diff --git a/src/.docker_modules/fastp/0.20.1/Dockerfile b/src/.docker_modules/fastp/0.20.1/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..0461d5ea260b3e894af982a27d1dc8d3b2860c16 --- /dev/null +++ b/src/.docker_modules/fastp/0.20.1/Dockerfile @@ -0,0 +1,2 @@ +FROM quay.io/biocontainers/fastp:0.20.1--h8b12597_0 +MAINTAINER Laurent Modolo diff --git a/src/.docker_modules/fastp/0.20.1/docker_init.sh b/src/.docker_modules/fastp/0.20.1/docker_init.sh new file mode 100755 index 0000000000000000000000000000000000000000..2b1f3bee40fb05504488fe026ff39811f9fef47d --- /dev/null +++ b/src/.docker_modules/fastp/0.20.1/docker_init.sh @@ -0,0 +1,4 @@ +#!/bin/sh +docker pull lbmc/fastp:0.20.1 +docker build src/.docker_modules/fastp/0.20.1 -t 'lbmc/fastp:0.20.1' +docker push lbmc/fastp:0.20.1 diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..c69412e430ad59ad9b62718329771f64a928a190 --- /dev/null +++ b/src/nf_modules/fastp/main.nf @@ -0,0 +1,55 @@ +version = "0.20.1" +container_url = "lbmc/fastp:${version}" + + +process fastp_pairedend { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "$pair_id" + + input: + tuple val(pair_id), path(reads) + + output: + tuple val(pair_id), path("*.fastq.gz"), emit: fastq + tuple val(pair_id), path("*.{zip,html}"), emit: report + + script: +""" +fastp --thread ${task.cpus} \ +--qualified_quality_phred 20 \ +--disable_length_filtering \ +--detect_adapter_for_pe \ +--in1 ${reads[0]} \ +--in2 ${reads[1]} \ +--out1 ${pair_id}_R1_trim.fastq.gz \ +--out2 ${pair_id}_R2_trim.fastq.gz \ +--html ${pair_id}.html \ +--report_title ${pair_id} +""" +} + +process fastp_singleend { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "$pair_id" + + input: + tuple val(pair_id), path(reads) + + output: + tuple val(pair_id), path("*.fastq.gz"), emit: fastq + tuple val(pair_id), path("*.{zip,html}"), emit: report + + script: +""" +fastp --thread ${task.cpus} \ +--qualified_quality_phred 20 \ +--disable_length_filtering \ +--detect_adapter_for_pe \ +--in1 ${reads} \ +--out1 ${pair_id}_trim.fastq.gz \ +--html ${pair_id}.html \ +--report_title ${pair_id} +""" +}