From a27d714c5cf61dfd36ec73c003972ec91809fbad Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Fri, 25 Sep 2020 11:21:00 +0200
Subject: [PATCH] src/RNAseq.nf : add multiqc module
---
src/RNAseq.config | 4 ++++
src/RNAseq.nf | 34 ++++++++++++++++++++++++++++++++--
2 files changed, 36 insertions(+), 2 deletions(-)
diff --git a/src/RNAseq.config b/src/RNAseq.config
index c8f39d48..d15b85fd 100644
--- a/src/RNAseq.config
+++ b/src/RNAseq.config
@@ -104,6 +104,10 @@ profiles {
container = "lbmc/htseq:0.11.2"
cpus = 1
}
+ withName: multiqc {
+ container = "ewels/multiqc:1.9"
+ cpus = 1
+ }
}
}
}
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index 8022c44a..e96e2fe5 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -45,7 +45,7 @@ process fastqc_raw {
set file_id, file(reads) from INPUT_FASTQC_RAW
output:
- set file_id, "*.{html,zip}" into OUTPUT_FASTQC_RAW
+ file "*_fastqc.{html,zip}" into OUTPUT_FASTQC_RAW
when:
params.do_fastqc
@@ -104,7 +104,7 @@ process fastqc_cut {
set file_id, file(reads) from CUTADAPT_OUTPUT_FASTQC
output:
- set file_id, "*.{html,zip}" into OUTPUT_FASTQC_CUT
+ file "*.{html,zip}" into OUTPUT_FASTQC_CUT
when:
params.do_fastqc
@@ -265,6 +265,9 @@ if (! params.do_dedup) {
HISAT_ALIGNED_DEDUP.into{DEDUP_GENOME}
}
+
+
+
/* HTseq
process sort_bam {
@@ -349,3 +352,30 @@ bash ${script} -b ${bam} \
"""
}
*/
+
+/* MultiQC */
+
+
+process multiqc {
+ tag "multiqc"
+ publishDir "${params.output}/multiqc", mode: 'copy'
+
+ input:
+ file ('fastqc/*') from OUTPUT_FASTQC_RAW.collect().ifEmpty([])
+ file ('*') from CUTADAPT_LOG.collect().ifEmpty([])
+ file ('fastqc/*') from OUTPUT_FASTQC_CUT.collect().ifEmpty([])
+ file ('*') from FILTER_LOG.collect().ifEmpty([])
+ file ('fastqc/*') from OUTPUT_FASTQC_FILTER.collect().ifEmpty([])
+ file ('*') from HISAT_LOG.collect().ifEmpty([])
+ file ('fastqc/*') from OUTPUT_FASTQC_GENOME.collect().ifEmpty([])
+
+
+ output:
+ file "multiqc_report.html" into multiqc_report
+ file "multiqc_data"
+
+ script:
+"""
+multiqc ./
+"""
+}
--
GitLab