diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf index 82f8d88062e982cd784f8673bc0267507dce3e69..267b7d86bff46ebb724709bbd3d253b2d6a26f0e 100644 --- a/src/nf_modules/fastp/main.nf +++ b/src/nf_modules/fastp/main.nf @@ -1,6 +1,10 @@ version = "0.20.1" container_url = "lbmc/fastp:${version}" +params.fastp = "" +params.fastp_pairedend = "" +params.fastp_singleend = "" + process fastp { container = "${container_url}" label "big_mem_multi_cpus" @@ -22,6 +26,7 @@ fastp --thread ${task.cpus} \ --qualified_quality_phred 20 \ --disable_length_filtering \ --detect_adapter_for_pe \ +${params.fastp} \ --in1 ${reads[0]} \ --in2 ${reads[1]} \ --out1 ${pair_id}_R1_trim.fastq.gz \ @@ -36,6 +41,7 @@ fastp --thread ${task.cpus} \ --qualified_quality_phred 20 \ --disable_length_filtering \ --detect_adapter_for_pe \ +${params.fastp} \ --in1 ${reads} \ --out1 ${pair_id}_trim.fastq.gz \ --html ${pair_id}.html \ @@ -64,6 +70,7 @@ fastp --thread ${task.cpus} \ --qualified_quality_phred 20 \ --disable_length_filtering \ --detect_adapter_for_pe \ +${params.fastp_pairedend} \ --in1 ${reads[0]} \ --in2 ${reads[1]} \ --out1 ${pair_id}_R1_trim.fastq.gz \ @@ -94,6 +101,7 @@ fastp --thread ${task.cpus} \ --qualified_quality_phred 20 \ --disable_length_filtering \ --detect_adapter_for_pe \ +${params.fastp_singleend} \ --in1 ${reads} \ --out1 ${pair_id}_trim.fastq.gz \ --html ${pair_id}.html \