From da619d52fe074200e7b138a74626fb8c995f2588 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 30 Jan 2024 10:46:00 +0000 Subject: [PATCH] Small modifications to make mirtrace run again --- modules/nf-core/umicollapse/main.nf | 2 +- workflows/smrnaseq.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/umicollapse/main.nf b/modules/nf-core/umicollapse/main.nf index 321ffd84..01915edb 100644 --- a/modules/nf-core/umicollapse/main.nf +++ b/modules/nf-core/umicollapse/main.nf @@ -14,7 +14,7 @@ process UMICOLLAPSE { output: tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("${prefix}.${extension}"), emit: fastq, optional: true + tuple val(meta), path("*dedup*fastq.gz"), emit: fastq, optional: true tuple val(meta), path("*_UMICollapse.log"), emit: log path "versions.yml" , emit: versions diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index f84b8f86..39776476 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -182,9 +182,9 @@ workflow SMRNASEQ { // FASTQ_FASTQC_UMITOOLS_FASTP.out.adapter_seq .join( ch_reads_for_mirna ) + .dump() .map { meta, adapter_seq, reads -> [adapter_seq, meta.id, reads] } .groupTuple() - .dump() .set { ch_mirtrace_inputs } MIRTRACE(ch_mirtrace_inputs)