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allowing retrieval of mask info
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lucacozzuto committed Mar 28, 2022
1 parent bdee0d3 commit 6f9be7a
Showing 1 changed file with 12 additions and 1 deletion.
13 changes: 12 additions & 1 deletion subworkflows/basecalling/bcl2fastq.nf
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ params.EXTRAPARS = ""
params.OUTPUTMODE = "copy"
params.OUTPUT = ""
params.CONTAINER = "centos:centos6.10"
params.PARSING = "false"


process getVersion {
Expand Down Expand Up @@ -41,18 +42,28 @@ process baseCall {
tuple val(idfile), path("${idfile}_ouput/Stats"), emit: statfolder

script:

def parsing_cmd = "par_cmd=''"

if (params.PARSING == "true") {
parsing_cmd = "par_cmd=`grep OverrideCycles ${samplesheet} | awk -F ',' '{print \"--use-bases-mask \" \$2 }' | sed s@';'@,@g`"
}

"""
bcl2fastq ${params.EXTRAPARS} --sample-sheet ${samplesheet} \
${parsing_cmd}
bcl2fastq ${params.EXTRAPARS} \$par_cmd --sample-sheet ${samplesheet} \
--output-dir ${idfile}_ouput \
--runfolder-dir ${infolder} \
-p ${task.cpus} -r ${task.cpus} -w ${task.cpus}
"""
}


workflow BASECALL {
take:
input_data


main:
baseCall(input_data)

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