From 322fdcd857aaa06cf8ca7247db3614a717c85e91 Mon Sep 17 00:00:00 2001 From: Thiseas Christos Lamnidis Date: Fri, 27 Oct 2023 10:54:17 +0200 Subject: [PATCH] tweak mqc mapdamage linking --- main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 1b238cdaf..2d597795f 100644 --- a/main.nf +++ b/main.nf @@ -2122,11 +2122,11 @@ process mapdamage_calculation { file fasta from ch_fasta_for_mapdamage.collect() output: - tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("results_*") into ch_output_from_mapdamage - path ("results_*") into ch_mapdamage_for_multiqc + tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("results_${base}") into ch_output_from_mapdamage + path ("results_${base}") into ch_mapdamage_for_multiqc script: - def base = "${bam.baseName}" + base = "${bam.baseName}" def singlestranded = strandedness == "single" ? '--single-stranded' : '' def downsample = params.mapdamage_downsample != 0 ? "-n ${params.mapdamage_downsample} --downsample-seed=1" : '' // Include seed to make results consistent between runs """ @@ -3258,7 +3258,7 @@ process multiqc { file ('flagstat_filtered/*') from ch_bam_filtered_flagstat_for_multiqc.collect().ifEmpty([]) file ('preseq/*') from ch_preseq_for_multiqc.collect().ifEmpty([]) file ('damageprofiler/dmgprof*/*') from ch_damageprofiler_results.collect().ifEmpty([]) - path ('mapdamage/*') from ch_mapdamage_for_multiqc.collect().ifEmpty([]).dump(tag:'ch_mapdamage_for_multiqc') + file ('mapdamage/*') from ch_mapdamage_for_multiqc.collect().ifEmpty([]).dump(tag:'ch_mapdamage_for_multiqc') file ('qualimap/qualimap*/*') from ch_qualimap_results.collect().ifEmpty([]) file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([]) file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([])