ ch_samtools_bam .map { row -> [ row[0].id, params.normalisation_c / (row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger()) ] } .map { row -> def denominator = row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger() [ row[0].id, params.normalisation_c / (denominator != 0 ? denominator : 1) ] } .set { ch_scale_factor } // EXAMPLE CHANNEL STRUCT: [id, scale_factor] //ch_scale_factor | view Loading
