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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

@bwlang bwlang May 27, 2026

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@lnblum this seems like a good thing to fix...

@lnblum lnblum May 27, 2026

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Probably the test is failing because the snapshot needs to be updated for the fastp version change (which gets us back to the bioconda fastp rather than our local install since the adapter dimer fix was merged). But I'm waiting on the bwameth change -- until then this UMI fix won't work and it breaks.

-l 2 -Q \${trim_polyg} \\
--thread 1 \\
--overrepresentation_analysis \\
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