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so RX tags are copied for UMIs #57

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1 change: 0 additions & 1 deletion conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ params {
max_time = '6.h'

outputDir = "test_output"
fastp_path = null

}

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7 changes: 3 additions & 4 deletions modules/fastp.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process fastp {
tag "${library}"
label 'low_cpu'
conda "bioconda::samtools=1.21 bioconda::fastp=1.0.1"
conda "bioconda::samtools=1.21 bioconda::fastp=1.1.0"
publishDir "${params.outputDir}/fastp"

input:
Expand All @@ -14,7 +14,6 @@ process fastp {
tuple val("${task.process}"), val('fastp'), eval('fastp --version 2>&1 | cut -f 2 -d " "'), topic: versions

script:
def fastp_path = params.fastp_path ? params.fastp_path : ''
def fastp_args = params.single_end ? "--out1 ${library}.1.trimmed.fastq.gz" : "--interleaved_in --out1 ${library}.1.trimmed.fastq.gz --out2 ${library}.2.trimmed.fastq.gz"
"""
set +o pipefail
Expand All @@ -24,8 +23,8 @@ process fastp {
trim_polyg=\$(echo "\${inst_name}" | awk '{if (\$1~/^A0|^NB|^NS|^VH/) {print "--trim_poly_g"} else {print ""}}')
echo \${trim_polyg} | awk '{ if (length(\$1)>0) { print "2-color instrument: poly-g trim mode on" } }'

samtools fastq -n ${bam} | \\
${fastp_path}fastp --stdin \\
samtools fastq -T RX -n ${bam} | \\
fastp --stdin \\
Comment on lines +26 to +27
-l 2 -Q \${trim_polyg} \\
--thread 1 \\
--overrepresentation_analysis \\
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