Remove def from module options definition in main (#270)

* Remove def from module options definition in main

* Fix bismark_deduplicate tests

* Fix bwameth_align tests

* Fixing gatk4 conda tests ("=" instead of ':' in build id)

* Same as previous commit (Fix gatk4 test)

* Fix qualimap bamqc test (no md5 check for pngs)

* Fix seqkit split2 tests. Changed to new test data

* Fix samtools tests. Some were missing initOptions include

* Removing TOOL SUBTOOL template module since now it is included on tools repo

.github/filters.yml

@@ -309,10 +309,6 @@ tiddit_sv:
   - software/tiddit/sv/**
   - tests/software/tiddit/sv/**
 
-tool_subtool:
-  - software/TOOL/SUBTOOL/**
-  - tests/software/TOOL/SUBTOOL/**
-
 trimgalore:
   - software/trimgalore/**
   - tests/software/trimgalore/**

software/TOOL/SUBTOOL/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/TOOL/SUBTOOL/main.nf

@@ -1,90 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-// TODO nf-core: All of these TODO statements can be deleted after the relevant changes have been made.
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/software
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-
-// TODO nf-core: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119).
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided as a string i.e. "options.args"
-//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-// TODO nf-core: Process name MUST be all uppercase,
-//               "TOOL" and (ideally) "SUBTOOL" MUST be all one word separated by an "_".
-process TOOL_SUBTOOL {
-    // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section
-    //               change tag value to another appropriate input value e.g. tag "$fasta"
-    tag "$meta.id"
-    // TODO nf-core: Provide appropriate resource label for process as listed in the nf-core pipeline template below:
-    //               https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config#L29
-    label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section
-        //               change "publish_id:meta.id" to initialise an empty string e.g. "publish_id:''".
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
-
-    // TODO nf-core: List required Conda packages.
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be excluded to support installation on different OS.
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
-
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
-    } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
-    }
-
-    input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(bam)
-
-    output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    // TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version)
-    tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "*.version.txt"          , emit: version
-
-
-    script:
-    def software = getSoftwareName(task.process)
-    // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section delete the line below
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
-    """
-    samtools \\
-        sort \\
-        $options.args \\
-        -@ $task.cpus \\
-        -o ${prefix}.bam \\
-        -T $prefix \\
-        $bam
-
-    echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
-    """
-}

software/TOOL/SUBTOOL/meta.yml

@@ -1,72 +0,0 @@
-## TODO nf-core: Please delete all of these TODO statements once the file has been curated
-## TODO nf-core: Change the name of "tool_subtool" below
-name: tool_subtool
-## TODO nf-core: Add a description and keywords
-description: Sort SAM/BAM/CRAM file
-keywords:
-    - sort
-    - bam
-    - sam
-    - cram
-tools:
-    ## TODO nf-core: Change the name of the tool below
-    - samtools:
-        ## TODO nf-core: Add a description and other details for the software below
-        description: |
-            SAMtools is a set of utilities for interacting with and post-processing
-            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
-            These files are generated as output by short read aligners like BWA.
-        homepage: http://www.htslib.org/
-        documentation: http://www.htslib.org/doc/samtools.html
-        doi: 10.1093/bioinformatics/btp352
-## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below
-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.
-## TODO nf-core: Add a description of all of the variables used as input
-input:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bam:
-        type: file
-        description: BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-## TODO nf-core: Add a description of all of the variables used as output
-output:
-    - meta:
-        type: map
-        description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-    - bam:
-        type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
-## TODO nf-core: Add your GitHub username below
-authors:
-    - "@your_github_username"

software/bandage/image/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BANDAGE_IMAGE {
     tag "${meta.id}"

software/bcftools/consensus/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BCFTOOLS_CONSENSUS {
     tag "$meta.id"

software/bcftools/filter/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BCFTOOLS_FILTER {
     tag "$meta.id"

software/bcftools/isec/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BCFTOOLS_ISEC {
     tag "$meta.id"

software/bcftools/merge/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BCFTOOLS_MERGE {
     tag "$meta.id"

software/bcftools/mpileup/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BCFTOOLS_MPILEUP {
     tag "$meta.id"

software/bcftools/stats/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BCFTOOLS_STATS {
     tag "$meta.id"

software/bedtools/complement/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_COMPLEMENT {
     tag "$meta.id"

software/bedtools/genomecov/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_GENOMECOV {
     tag "$meta.id"

software/bedtools/getfasta/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_GETFASTA {
     tag "$bed"

software/bedtools/intersect/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_INTERSECT {
     tag "$meta.id"

software/bedtools/maskfasta/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_MASKFASTA {
     tag "$meta.id"

software/bedtools/merge/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_MERGE {
     tag "$meta.id"

software/bedtools/slop/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_SLOP {
     tag "$meta.id"

software/bedtools/sort/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BEDTOOLS_SORT {
     tag "$meta.id"

software/bismark/deduplicate/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BISMARK_DEDUPLICATE {
     tag "$meta.id"

software/bismark/genome_preparation/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BISMARK_GENOME_PREPARATION {
     tag "$fasta"

software/blast/blastn/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BLAST_BLASTN {
     tag "$meta.id"

software/blast/makeblastdb/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BLAST_MAKEBLASTDB {
     tag "$fasta"

software/bowtie/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BOWTIE_ALIGN {
     tag "$meta.id"

software/bowtie/build/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BOWTIE_BUILD {
     tag "$fasta"

software/bowtie2/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BOWTIE2_ALIGN {
     tag "$meta.id"

software/bowtie2/build/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BOWTIE2_BUILD {
     tag "$fasta"

software/bwa/index/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWA_INDEX {
     tag "$fasta"

software/bwa/mem/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWA_MEM {
     tag "$meta.id"

software/bwamem2/index/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWAMEM2_INDEX {
     tag "$fasta"

software/bwamem2/mem/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWAMEM2_MEM {
     tag "$meta.id"

software/bwameth/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWAMETH_ALIGN {
     tag "$meta.id"

software/bwameth/index/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process BWAMETH_INDEX {
     tag "$fasta"

software/cat/fastq/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process CAT_FASTQ {
     tag "$meta.id"

software/cutadapt/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process CUTADAPT {
     tag "$meta.id"

software/deeptools/computematrix/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process DEEPTOOLS_COMPUTEMATRIX {
     tag "$meta.id"

software/deeptools/plotfingerprint/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process DEEPTOOLS_PLOTFINGERPRINT {
     tag "$meta.id"

software/deeptools/plotheatmap/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process DEEPTOOLS_PLOTHEATMAP {
     tag "$meta.id"

software/deeptools/plotprofile/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process DEEPTOOLS_PLOTPROFILE {
     tag "$meta.id"

software/dsh/filterbed/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process DSH_FILTERBED {
     tag "${meta.id}"

software/dsh/splitbed/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process DSH_SPLITBED {
     tag "${meta.id}"

software/fastp/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process FASTP {
     tag "$meta.id"

software/fastqc/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process FASTQC {
     tag "$meta.id"

software/gatk4/bedtointervallist/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_BEDTOINTERVALLIST {
     tag "$meta.id"
@@ -11,7 +11,7 @@ process GATK4_BEDTOINTERVALLIST {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
     } else {

software/gatk4/createsequencedictionary/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"

software/gatk4/mergevcfs/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_MERGEVCFS {
     tag "$meta.id"
@@ -11,7 +11,7 @@ process GATK4_MERGEVCFS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
     } else {

software/gatk4/revertsam/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_REVERTSAM {
     tag "$meta.id"
@@ -11,7 +11,7 @@ process GATK4_REVERTSAM {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
     } else {

software/gatk4/samtofastq/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_SAMTOFASTQ {
     tag "$meta.id"
@@ -11,7 +11,7 @@ process GATK4_SAMTOFASTQ {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
     } else {

software/gatk4/splitncigarreads/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GATK4_SPLITNCIGARREADS {
     tag "$meta.id"
@@ -11,7 +11,7 @@ process GATK4_SPLITNCIGARREADS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null)
+    conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0'
     } else {

software/gffread/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GFFREAD {
     tag "$gff"

software/gunzip/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process GUNZIP {
     tag "$archive"

software/hisat2/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 def VERSION = '2.2.0'
 

software/hisat2/build/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 def VERSION = '2.2.0'
 

software/hisat2/extractsplicesites/main.nf

@@ -2,6 +2,7 @@
 include { saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 def VERSION = '2.2.0'
 

software/homer/annotatepeaks/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 def VERSION = '4.11'
 

software/ivar/consensus/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process IVAR_CONSENSUS {
     tag "$meta.id"

software/ivar/trim/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process IVAR_TRIM {
     tag "$meta.id"

software/ivar/variants/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process IVAR_VARIANTS {
     tag "$meta.id"

software/macs2/callpeak/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process MACS2_CALLPEAK {
     tag "$meta.id"

software/methyldackel/extract/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process METHYLDACKEL_EXTRACT {
     tag "$meta.id"

software/methyldackel/mbias/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process METHYLDACKEL_MBIAS {
     tag "$meta.id"

software/minimap2/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options = initOptions(params.options)
+options        = initOptions(params.options)
 
 process MINIMAP2_ALIGN {
     tag "$meta.id"

software/mosdepth/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process MOSDEPTH {
     tag "$meta.id"

software/multiqc/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process MULTIQC {
     label 'process_medium'

software/pangolin/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process PANGOLIN {
     tag "$meta.id"

software/phantompeakqualtools/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 def VERSION = '1.2.2'
 

software/picard/collectmultiplemetrics/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"

software/picard/markduplicates/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process PICARD_MARKDUPLICATES {
     tag "$meta.id"

software/picard/mergesamfiles/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process PICARD_MERGESAMFILES {
     tag "$meta.id"

software/preseq/lcextrap/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process PRESEQ_LCEXTRAP {
     tag "$meta.id"

software/qualimap/bamqc/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process QUALIMAP_BAMQC {
     tag "$meta.id"

software/qualimap/rnaseq/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process QUALIMAP_RNASEQ {
     tag "$meta.id"

software/quast/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process QUAST {
     label 'process_medium'

software/rsem/calculateexpression/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEM_CALCULATEEXPRESSION {
     tag "$meta.id"

software/rsem/preparereference/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEM_PREPAREREFERENCE {
     tag "$fasta"

software/rseqc/bamstat/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_BAMSTAT {
     tag "$meta.id"

software/rseqc/inferexperiment/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_INFEREXPERIMENT {
     tag "$meta.id"

software/rseqc/innerdistance/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_INNERDISTANCE {
     tag "$meta.id"

software/rseqc/junctionannotation/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_JUNCTIONANNOTATION {
     tag "$meta.id"

software/rseqc/junctionsaturation/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_JUNCTIONSATURATION {
     tag "$meta.id"

software/rseqc/readdistribution/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_READDISTRIBUTION {
     tag "$meta.id"

software/rseqc/readduplication/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process RSEQC_READDUPLICATION {
     tag "$meta.id"

software/salmon/index/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SALMON_INDEX {
     tag "$transcript_fasta"

software/salmon/quant/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SALMON_QUANT {
     tag "$meta.id"

software/samtools/faidx/main.nf

@@ -1,7 +1,8 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_FAIDX {
     tag "$fasta"

software/samtools/flagstat/main.nf

@@ -1,7 +1,8 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"

software/samtools/idxstats/main.nf

@@ -1,7 +1,8 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_IDXSTATS {
     tag "$meta.id"

software/samtools/index/main.nf

@@ -1,7 +1,8 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_INDEX {
     tag "$meta.id"

software/samtools/mpileup/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SAMTOOLS_MPILEUP {
     tag "$meta.id"

software/samtools/sort/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SAMTOOLS_SORT {
     tag "$meta.id"

software/samtools/stats/main.nf

@@ -1,7 +1,8 @@
 // Import generic module functions
-include { saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
+options        = initOptions(params.options)
 
 process SAMTOOLS_STATS {
     tag "$meta.id"

software/samtools/view/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SAMTOOLS_VIEW {
     tag "$meta.id"

software/seacr/callpeak/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 def VERSION = '1.3'
 

software/seqkit/split2/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SEQKIT_SPLIT2 {
     tag "$meta.id"

software/seqwish/induce/main.nf

@@ -1,7 +1,7 @@
 // Import generic module functions
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 def VERSION = '0.4.1'
 

software/sortmerna/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SORTMERNA {
     tag "$meta.id"

software/star/align/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process STAR_ALIGN {
     tag "$meta.id"

software/star/genomegenerate/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process STAR_GENOMEGENERATE {
     tag "$fasta"

software/stringtie/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process STRINGTIE {
     tag "$meta.id"

software/subread/featurecounts/main.nf

@@ -2,7 +2,7 @@
 include { initOptions; saveFiles; getSoftwareName } from './functions'
 
 params.options = [:]
-def options    = initOptions(params.options)
+options        = initOptions(params.options)
 
 process SUBREAD_FEATURECOUNTS {
     tag "$meta.id"