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Verified Commit fdb5acb8 authored by Laurent Modolo's avatar Laurent Modolo
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nf_modules: update last main.nf to change in CONTRIBUTING.md

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src/nf_modules/samtools/main.nf
+ 72
− 20
View file @ fdb5acb8
version = "1.11"
container_url = "lbmc/samtools:${version}"
params.index_fasta = ""
params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(fasta)
......@@ -13,16 +18,20 @@ process index_fasta {
script:
"""
samtools faidx ${fasta}
samtools faidx ${params.index_fasta} ${fasta}
"""
}
filter_bam_quality_threshold = 30
params.filter_bam_quality_threshold = 30
params.filter_bam_quality = "-q ${filter_bam_quality_threshold}"
params.filter_bam_quality_out = ""
process filter_bam_quality {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -31,16 +40,20 @@ process filter_bam_quality {
tuple val(file_id), path("*_filtered.bam"), emit: bam
script:
"""
samtools view -@ ${task.cpus} -hb ${bam} -q ${filter_bam_quality_threshold} > \
samtools view -@ ${task.cpus} -hb ${bam} ${params.filter_bam_quality} > \
${bam.simpleName}_filtered.bam
"""
}
params.filter_bam = ""
params.filter_bam_out = ""
process filter_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -50,11 +63,13 @@ process filter_bam {
tuple val(file_id), path("*_filtered.bam"), emit: bam
script:
"""
samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > \
samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} ${params.filter_bam} > \
${bam.simpleName}_filtered.bam
"""
}
params.filter_bam_mapped = "-F 4"
params.filter_bam_mapped_out = ""
process filter_bam_mapped {
container = "${container_url}"
label "big_mem_multi_cpus"
......@@ -67,15 +82,20 @@ process filter_bam_mapped {
tuple val(file_id), path("*_mapped.bam"), emit: bam
script:
"""
samtools view -@ ${task.cpus} -F 4 -hb ${bam} > \
samtools view -@ ${task.cpus} ${params.filter_bam_mapped} -hb ${bam} > \
${bam.simpleName}_mapped.bam
"""
}
params.filter_bam_unmapped = "-f 4"
params.filter_bam_unmapped_out = ""
process filter_bam_unmapped {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -84,11 +104,12 @@ process filter_bam_unmapped {
tuple val(file_id), path("*_unmapped.bam"), emit: bam
script:
"""
samtools view -@ ${task.cpus} -f 4 -hb ${bam} > ${bam.simpleName}_unmapped.bam
samtools view -@ ${task.cpus} ${params.filter_bam_unmapped} -hb ${bam} > ${bam.simpleName}_unmapped.bam
"""
}
params.index_bam = ""
params.index_bam_out = ""
process index_bam {
container = "${container_url}"
label "big_mem_mono_cpus"
......@@ -103,14 +124,19 @@ process index_bam {
script:
"""
samtools index ${bam}
samtools index ${params.index_bam} ${bam}
"""
}
params.sort_bam = ""
params.sort_bam_out = ""
process sort_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -120,15 +146,19 @@ process sort_bam {
script:
"""
samtools sort -@ ${task.cpus} -O BAM -o ${bam.simpleName}_sorted.bam ${bam}
samtools sort -@ ${task.cpus} ${params.sort_bam} -O BAM -o ${bam.simpleName}_sorted.bam ${bam}
"""
}
params.split_bam = ""
params.split_bam_out = ""
process split_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -138,19 +168,22 @@ process split_bam {
tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
script:
"""
samtools view --@ ${Math.round(task.cpus/2)} \
samtools view --@ ${Math.round(task.cpus/2)} ${params.split_bam} \
-hb -F 0x10 ${bam} > ${bam.simpleName}_forward.bam &
samtools view --@ ${Math.round(task.cpus/2)} \
samtools view --@ ${Math.round(task.cpus/2)} ${params.split_bam} \
-hb -f 0x10 ${bam} > ${bam.simpleName}_reverse.bam
"""
}
params.merge_bam = ""
params.merge_bam_out = ""
process merge_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
cpus = 2
if (params.mapping_fastq_out != "") {
publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(first_file_id), path(first_bam)
......@@ -160,16 +193,20 @@ process merge_bam {
tuple val(file_id), path("*.bam*"), emit: bam
script:
"""
samtools merge ${first_bam} ${second_bam} \
samtools merge -@ ${task.cpus} ${params.merge_bam} ${first_bam} ${second_bam} \
${first_bam.simpleName}_${second_file.simpleName}.bam
"""
}
params.merge_multi_bam = ""
params.merge_multi_bam_out = ""
process merge_multi_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
cpus = 2
if (params.mapping_fastq_out != "") {
publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bams)
......@@ -179,16 +216,21 @@ process merge_multi_bam {
script:
"""
samtools merge -@ ${task.cpus} \
${params.merge_multi_bam} \
${bams[0].simpleName}_merged.bam \
${bams}
"""
}
params.stats_bam = ""
params.stats_bam_out = ""
process stats_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
cpus = 2
if (params.mapping_fastq_out != "") {
publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(bam)
......@@ -197,12 +239,17 @@ process stats_bam {
tuple val(file_id), path("*.tsv"), emit: tsv
script:
"""
samtools flagstat -@ ${task.cpus} -O tsv ${bam} > ${bam.simpleName}_stats.tsv
samtools flagstat -@ ${task.cpus} ${params.stats_bam} -O tsv ${bam} > ${bam.simpleName}_stats.tsv
"""
}
params.flagstat_2_multiqc = ""
params.flagstat_2_multiqc_out = ""
process flagstat_2_multiqc {
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(tsv)
......@@ -214,8 +261,13 @@ mv ${tsv} ${tsv.simpleName}.flagstat.txt
"""
}
params.idxstat_2_multiqc = ""
params.idxstat_2_multiqc_out = ""
process idxstat_2_multiqc {
tag "$file_id"
if (params.mapping_fastq_out != "") {
publishdir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
tuple val(file_id), path(tsv)
......
src/nf_modules/sratoolkit/main.nf
+ 6
− 1
View file @ fdb5acb8
version = "2.8.2"
container_url = "lbmc/sratoolkit:${version}"
params.fastq_dump = ""
params.fastq_dump_out = ""
process fastq_dump {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "$sra"
if (params.fastq_dump_out != "") {
publishDir "results/${params.fastq_dump_out}", mode: 'copy'
}
input:
val sra
......@@ -14,7 +19,7 @@ process fastq_dump {
script:
"""
fastq-dump --split-files --gzip ${sra}
fastq-dump ${params.fastq_dump} --split-files --gzip ${sra}
if [ -f ${sra}_1.fastq ]
then
mv ${sra}_1.fastq ${sra}_R1.fastq
......
src/nf_modules/ucsc/main.nf
+ 4
− 0
View file @ fdb5acb8
......@@ -2,10 +2,14 @@ version = "407"
container_url = "lbmc/ucsc:${version}"
params.bedgraph_to_bigwig = ""
params.bedgraph_to_bigwig_out = ""
process bedgraph_to_bigwig {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${file_id}"
if (params.bedgraph_to_bigwig_out != "") {
publishDir "results/${params.bedgraph_to_bigwig_out}", mode: 'copy'
}
input:
tuple val(file_id) path(bg)
......
src/nf_modules/urqt/main.nf
+ 18
− 55
View file @ fdb5acb8
......@@ -3,74 +3,37 @@ container_url = "lbmc/urqt:${version}"
trim_quality = "20"
params.trimming = "--t 20"
process trimming {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "${reads}"
tag "${file_id}"
input:
tuple val(pair_id), path(reads)
output:
tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit: fastq
path "*_report.txt", emit: report
script:
if (reads instanceof List)
"""
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
"""
else
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads} \
--out ${file_id}_trim.fastq.gz \
> ${file_id}_trimming_report.txt
"""
}
process trimming_pairedend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "${reads}"
input:
tuple val(pair_id), path(reads)
tuple val(file_id), path(reads)
output:
tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit: fastq
path "*_report.txt", emit: report
script:
"""
UrQt --t 20 --m ${task.cpus} --gz \
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
if (reads.size() == 2)
"""
UrQt ${params.trimming} --m ${task.cpus} --gz \
--in ${reads[0]} --inpair ${reads[1]} \
--out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \
--out ${file_prefix}_trim_R1.fastq.gz --outpair ${file_prefix}_trim_R2.fastq.gz \
> ${pair_id}_trimming_report.txt
"""
}
process trimming_singleend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
input:
tuple val(file_id), path(reads)
output:
tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq
path "*_report.txt", emit: report
script:
else if (reads.size() == 1)
"""
UrQt --t 20 --m ${task.cpus} --gz \
--in ${reads} \
--out ${file_id}_trim.fastq.gz \
> ${file_id}_trimming_report.txt
UrQt ${params.trimming} --m ${task.cpus} --gz \
--in ${reads[0]} \
--out ${file_prefix}_trim.fastq.gz \
> ${file_prefix}_trimming_report.txt
"""
}
}
\ No newline at end of file
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