Commit 8e6edae0 authored by Xavier Grand's avatar Xavier Grand
Browse files

Test ChIPseq CTCF

parent 50014602
......@@ -100,3 +100,73 @@ process mapping_fastq {
${file_prefix}_bowtie2_mapping_report.txt
"""
}
process mapping_fastq_chipster {
container = "${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(index_id), path(index)
tuple val(file_id), path(reads), val(condition), val(type)
output:
tuple val(file_id), path("*.bam"), val(condition), val(type), 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]
}
}
switch(file_id) {
case {it instanceof List}:
file_prefix = file_id[0]
break
case {it instanceof Map}:
file_prefix = file_id.values()[0]
break
default:
file_prefix = file_id
break
}
if (reads.size() == 2)
"""
bowtie2 ${params.mapping_fastq} \
-p ${task.cpus} \
-x ${index_id} \
-1 ${reads[0]} \
-2 ${reads[1]} 2> \
${file_prefix}_bowtie2_mapping_report_tmp.txt | \
samtools view -Sb - > ${file_prefix}.bam
if grep -q "Error" ${file_prefix}_bowtie2_mapping_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
${file_prefix}_bowtie2_mapping_report.txt
"""
else
"""
bowtie2 ${params.mapping_fastq} \
-p ${task.cpus} \
-x ${index_id} \
-U ${reads} 2> \
${file_prefix}_bowtie2_mapping_report_tmp.txt | \
samtools view -Sb - > ${file_prefix}.bam
if grep -q "Error" ${file_prefix}_bowtie2_mapping_report_tmp.txt; then
exit 1
fi
tail -n 19 ${file_prefix}_bowtie2_mapping_report_tmp.txt > \
${file_prefix}_bowtie2_mapping_report.txt
"""
}
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