feat: add module for seqkit stats (#1466)
Moritz E. Beber
2 years ago
committed by
GitHub
parent
fd5f6f5f4f
commit
0de6406217
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process SEQKIT_STATS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0':
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'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.tsv"), emit: stats
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: '--all'
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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seqkit stats \\
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--tabular \\
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$args \\
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$reads > '${prefix}.tsv'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seqkit: \$( seqkit version | sed 's/seqkit v//' )
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END_VERSIONS
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"""
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}
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name: "seqkit_stats"
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description: simple statistics of FASTA/Q files
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keywords:
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- seqkit
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- stats
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tools:
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- "seqkit":
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description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
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homepage: https://bioinf.shenwei.me/seqkit/usage/
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documentation: https://bioinf.shenwei.me/seqkit/usage/
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tool_dev_url: https://github.com/shenwei356/seqkit/
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doi: "10.1371/journal.pone.0163962"
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: >
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: >
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Either FASTA or FASTQ files.
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pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]"
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output:
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- meta:
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type: map
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description: >
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- stats:
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type: file
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description: >
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Tab-separated output file with basic sequence statistics.
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pattern: "*.tsv"
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authors:
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- "@Midnighter"
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@ -0,0 +1,58 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SEQKIT_STATS } from '../../../../modules/seqkit/stats/main.nf'
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workflow test_seqkit_stats_single_end {
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input = [
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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SEQKIT_STATS ( input )
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}
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workflow test_seqkit_stats_paired_end {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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SEQKIT_STATS ( input )
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}
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workflow test_seqkit_stats_nanopore {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
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]
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SEQKIT_STATS ( input )
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}
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workflow test_seqkit_stats_genome_fasta {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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]
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SEQKIT_STATS ( input )
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}
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workflow test_seqkit_stats_transcriptome_fasta {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true),
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]
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SEQKIT_STATS ( input )
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}
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@ -0,0 +1,5 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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@ -0,0 +1,54 @@
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- name: seqkit stats test_seqkit_stats_single_end
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command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_single_end -c tests/config/nextflow.config
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tags:
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- seqkit/stats
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- seqkit
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files:
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- path: output/seqkit/test.tsv
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md5sum: e23227d089a7e04b0ec0cb547c4aadff
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- path: output/seqkit/versions.yml
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md5sum: d67f0c16feb9df77b11f6c91bbdf9926
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- name: seqkit stats test_seqkit_stats_paired_end
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command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_paired_end -c tests/config/nextflow.config
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tags:
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- seqkit/stats
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- seqkit
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files:
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- path: output/seqkit/test.tsv
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md5sum: 9de20dc39fb01285e3f0c382fda9db52
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- path: output/seqkit/versions.yml
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md5sum: bd8881933b953d07f2600e2e6a88ebf3
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- name: seqkit stats test_seqkit_stats_nanopore
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command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_nanopore -c tests/config/nextflow.config
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tags:
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- seqkit/stats
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- seqkit
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files:
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- path: output/seqkit/test.tsv
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md5sum: 5da1709eb5ae64fa3b2d624bffe2e7aa
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- path: output/seqkit/versions.yml
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md5sum: 565632701fbe048f7ba99f1865bd48ca
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- name: seqkit stats test_seqkit_stats_genome_fasta
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command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_genome_fasta -c tests/config/nextflow.config
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tags:
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- seqkit/stats
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- seqkit
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files:
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- path: output/seqkit/test.tsv
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md5sum: f64489767a4e769539ef3faf83260184
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- path: output/seqkit/versions.yml
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md5sum: 782fcdeaa922c8bb532ffa5808849d87
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- name: seqkit stats test_seqkit_stats_transcriptome_fasta
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command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c tests/config/nextflow.config
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tags:
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- seqkit/stats
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- seqkit
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files:
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- path: output/seqkit/test.tsv
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md5sum: fbb975b665a08c8862fcd1268613a945
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- path: output/seqkit/versions.yml
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md5sum: db99b016d986d26102ec398264a58410
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