From b58233794b05b287d0887c6803c6c2f7abf10db4 Mon Sep 17 00:00:00 2001 From: Sviatoslav Sidorov Date: Tue, 16 Mar 2021 13:14:43 +0000 Subject: [PATCH] Add hifiasm version printing --- software/hifiasm/main.nf | 33 +++++++++++++++++++-------------- tests/software/hifiasm/test.yml | 4 ++-- 2 files changed, 21 insertions(+), 16 deletions(-) diff --git a/software/hifiasm/main.nf b/software/hifiasm/main.nf index 4e847876..7a364be2 100644 --- a/software/hifiasm/main.nf +++ b/software/hifiasm/main.nf @@ -4,33 +4,34 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] options = initOptions(params.options) -process FASTQC { - tag "$meta.id" - label 'process_medium' +process HIFIASM { + //tag "$meta.id" + label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } // publish_id:meta.id) } - conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null) + conda (params.enable_conda ? "bioconda::hifiasm=0.14" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { - container "https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0" + container "https://depot.galaxyproject.org/singularity/hifiasm:0.14--h8b12597_0" } else { - container "quay.io/biocontainers/fastqc:0.11.9--0" + container "quay.io/biocontainers/hifiasm:0.14--h8b12597_0" } - input: - tuple val(meta), path(reads) +/* input: + tuple val(meta), path(reads) */ output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip +/* tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip") , emit: zip */ path "*.version.txt" , emit: version script: // Add soft-links to original FastQs for consistent naming in pipeline def software = getSoftwareName(task.process) - def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" - if (meta.single_end) { + //def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" + +/* if (meta.single_end) { """ [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz @@ -43,5 +44,9 @@ process FASTQC { fastqc $options.args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt """ - } + } */ + + """ + hifiasm --version > ${software}.version.txt || exit 0 + """ } diff --git a/tests/software/hifiasm/test.yml b/tests/software/hifiasm/test.yml index 3825b238..e639f099 100644 --- a/tests/software/hifiasm/test.yml +++ b/tests/software/hifiasm/test.yml @@ -1,7 +1,7 @@ - name: hifiasm - command: nextflow run ./tests/software/hifiasm/ -entry test_hifiasm_version -c tests/config/nextflow.config + command: nextflow run ./tests/software/hifiasm -entry test_hifiasm_version -c tests/config/nextflow.config tags: - hifiasm - hifiasm_version files: - - path: ./output/hifiasm/VERSION.txt + - path: ./output/hifiasm/hifiasm.version.txt