From e7f65eb4ba9df1efb9666620cb76ad504bb031a5 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Sun, 8 Sep 2024 17:07:42 +0200 Subject: [PATCH] tweak the channel dumps [ci skip] --- subworkflows/local/quality_check/main.nf | 2 +- workflows/mtbseqnf.nf | 5 ++--- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/quality_check/main.nf b/subworkflows/local/quality_check/main.nf index 46df614..10556e6 100644 --- a/subworkflows/local/quality_check/main.nf +++ b/subworkflows/local/quality_check/main.nf @@ -30,7 +30,7 @@ workflow QUALITY_CHECK { emit: reads_and_meta_ch = RENAME_FILES.out.meta_and_files - reads_ch = RENAME_FILES.out.files.collect() + reads_ch = RENAME_FILES.out.files multiqc_files = FASTQC.out.zip.collect{it[1]} versions = FASTQC.out.versions.first() derived_cohort_tsv = samples_tsv_file diff --git a/workflows/mtbseqnf.nf b/workflows/mtbseqnf.nf index a2f37ea..0cea2cd 100644 --- a/workflows/mtbseqnf.nf +++ b/workflows/mtbseqnf.nf @@ -49,9 +49,6 @@ workflow MTBSEQ_NF { ch_multiqc_files = ch_multiqc_files.mix(QUALITY_CHECK.out.multiqc_files) - QUALITY_CHECK.out.reads_and_meta_ch.dump(tag: 'QUALITY_CHECK.out.reads_and_meta_ch') - - if(!params.only_qc) { if( params.parallel ) { @@ -75,6 +72,8 @@ workflow MTBSEQ_NF { ch_reads = QUALITY_CHECK.out.reads_ch.collect() + ch_reads.dump(tag: 'ch_reads') + TBFULL( ch_reads, params.user, ch_reference_files )