diff --git a/src/nf_modules/cutadapt/main.nf b/src/nf_modules/cutadapt/main.nf index 74c37be028cf23f8af64b4d9ff7efa492e9a8c19..0859ea9232e284713adaf19a69f8b96f4b7e760e 100644 --- a/src/nf_modules/cutadapt/main.nf +++ b/src/nf_modules/cutadapt/main.nf @@ -6,7 +6,7 @@ adapter_5_prim = "CTCTTCCGATCT" trim_quality = "20" -process adaptor_removal_paired { +process adaptor_removal_pairedend { container = "${container_url}" label "big_mem_mono_cpus" tag "$pair_id" diff --git a/src/nf_modules/urqt/main.nf b/src/nf_modules/urqt/main.nf new file mode 100644 index 0000000000000000000000000000000000000000..48a1a3ecb75a17ecab60dc0735df715afbf5ec9e --- /dev/null +++ b/src/nf_modules/urqt/main.nf @@ -0,0 +1,49 @@ +version = "d62c1f8" +container_url = "lbmc/urqt:${version}" + +trim_quality = "20" + +process trimming_pairedend { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "${reads}" + publishDir "results/fastq/trimming/", mode: 'copy' + + input: + tuple val(pair_id), path(reads) + + output: + tuple val(pair_id), path("*_trim_R{1,2}.fastq.gz"), emit: fastq + path "*_report.txt", emit: report + + script: +""" +UrQt --t 20 --m ${task.cpus} --gz \ + --in ${reads[0]} --inpair ${reads[1]} \ + --out ${pair_id}_trim_R1.fastq.gz --outpair ${pair_id}_trim_R2.fastq.gz \ + > ${pair_id}_trimming_report.txt +""" +} + +process trimming_singleend { + container = "${container_url}" + label "big_mem_multi_cpus" + tag "$file_id" + publishDir "results/fastq/trimming/", mode: 'copy' + + input: + tuple val(file_id), path(reads) + + output: + tuple val(file_id), path("*_trim.fastq.gz"), emit: fastq + path "*_report.txt", emit: report + + script: +""" +UrQt --t 20 --m ${task.cpus} --gz \ + --in ${reads} \ + --out ${file_id}_trim.fastq.gz \ + > ${file_id}_trimming_report.txt +""" +} +