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nextflow
Commits
a6ae64ae
Verified
Commit
a6ae64ae
authored
Aug 02, 2018
by
Laurent Modolo
Browse files
cutadapt: nf file add file_id var for single-end like for paired
parent
f9a6c22f
Changes
4
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src/nf_modules/cutadapt/cutadapt.nf
View file @
a6ae64ae
...
...
@@ -41,33 +41,32 @@ process adaptor_removal {
* 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: ${params.fastq}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process adaptor_removal {
tag "$reads.baseName"
publishDir "results/fastq/adaptor_removal/", mode: 'copy'
tag "$file_id"
input:
file
reads from fastq_files
set file_id, file(
reads
)
from fastq_files
output:
file
"*_cut.fastq.gz" into fastq_files_cut
set file_id,
"*_cut.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
-o ${
reads.baseName
}_cut.fastq.gz \
${reads} > ${
reads.baseName
}_report.txt
-o ${
file_id
}_cut.fastq.gz \
${reads} > ${
file_id
}_report.txt
"""
}
/* quality trimming */
/*
...
...
@@ -105,30 +104,28 @@ process trimming {
* for single-end data
*/
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process trimming {
tag "$reads.baseName"
publishDir "results/fastq/trimming/", mode: 'copy'
tag "$file_id"
input:
file
reads from fastq_files
set file_id, file(
reads
)
from fastq_files
output:
file
"*_trim.fastq.gz" into fastq_files_
trim
set file_id,
"*_trim.fastq.gz" into fastq_files_
cut
script:
"""
cutadapt -q 20,20 \
-o ${
reads.baseName
}_trim.fastq.gz \
${reads} > ${
reads.baseName
}_report.txt
-o ${
file_id
}_trim.fastq.gz \
${reads} > ${
file_id
}_report.txt
"""
}
src/nf_modules/cutadapt/tests/adaptor_removal_single.nf
View file @
a6ae64ae
...
...
@@ -3,22 +3,23 @@ log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process adaptor_removal {
tag "$
reads.baseName
"
tag "$
file_id
"
input:
file
reads from fastq_files
set file_id, file(
reads
)
from fastq_files
output:
file
"*_cut.fastq.gz" into fastq_files_cut
set file_id,
"*_cut.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -a AGATCGGAAGAG -g CTCTTCCGATCT\
-o ${
reads.baseName
}_cut.fastq.gz \
${reads} > ${
reads.baseName
}_report.txt
-o ${
file_id
}_cut.fastq.gz \
${reads} > ${
file_id
}_report.txt
"""
}
src/nf_modules/cutadapt/tests/tests.sh
View file @
a6ae64ae
...
...
@@ -6,7 +6,7 @@ nextflow src/nf_modules/cutadapt/tests/adaptor_removal_paired.nf \
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
_R{1,2}
.fastq"
--fastq
"data/tiny_dataset/fastq/tiny
*_S
.fastq"
nextflow src/nf_modules/cutadapt/tests/trimming_paired.nf
\
-c
src/nf_modules/cutadapt/cutadapt.config
\
...
...
@@ -16,4 +16,4 @@ nextflow src/nf_modules/cutadapt/tests/trimming_paired.nf \
nextflow src/nf_modules/cutadapt/tests/trimming_single.nf
\
-c
src/nf_modules/cutadapt/cutadapt.config
\
-profile
docker
\
--fastq
"data/tiny_dataset/fastq/tiny
_R{1,2}
.fastq"
--fastq
"data/tiny_dataset/fastq/tiny
*_S
.fastq"
src/nf_modules/cutadapt/tests/trimming_single.nf
View file @
a6ae64ae
...
...
@@ -3,22 +3,23 @@ log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { fastq_files }
process trimming {
tag "$
reads.baseName
"
tag "$
file_id
"
input:
file
reads from fastq_files
set file_id, file(
reads
)
from fastq_files
output:
file
"*_trim.fastq.gz" into fastq_files_cut
set file_id,
"*_trim.fastq.gz" into fastq_files_cut
script:
"""
cutadapt -q 20,20 \
-o ${
reads.baseName
}_trim.fastq.gz \
${reads} > ${
reads.baseName
}_report.txt
-o ${
file_id
}_trim.fastq.gz \
${reads} > ${
file_id
}_report.txt
"""
}
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