From 927521d7271ea92807d969720444a37172fa8849 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 15:49:03 +0200
Subject: [PATCH] MultiQC: update nf structure
---
src/nf_modules/MultiQC/multiqc.nf | 25 ------------
.../{multiqc.config => multiqc_paired.config} | 0
.../MultiQC/{tests => }/multiqc_paired.nf | 0
src/nf_modules/MultiQC/multiqc_single.config | 38 +++++++++++++++++++
.../MultiQC/{tests => }/multiqc_single.nf | 0
src/nf_modules/MultiQC/tests.sh | 9 +++++
src/nf_modules/MultiQC/tests/tests.sh | 9 -----
7 files changed, 47 insertions(+), 34 deletions(-)
delete mode 100644 src/nf_modules/MultiQC/multiqc.nf
rename src/nf_modules/MultiQC/{multiqc.config => multiqc_paired.config} (100%)
rename src/nf_modules/MultiQC/{tests => }/multiqc_paired.nf (100%)
create mode 100644 src/nf_modules/MultiQC/multiqc_single.config
rename src/nf_modules/MultiQC/{tests => }/multiqc_single.nf (100%)
create mode 100755 src/nf_modules/MultiQC/tests.sh
delete mode 100755 src/nf_modules/MultiQC/tests/tests.sh
diff --git a/src/nf_modules/MultiQC/multiqc.nf b/src/nf_modules/MultiQC/multiqc.nf
deleted file mode 100644
index b64d7f6..0000000
--- a/src/nf_modules/MultiQC/multiqc.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
-* multiqc :
-* Imputs : report files
-* Output : multiqc report
-*/
-
-/* MultiQC */
-
-process multiqc {
- tag "$report.baseName"
- publishDir "results/fastq/multiqc/", mode: 'copy'
- cpus = 1
-
- input:
- file report from fastqc_report.collect()
-
- output:
- file "*multiqc_*" into multiqc_report
-
- script:
-"""
-multiqc -f .
-"""
-}
-
diff --git a/src/nf_modules/MultiQC/multiqc.config b/src/nf_modules/MultiQC/multiqc_paired.config
similarity index 100%
rename from src/nf_modules/MultiQC/multiqc.config
rename to src/nf_modules/MultiQC/multiqc_paired.config
diff --git a/src/nf_modules/MultiQC/tests/multiqc_paired.nf b/src/nf_modules/MultiQC/multiqc_paired.nf
similarity index 100%
rename from src/nf_modules/MultiQC/tests/multiqc_paired.nf
rename to src/nf_modules/MultiQC/multiqc_paired.nf
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
new file mode 100644
index 0000000..c1bda95
--- /dev/null
+++ b/src/nf_modules/MultiQC/multiqc_single.config
@@ -0,0 +1,38 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $fastqc_fastq {
+ container = "fastqc:0.11.5"
+ }
+ $multiqc {
+ container = "multiqc:1.0"
+ }
+ }
+ }
+ sge {
+ process{
+ $fastqc_fastq {
+ beforeScript = "module purge; module load FastQC/0.11.5"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ $multiqc {
+ beforeScript = "module purge; module load FastQC/1.0"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'monointeldeb128'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/MultiQC/tests/multiqc_single.nf b/src/nf_modules/MultiQC/multiqc_single.nf
similarity index 100%
rename from src/nf_modules/MultiQC/tests/multiqc_single.nf
rename to src/nf_modules/MultiQC/multiqc_single.nf
diff --git a/src/nf_modules/MultiQC/tests.sh b/src/nf_modules/MultiQC/tests.sh
new file mode 100755
index 0000000..40b6522
--- /dev/null
+++ b/src/nf_modules/MultiQC/tests.sh
@@ -0,0 +1,9 @@
+nextflow src/nf_modules/MultiQC/multiqc_paired.nf \
+ -c src/nf_modules/MultiQC/multiqc_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/MultiQC/multiqc_single.nf \
+ -c src/nf_modules/MultiQC/multiqc_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
diff --git a/src/nf_modules/MultiQC/tests/tests.sh b/src/nf_modules/MultiQC/tests/tests.sh
deleted file mode 100755
index 8aaa83c..0000000
--- a/src/nf_modules/MultiQC/tests/tests.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-nextflow src/nf_modules/MultiQC/tests/multiqc_paired.nf \
- -c src/nf_modules/MultiQC/multiqc.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/MultiQC/tests/multiqc_single.nf \
- -c src/nf_modules/MultiQC/multiqc.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
--
GitLab