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Verified Commit d69ff6ea authored by Laurent Modolo's avatar Laurent Modolo
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cutadapt: fix typo :34

parent 18e214ae
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...@@ -19,18 +19,19 @@ process adaptor_removal { ...@@ -19,18 +19,19 @@ process adaptor_removal {
path "*_report.txt", emit: report path "*_report.txt", emit: report
script: script:
if (reads instanceof List) { if (reads instanceof List) {
""" """
cutadapt ${params.adaptor_removal} \ cutadapt ${params.adaptor_removal} \
-o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \ -o ${pair_id}_cut_R1.fastq.gz -p ${pair_id}_cut_R2.fastq.gz \
${reads[0]} ${reads[1]} > ${pair_id}_report.txt ${reads[0]} ${reads[1]} > ${pair_id}_report.txt
""" """
} else { } else {
""" """
cutadapt ${params.adaptor_removal} \ cutadapt ${params.adaptor_removal} \
-o ${file_id}_cut.fastq.gz \ -o ${file_id}_cut.fastq.gz \
${reads} > ${file_id}_report.txt ${reads} > ${file_id}_report.txt
""" """
}
} }
params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}" params.adaptor_removal_pairedend = "-a ${adapter_3_prim} -g ${adapter_5_prim} -A ${adapter_3_prim} -G ${adapter_5_prim}"
......
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