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Unverified Commit 209cb4b1 authored by Laurent Modolo's avatar Laurent Modolo
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nf_modules: add DSL2 module for bowtie2

parent 9b4d697a
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bowtie_version = "2.3.4.1"
container_url = "lbmc/bowtie2:${bowtie_version}"
process index_fasta {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$fasta.baseName"
publishDir "results/mapping/index/", mode: 'copy'
input:
path fasta
output:
path "*.index*", emit: index
path "*_report.txt", emit: report
script:
"""
bowtie2-build --threads ${task.cpus} \
${fasta} \
${fasta.baseName}.index &> \
${fasta.baseName}_bowtie2_index_report.txt
if grep -q "Error" ${fasta.baseName}_bowtie2_index_report.txt; then
exit 1
fi
"""
}
process mapping_fastq_pairedend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
publishDir "results/mapping/bams/", mode: 'copy'
input:
tuple val(pair_id), path(reads)
path index.collect()
output:
tuple val(pair_id), path("*.bam"), emit: bam
path "*_report.txt", emit: report
script:
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
"""
bowtie2 --very-sensitive \
-p ${task.cpus} \
-x ${index_id} \
-1 ${reads[0]} \
-2 ${reads[1]} 2> \
${pair_id}_bowtie2_mapping_report_tmp.txt | \
samtools view -Sb - > ${pair_id}.bam
if grep -q "Error" ${pair_id}_bowtie2_mapping_report_tmp.txt; then
exit 1
fi
tail -n 19 ${pair_id}_bowtie2_mapping_report_tmp.txt > \
${pair_id}_bowtie2_mapping_report.txt
"""
}
process mapping_fastq_singleend {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
publishDir "results/mapping/bams/", mode: 'copy'
input:
tuple val(file_id), path(reads)
path index.collect()
output:
set file_id, "*.bam", emit: bam
file "*_report.txt", emit: report
script:
index_id = index[0]
for (index_file in index) {
if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
}
}
"""
bowtie2 --very-sensitive \
-p ${task.cpus} \
-x ${index_id} \
-U ${reads} 2> \
${file_id}_bowtie2_mapping_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
if grep -q "Error" ${file_id}_bowtie2_mapping_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_id}_bowtie2_mapping_report_tmp.txt > \
${file_id}_bowtie2_mapping_report.txt
"""
}
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