From 4c59984d7bcc772598ba44fb8289051352c7a6c6 Mon Sep 17 00:00:00 2001 From: Sateesh <33637490+sateeshperi@users.noreply.github.com> Date: Thu, 24 Feb 2022 09:07:35 -0500 Subject: [PATCH] Seqkit pair (#1348) * add seqkit pair module * local tests * local tests * fix workflow name * fix workflow name * fix version indentation * fix version indentation * fix version indentation * fix review comments * fix review comments * fix github usernames * minor fix * add meta unpaired output Co-authored-by: Peri --- modules/seqkit/pair/main.nf | 40 +++++++++++++++++++ modules/seqkit/pair/meta.yml | 48 +++++++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/seqkit/pair/main.nf | 16 ++++++++ tests/modules/seqkit/pair/nextflow.config | 6 +++ tests/modules/seqkit/pair/test.yml | 12 ++++++ 6 files changed, 126 insertions(+) create mode 100644 modules/seqkit/pair/main.nf create mode 100644 modules/seqkit/pair/meta.yml create mode 100644 tests/modules/seqkit/pair/main.nf create mode 100644 tests/modules/seqkit/pair/nextflow.config create mode 100644 tests/modules/seqkit/pair/test.yml diff --git a/modules/seqkit/pair/main.nf b/modules/seqkit/pair/main.nf new file mode 100644 index 00000000..228b98bd --- /dev/null +++ b/modules/seqkit/pair/main.nf @@ -0,0 +1,40 @@ +process SEQKIT_PAIR { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::seqkit=2.1.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': + 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.paired.fastq.gz") , emit: reads + tuple val(meta), path("*.unpaired.fastq.gz"), optional: true, emit: unpaired_reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + seqkit \\ + pair \\ + -1 ${reads[0]} \\ + -2 ${reads[1]} \\ + $args \\ + --threads $task.cpus + + # gzip fastq + find . -maxdepth 1 -name "*.fastq" -exec gzip {} \; + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$( seqkit | sed '3!d; s/Version: //' ) + END_VERSIONS + """ +} diff --git a/modules/seqkit/pair/meta.yml b/modules/seqkit/pair/meta.yml new file mode 100644 index 00000000..3b35d908 --- /dev/null +++ b/modules/seqkit/pair/meta.yml @@ -0,0 +1,48 @@ +name: seqkit_pair +description: match up paired-end reads from two fastq files +keywords: + - seqkit + - pair +tools: + - seqkit: + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + homepage: https://bioinf.shenwei.me/seqkit/usage/ + documentation: https://bioinf.shenwei.me/seqkit/usage/ + tool_dev_url: https://github.com/shenwei356/seqkit/ + doi: "10.1371/journal.pone.0163962" + licence: ['MIT'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input paired-end FastQ files. + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - reads: + type: file + description: Paired fastq reads + pattern: "*.paired.fastq.gz" + - unpaired_reads: + type: file + description: Unpaired reads (optional) + pattern: "*.unpaired.fastq.gz" + +authors: + - "@sateeshperi" + - "@mjcipriano" + - "@hseabolt" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index cda6d98d..5ae30708 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1445,6 +1445,10 @@ seacr/callpeak: - modules/seacr/callpeak/** - tests/modules/seacr/callpeak/** +seqkit/pair: + - modules/seqkit/pair/** + - tests/modules/seqkit/pair/** + seqkit/split2: - modules/seqkit/split2/** - tests/modules/seqkit/split2/** diff --git a/tests/modules/seqkit/pair/main.nf b/tests/modules/seqkit/pair/main.nf new file mode 100644 index 00000000..42bc9587 --- /dev/null +++ b/tests/modules/seqkit/pair/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SEQKIT_PAIR } from '../../../../modules/seqkit/pair/main.nf' + +workflow test_seqkit_pair { + + input = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + + SEQKIT_PAIR ( input ) +} diff --git a/tests/modules/seqkit/pair/nextflow.config b/tests/modules/seqkit/pair/nextflow.config new file mode 100644 index 00000000..49de9240 --- /dev/null +++ b/tests/modules/seqkit/pair/nextflow.config @@ -0,0 +1,6 @@ +process { + + ext.args = "-u" + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/seqkit/pair/test.yml b/tests/modules/seqkit/pair/test.yml new file mode 100644 index 00000000..30373d69 --- /dev/null +++ b/tests/modules/seqkit/pair/test.yml @@ -0,0 +1,12 @@ +- name: seqkit pair test_seqkit_pair + command: nextflow run tests/modules/seqkit/pair -entry test_seqkit_pair -c tests/config/nextflow.config + tags: + - seqkit/pair + - seqkit + files: + - path: output/seqkit/test_1.paired.fastq.gz + md5sum: fbfe7e8bdbc29abaaf58b6f1a32448e5 + - path: output/seqkit/test_2.paired.fastq.gz + md5sum: 7d3c0912e5adc2674e8ecc1e647381b3 + - path: output/seqkit/versions.yml + md5sum: 3086293bc986fc2ece38b1951d090819