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Verified Commit 86a16ba6 authored by Laurent Modolo's avatar Laurent Modolo
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UrQt: add tests, nf and config

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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"
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"
cpus 4
input:
set pair_id, file(reads) from fastq_files
output:
file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
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 \
> ${pair_id}_trimming_report.txt
"""
}
params.fastq = "$baseDir/data/fastq/*.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromPath( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process trimming {
tag "$reads.baseName"
cpus 4
input:
file reads from fastq_files
output:
file "*_trim.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads} \
--out ${reads.baseName}_trim.fastq.gz \
> ${reads.baseName}_trimming_report.txt
"""
}
profiles {
docker {
process {
$trimming {
container = "urqt:d62c1f8"
}
}
}
sge {
process{
$trimming {
beforeScript = "module purge; module load UrQt/d62c1f8"
}
}
}
}
/*
* urqt :
* Imputs : fastq files
* Output : fastq files
*/
/* quality trimming */
/*
* for paired-end data
*/
params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
log.info "fastq files : ${params.fastq}"
Channel
.fromFilePairs( params.fastq )
.ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
.set { fastq_files }
process trimming {
tag "$pair_id"
cpus 4
input:
set pair_id, file(reads) from fastq_files
output:
file "*_trim_R{1,2}.fastq.gz" into fastq_files_cut
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: ${params.fastq}" }
.set { fastq_files }
process trimming {
tag "$reads.baseName"
cpus 4
input:
file reads from fastq_files
output:
file "*_trim.fastq.gz" into fastq_files_trim
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads} \
--out ${reads.baseName}_trim.fastq.gz \
> ${reads.baseName}_trimming_report.txt
"""
}
nextflow src/nf_modules/cutadapt/test/adaptor_removal_paired.nf \
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/test/adaptor_removal_single.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"
nextflow src/nf_modules/cutadapt/test/trimming_paired.nf \
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/test/trimming_single.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"
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