From b5a93ee3418d8d1511d280b9b4f1a8ebfbd9a4eb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 18 Feb 2021 17:29:36 +0100
Subject: [PATCH] fastp: fix output name to be catched by multiqc
---
src/nf_modules/fastp/main.nf | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index a44e6e89..8b264375 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -6,13 +6,15 @@ process fastp_pairedend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
+ publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html"
input:
tuple val(pair_id), path(reads)
output:
tuple val(pair_id), path("*.fastq.gz"), emit: fastq
- tuple val(pair_id), path("*.{zip,html,json}"), emit: report
+ tuple val(pair_id), path("*.html"), emit: html
+ tuple val(pair_id), path("*.json"), emit: report
script:
"""
@@ -25,7 +27,7 @@ fastp --thread ${task.cpus} \
--out1 ${pair_id}_R1_trim.fastq.gz \
--out2 ${pair_id}_R2_trim.fastq.gz \
--html ${pair_id}.html \
---json ${pair_id}.json \
+--json ${pair_id}_fastp.json \
--report_title ${pair_id}
"""
}
@@ -34,13 +36,15 @@ process fastp_singleend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
+ publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html"
input:
tuple val(pair_id), path(reads)
output:
tuple val(pair_id), path("*.fastq.gz"), emit: fastq
- tuple val(pair_id), path("*.{zip,html,json}"), emit: report
+ tuple val(pair_id), path("*.html"), emit: html
+ tuple val(pair_id), path("*.json"), emit: report
script:
"""
@@ -51,7 +55,7 @@ fastp --thread ${task.cpus} \
--in1 ${reads} \
--out1 ${pair_id}_trim.fastq.gz \
--html ${pair_id}.html \
---json ${pair_id}.json \
+--json ${pair_id}_fastp.json \
--report_title ${pair_id}
"""
}
--
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