From 12e1d05afc183b3c006cafb90832e5431d8354a7 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 17:19:22 +0200
Subject: [PATCH] UrQt: update nf structure
---
src/nf_modules/UrQt/tests.sh | 9 +++
src/nf_modules/UrQt/tests/tests.sh | 9 ---
src/nf_modules/UrQt/trimming_paired.config | 26 +++++++
.../UrQt/{tests => }/trimming_paired.nf | 0
src/nf_modules/UrQt/trimming_single.config | 26 +++++++
.../UrQt/{tests => }/trimming_single.nf | 0
src/nf_modules/UrQt/urqt.nf | 72 -------------------
7 files changed, 61 insertions(+), 81 deletions(-)
create mode 100755 src/nf_modules/UrQt/tests.sh
delete mode 100755 src/nf_modules/UrQt/tests/tests.sh
create mode 100644 src/nf_modules/UrQt/trimming_paired.config
rename src/nf_modules/UrQt/{tests => }/trimming_paired.nf (100%)
create mode 100644 src/nf_modules/UrQt/trimming_single.config
rename src/nf_modules/UrQt/{tests => }/trimming_single.nf (100%)
delete mode 100644 src/nf_modules/UrQt/urqt.nf
diff --git a/src/nf_modules/UrQt/tests.sh b/src/nf_modules/UrQt/tests.sh
new file mode 100755
index 0000000..436e9cb
--- /dev/null
+++ b/src/nf_modules/UrQt/tests.sh
@@ -0,0 +1,9 @@
+nextflow src/nf_modules/UrQt/trimming_paired.nf \
+ -c src/nf_modules/UrQt/trimming_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/UrQt/trimming_single.nf \
+ -c src/nf_modules/UrQt/trimming_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
diff --git a/src/nf_modules/UrQt/tests/tests.sh b/src/nf_modules/UrQt/tests/tests.sh
deleted file mode 100755
index ebad731..0000000
--- a/src/nf_modules/UrQt/tests/tests.sh
+++ /dev/null
@@ -1,9 +0,0 @@
-nextflow src/nf_modules/UrQt/tests/trimming_paired.nf \
- -c src/nf_modules/UrQt/urqt.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/UrQt/tests/trimming_single.nf \
- -c src/nf_modules/UrQt/urqt.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
diff --git a/src/nf_modules/UrQt/trimming_paired.config b/src/nf_modules/UrQt/trimming_paired.config
new file mode 100644
index 0000000..46a8672
--- /dev/null
+++ b/src/nf_modules/UrQt/trimming_paired.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $trimming {
+ container = "urqt:d62c1f8"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load UrQt/d62c1f8"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/UrQt/tests/trimming_paired.nf b/src/nf_modules/UrQt/trimming_paired.nf
similarity index 100%
rename from src/nf_modules/UrQt/tests/trimming_paired.nf
rename to src/nf_modules/UrQt/trimming_paired.nf
diff --git a/src/nf_modules/UrQt/trimming_single.config b/src/nf_modules/UrQt/trimming_single.config
new file mode 100644
index 0000000..46a8672
--- /dev/null
+++ b/src/nf_modules/UrQt/trimming_single.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $trimming {
+ container = "urqt:d62c1f8"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load UrQt/d62c1f8"
+ executor = "sge"
+ cpus = 4
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/UrQt/tests/trimming_single.nf b/src/nf_modules/UrQt/trimming_single.nf
similarity index 100%
rename from src/nf_modules/UrQt/tests/trimming_single.nf
rename to src/nf_modules/UrQt/trimming_single.nf
diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
deleted file mode 100644
index 3a0e7d8..0000000
--- a/src/nf_modules/UrQt/urqt.nf
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
-* urqt :
-* Imputs : fastq files
-* Output : fastq files
-*/
-/* quality trimming */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process trimming {
- tag "${reads}"
- cpus 4
- publishDir "results/fastq/trimming/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- set pair_id, "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
-
- script:
-"""
-UrQt --t 20 --m ${task.cpus} --gz \
---in ${reads[0]} --inpair ${reads[1]} \
---out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
-> ${pair_id}_trimming_report.txt
-"""
-}
-
-/*
-* for single-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process trimming {
- tag "$file_id"
- cpus 4
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- set file_id, "*_trim.fastq.gz" into fastq_files_trim
-
- script:
- """
- UrQt --t 20 --m ${task.cpus} --gz \
- --in ${reads} \
- --out ${file_id}_trim.fastq.gz \
- > ${file_id}_trimming_report.txt
- """
-}
--
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