diff --git a/modules/local/exomedepth/merge_count/main.nf b/modules/local/exomedepth/merge_count/main.nf index 771ee2c..333652b 100644 --- a/modules/local/exomedepth/merge_count/main.nf +++ b/modules/local/exomedepth/merge_count/main.nf @@ -12,10 +12,10 @@ process EXOMEDEPTH_COUNT_MERGE { """ for file in $files; do if [ -f ${meta.id}_${meta.chr}.txt ]; then - paste ${meta.id}_${meta.chr}.txt <(awk '{print \$5}' \$file) > temp_auto.txt - mv temp_auto.txt ${meta.id}_${meta.chr}.txt - else - cp \$file ${meta.id}_${meta.chr}.txt + paste ${meta.id}_${meta.chr}.txt <(awk '{print \$5}' \$file) > temp_auto.txt + mv temp_auto.txt ${meta.id}_${meta.chr}.txt + else + cp \$file ${meta.id}_${meta.chr}.txt fi done """ diff --git a/workflows/exomecnv.nf b/workflows/exomecnv.nf index a5968c3..d39b913 100644 --- a/workflows/exomecnv.nf +++ b/workflows/exomecnv.nf @@ -47,8 +47,8 @@ workflow EXOMECNV { .set{ ch_input_prepare } - //ch_input_prepare.BAM.view { "BAM: $it" } - //ch_input_prepare.CRAM.view { "CRAM: $it" } + //ch_input_prepare.BAM.view { "BAM: $it" } + //ch_input_prepare.CRAM.view { "CRAM: $it" } ch_fasta = Channel.fromPath(params.fasta).map{ [[id:"reference"], it]}.collect()