diff --git a/conf/test.config b/conf/test.config index a06664f..734ff99 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,7 +24,6 @@ params { max_time = '6.h' outputDir = "test_output" - fastp_path = null } diff --git a/modules/fastp.nf b/modules/fastp.nf index fb38b1f..c9a8ddf 100644 --- a/modules/fastp.nf +++ b/modules/fastp.nf @@ -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: @@ -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 @@ -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 \\ -l 2 -Q \${trim_polyg} \\ --thread 1 \\ --overrepresentation_analysis \\