Reverted hifiasm from main

software/hifiasm/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/hifiasm/main.nf

@@ -1,52 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-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:'') } // publish_id:meta.id) }
-
-    conda (params.enable_conda ? "bioconda::hifiasm=0.14" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/hifiasm:0.14--h8b12597_0"
-    } else {
-        container "quay.io/biocontainers/hifiasm:0.14--h8b12597_0"
-    }
-
-/*     input:
-    tuple val(meta), path(reads) */
-
-    output:
-/*     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) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
-        fastqc --version | sed -e "s/FastQC v//g" > ${software}.version.txt
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        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
-    """
-}

software/hifiasm/meta.yml

@@ -1,69 +0,0 @@
-name: hifiasm
-description: Run hifiasm on Pacbio HiFi reads
-keywords:
-    - genome assembly
-    - pacbaio
-    - hifi
-    - long reads
-    - fastq
-tools:
-    - hifiasm:
-        description: |
-            hifiasm generates a genome assembly from long Pacbio HiFi reads. ...Haplotype resolution ...Using short reads.
-        homepage: https://github.com/chhylp123/hifiasm
-        documentation: https://github.com/chhylp123/hifiasm
-params:
-    - outdir:
-        type: string
-        description: |
-            The pipeline's output directory. By default, the module will
-            output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-            Value for the Nextflow `publishDir` mode parameter.
-            Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-            Run the module with Conda using the software specified
-            via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-            Instead of directly downloading Singularity images for use with Singularity,
-            force the workflow to pull and convert Docker containers instead.
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - reads:
-        type: file
-        description: |
-            List of input FastQ files of size 1 and 2 for single-end and paired-end data,
-            respectively.
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - html:
-        type: file
-        description: FastQC report
-        pattern: "*_{fastqc.html}"
-    - zip:
-        type: file
-        description: FastQC report archive
-        pattern: "*_{fastqc.zip}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
-authors:
-    - "@drpatelh"
-    - "@grst"
-    - "@ewels"
-    - "@FelixKrueger"

tests/software/hifiasm/main.nf

@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HIFIASM } from '../../../software/hifiasm/main.nf' addParams( options: [:] )
-
-/* 
- * Test with single-end data
- */
-/* workflow test_fastqc_single_end {
-
-    def input = []
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
-    FASTQC ( input )
-} */
-
-/*
- * Test version printing
- */
-workflow test_hifiasm_version {
-
-/*     def input = []
-    input = [[id: 'test', single_end: false], // meta map
-             [file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
-              file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true)]] */
-    HIFIASM ()
-}

tests/software/hifiasm/test.yml

@@ -1,7 +0,0 @@
-- name: hifiasm 
-  command: nextflow run ./tests/software/hifiasm -entry test_hifiasm_version -c tests/config/nextflow.config
-  tags:
-    - hifiasm
-    - hifiasm_version
-  files:
-    - path: ./output/hifiasm/hifiasm.version.txt