diff --git a/conf/test.config b/conf/test.config index 734ff99..a06664f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,6 +24,7 @@ params { max_time = '6.h' outputDir = "test_output" + fastp_path = null } diff --git a/modules/fastp.nf b/modules/fastp.nf index e401773..fb38b1f 100644 --- a/modules/fastp.nf +++ b/modules/fastp.nf @@ -14,6 +14,7 @@ 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 @@ -24,7 +25,7 @@ process fastp { echo \${trim_polyg} | awk '{ if (length(\$1)>0) { print "2-color instrument: poly-g trim mode on" } }' samtools fastq -n ${bam} | \\ - fastp --stdin \\ + ${fastp_path}fastp --stdin \\ -l 2 -Q \${trim_polyg} \\ --thread 1 \\ --overrepresentation_analysis \\