From 419991effa705af955b5383dc919e60ef0a4f6a3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 14:51:00 +0200
Subject: [PATCH] FastQC: update nf structure
---
src/nf_modules/FastQC/fastqc.nf | 71 -------------------
.../{fastqc.config => fastqc_paired.config} | 0
.../FastQC/{tests => }/fastqc_paired.nf | 0
src/nf_modules/FastQC/fastqc_single.config | 25 +++++++
.../FastQC/{tests => }/fastqc_single.nf | 0
src/nf_modules/FastQC/tests.sh | 9 +++
src/nf_modules/FastQC/tests/tests.sh | 9 ---
7 files changed, 34 insertions(+), 80 deletions(-)
delete mode 100644 src/nf_modules/FastQC/fastqc.nf
rename src/nf_modules/FastQC/{fastqc.config => fastqc_paired.config} (100%)
rename src/nf_modules/FastQC/{tests => }/fastqc_paired.nf (100%)
create mode 100644 src/nf_modules/FastQC/fastqc_single.config
rename src/nf_modules/FastQC/{tests => }/fastqc_single.nf (100%)
create mode 100755 src/nf_modules/FastQC/tests.sh
delete mode 100755 src/nf_modules/FastQC/tests/tests.sh
diff --git a/src/nf_modules/FastQC/fastqc.nf b/src/nf_modules/FastQC/fastqc.nf
deleted file mode 100644
index 6e90d45..0000000
--- a/src/nf_modules/FastQC/fastqc.nf
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
-* fastqc :
-* Imputs : fastq files
-* Output : pdf files
-*/
-
-/* fastQC */
-
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process fastqc_fastq {
- tag "$file_id"
- publishDir "results/fastq/fastqc/", mode: 'copy'
- cpus = 1
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastqc_report
-
- script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ ${reads}
-"""
-}
-
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process fastqc_fastq {
- tag "$pair_id"
- publishDir "results/fastq/fastqc/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- file "*.{zip,html}" into fastqc_report
-
- script:
-"""
-fastqc --quiet --threads ${task.cpus} --format fastq --outdir ./ \
-${reads[0]} ${reads[1]}
-"""
-}
-
diff --git a/src/nf_modules/FastQC/fastqc.config b/src/nf_modules/FastQC/fastqc_paired.config
similarity index 100%
rename from src/nf_modules/FastQC/fastqc.config
rename to src/nf_modules/FastQC/fastqc_paired.config
diff --git a/src/nf_modules/FastQC/tests/fastqc_paired.nf b/src/nf_modules/FastQC/fastqc_paired.nf
similarity index 100%
rename from src/nf_modules/FastQC/tests/fastqc_paired.nf
rename to src/nf_modules/FastQC/fastqc_paired.nf
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
new file mode 100644
index 0000000..a658984
--- /dev/null
+++ b/src/nf_modules/FastQC/fastqc_single.config
@@ -0,0 +1,25 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $fastqc_fastq {
+ container = "fastqc:0.11.5"
+ }
+ }
+ }
+ 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'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/FastQC/tests/fastqc_single.nf b/src/nf_modules/FastQC/fastqc_single.nf
similarity index 100%
rename from src/nf_modules/FastQC/tests/fastqc_single.nf
rename to src/nf_modules/FastQC/fastqc_single.nf
diff --git a/src/nf_modules/FastQC/tests.sh b/src/nf_modules/FastQC/tests.sh
new file mode 100755
index 0000000..b103ac7
--- /dev/null
+++ b/src/nf_modules/FastQC/tests.sh
@@ -0,0 +1,9 @@
+nextflow src/nf_modules/FastQC/fastqc_paired.nf \
+ -c src/nf_modules/FastQC/fastqc_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/FastQC/fastqc_single.nf \
+ -c src/nf_modules/FastQC/fastqc_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
diff --git a/src/nf_modules/FastQC/tests/tests.sh b/src/nf_modules/FastQC/tests/tests.sh
deleted file mode 100755
index 147503b..0000000
--- a/src/nf_modules/FastQC/tests/tests.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-nextflow src/nf_modules/FastQC/tests/fastqc_paired.nf \
- -c src/nf_modules/FastQC/fastqc.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/FastQC/tests/fastqc_single.nf \
- -c src/nf_modules/FastQC/fastqc.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_S.fastq"
--
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