From b5d577192a0ab64ed3919ec7fbe0d456e1eecf3e Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 22 Aug 2018 14:46:33 +0200
Subject: [PATCH] Cutadapt: update nf structure
---
...t.config => adaptor_removal_paired.config} | 27 ----
.../{tests => }/adaptor_removal_paired.nf | 0
.../cutadapt/adaptor_removal_single.config | 26 ++++
.../{tests => }/adaptor_removal_single.nf | 0
src/nf_modules/cutadapt/cutadapt.nf | 131 ------------------
src/nf_modules/cutadapt/tests.sh | 19 +++
src/nf_modules/cutadapt/tests/tests.sh | 19 ---
.../cutadapt/trimming_paired.config | 26 ++++
.../cutadapt/{tests => }/trimming_paired.nf | 0
.../cutadapt/trimming_single.config | 26 ++++
.../cutadapt/{tests => }/trimming_single.nf | 0
11 files changed, 97 insertions(+), 177 deletions(-)
rename src/nf_modules/cutadapt/{cutadapt.config => adaptor_removal_paired.config} (50%)
rename src/nf_modules/cutadapt/{tests => }/adaptor_removal_paired.nf (100%)
create mode 100644 src/nf_modules/cutadapt/adaptor_removal_single.config
rename src/nf_modules/cutadapt/{tests => }/adaptor_removal_single.nf (100%)
delete mode 100644 src/nf_modules/cutadapt/cutadapt.nf
create mode 100755 src/nf_modules/cutadapt/tests.sh
delete mode 100755 src/nf_modules/cutadapt/tests/tests.sh
create mode 100644 src/nf_modules/cutadapt/trimming_paired.config
rename src/nf_modules/cutadapt/{tests => }/trimming_paired.nf (100%)
create mode 100644 src/nf_modules/cutadapt/trimming_single.config
rename src/nf_modules/cutadapt/{tests => }/trimming_single.nf (100%)
diff --git a/src/nf_modules/cutadapt/cutadapt.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
similarity index 50%
rename from src/nf_modules/cutadapt/cutadapt.config
rename to src/nf_modules/cutadapt/adaptor_removal_paired.config
index 07efa9be..aa1a372b 100644
--- a/src/nf_modules/cutadapt/cutadapt.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -24,30 +24,3 @@ profiles {
}
}
}
-
-profiles {
- docker {
- docker.temp = 'auto'
- docker.enabled = true
- process {
- $trimming {
- container = "cutadapt:1.14"
- }
- }
- }
- sge {
- process{
- $trimming {
- beforeScript = "module purge; module load cutadapt/1.14"
- executor = "sge"
- cpus = 1
- memory = "5GB"
- time = "6h"
- queueSize = 1000
- pollInterval = '60sec'
- queue = 'h6-E5-2667v4deb128'
- penv = 'openmp8'
- }
- }
- }
-}
diff --git a/src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf b/src/nf_modules/cutadapt/adaptor_removal_paired.nf
similarity index 100%
rename from src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf
rename to src/nf_modules/cutadapt/adaptor_removal_paired.nf
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
new file mode 100644
index 00000000..aa1a372b
--- /dev/null
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $adaptor_removal {
+ container = "cutadapt:1.14"
+ }
+ }
+ }
+ sge {
+ process{
+ $adaptor_removal {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/cutadapt/tests/adaptor_removal_single.nf b/src/nf_modules/cutadapt/adaptor_removal_single.nf
similarity index 100%
rename from src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
rename to src/nf_modules/cutadapt/adaptor_removal_single.nf
diff --git a/src/nf_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
deleted file mode 100644
index c7428637..00000000
--- a/src/nf_modules/cutadapt/cutadapt.nf
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
-* cutadapt :
-* Imputs : fastq files
-* Output : fastq files
-*/
-
-/* Illumina adaptor removal */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process adaptor_removal {
- tag "$pair_id"
- publishDir "results/fastq/adaptor_removal/", mode: 'copy'
-
- input:
- set pair_id, file(reads) from fastq_files
-
- output:
- set pair_id, "*_cut_R{1,2}.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT -A AGATCGGAAGAG -G CTCTTCCGATCT \
- -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
- ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
- """
-}
-
-/*
-* for single-end data
-*/
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromPath( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
- .set { fastq_files }
-
-process adaptor_removal {
- tag "$file_id"
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- set file_id, "*_cut.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
- -o ${file_id}_cut.fastq.gz \
- ${reads} > ${file_id}_report.txt
- """
-}
-
-
-/* quality trimming */
-
-/*
-* for paired-end data
-*/
-
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
-process trimming {
- tag "$pair_id"
- 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:
- """
- cutadapt -q 20,20 \
- -o ${pair_id}_trim_R1.fastq.gz -p ${pair_id}_trim_R2.fastq.gz \
- ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
- """
-}
-
-/*
-* for single-end data
-*/
-
-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"
-
- input:
- set file_id, file(reads) from fastq_files
-
- output:
- set file_id, "*_trim.fastq.gz" into fastq_files_cut
-
- script:
- """
- cutadapt -q 20,20 \
- -o ${file_id}_trim.fastq.gz \
- ${reads} > ${file_id}_report.txt
- """
-}
-
diff --git a/src/nf_modules/cutadapt/tests.sh b/src/nf_modules/cutadapt/tests.sh
new file mode 100755
index 00000000..cf2b529e
--- /dev/null
+++ b/src/nf_modules/cutadapt/tests.sh
@@ -0,0 +1,19 @@
+nextflow src/nf_modules/cutadapt/adaptor_removal_paired.nf \
+ -c src/nf_modules/cutadapt/adaptor_removal_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/cutadapt/adaptor_removal_single.nf \
+ -c src/nf_modules/cutadapt/adaptor_removal_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
+
+nextflow src/nf_modules/cutadapt/trimming_paired.nf \
+ -c src/nf_modules/cutadapt/trimming_paired.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
+
+nextflow src/nf_modules/cutadapt/trimming_single.nf \
+ -c src/nf_modules/cutadapt/trimming_single.config \
+ -profile docker \
+ --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
diff --git a/src/nf_modules/cutadapt/tests/tests.sh b/src/nf_modules/cutadapt/tests/tests.sh
deleted file mode 100755
index 68623dbb..00000000
--- a/src/nf_modules/cutadapt/tests/tests.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-nextflow src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf \
- -c src/nf_modules/cutadapt/cutadapt.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/cutadapt/tests/adaptor_removal_single.nf \
- -c src/nf_modules/cutadapt/cutadapt.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
-
-nextflow src/nf_modules/cutadapt/tests/trimming_paired.nf \
- -c src/nf_modules/cutadapt/cutadapt.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny_R{1,2}.fastq"
-
-nextflow src/nf_modules/cutadapt/tests/trimming_single.nf \
- -c src/nf_modules/cutadapt/cutadapt.config \
- -profile docker \
- --fastq "data/tiny_dataset/fastq/tiny*_S.fastq"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
new file mode 100644
index 00000000..be03e9d7
--- /dev/null
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $trimming {
+ container = "cutadapt:1.14"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/cutadapt/tests/trimming_paired.nf b/src/nf_modules/cutadapt/trimming_paired.nf
similarity index 100%
rename from src/nf_modules/cutadapt/tests/trimming_paired.nf
rename to src/nf_modules/cutadapt/trimming_paired.nf
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
new file mode 100644
index 00000000..be03e9d7
--- /dev/null
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -0,0 +1,26 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ $trimming {
+ container = "cutadapt:1.14"
+ }
+ }
+ }
+ sge {
+ process{
+ $trimming {
+ beforeScript = "module purge; module load cutadapt/1.14"
+ executor = "sge"
+ cpus = 1
+ memory = "5GB"
+ time = "6h"
+ queueSize = 1000
+ pollInterval = '60sec'
+ queue = 'h6-E5-2667v4deb128'
+ penv = 'openmp8'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/cutadapt/tests/trimming_single.nf b/src/nf_modules/cutadapt/trimming_single.nf
similarity index 100%
rename from src/nf_modules/cutadapt/tests/trimming_single.nf
rename to src/nf_modules/cutadapt/trimming_single.nf
--
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