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Verified Commit b867bf9a authored by Laurent Modolo's avatar Laurent Modolo
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bowtie: update to match CONTRIBUTING.md

parent 1f72b2c4
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......@@ -2,17 +2,21 @@ version = "1.2.2"
container_url = "lbmc/bowtie:${version}"
params.index_fasta = ""
params.index_fasta_out = ""
process index_fasta {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$fasta.baseName"
tag "$file_id"
if (params.index_fasta_out != "") {
publishDir "results/${params.index_fasta_out}", mode: 'copy'
}
input:
path fasta
tuple val(file_id), path(fasta)
output:
path "*.index*", emit: index
path "*_report.txt", emit: report
tuple val(file_id), path("*.index*"), emit: index
tuple val(file_id), path("*_report.txt"), emit: report
script:
"""
......@@ -27,57 +31,66 @@ fi
"""
}
params.mapping_fastq = ""
params.mapping_fastq = "--very-sensitive"
params.mapping_fastq_out = ""
process mapping_fastq {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$pair_id"
if (params.mapping_fastq_out != "") {
publishDir "results/${params.mapping_fastq_out}", mode: 'copy'
}
input:
path index
tuple val(pair_id), path(reads)
tuple val(index_id), path(index)
tuple val(file_id), path(reads)
output:
tuple val(pair_id), path("*.bam"), emit: bam
tuple val(file_id), path("*.bam"), emit: bam
path "*_report.txt", emit: report
script:
if (file_id instanceof List){
file_prefix = file_id[0]
} else {
file_prefix = file_id
}
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]
}
}
if (reads instanceof List)
"""
# -v specify the max number of missmatch, -k the number of match reported per
# reads
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${pair_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${pair_id}.bam
if grep -q "Error" ${pair_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${pair_id}_bowtie_report_tmp.txt > \
${pair_id}_bowtie_mapping_report.txt
"""
else
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq}
-q ${reads} 2> \
${file_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
${file_id}_bowtie_mapping_report.txt
"""
if (reads.size() == 2)
"""
# -v specify the max number of missmatch, -k the number of match reported per
# reads
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq} \
-1 ${reads[0]} -2 ${reads[1]} 2> \
${file_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
${file_id}_bowtie_mapping_report.txt
"""
else if (reads.size() == 1)
"""
bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
${params.mapping_fastq}
-q ${reads} 2> \
${file_id}_bowtie_report_tmp.txt | \
samtools view -Sb - > ${file_id}.bam
if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_id}_bowtie_report_tmp.txt > \
${file_id}_bowtie_mapping_report.txt
"""
}
params.mapping_fastq_pairedend = ""
......
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