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
This commit is contained in:
Jose Espinosa-Carrasco 2021-03-15 13:16:43 +01:00 committed by GitHub
parent 0218824b86
commit 572abb00b3
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
115 changed files with 166 additions and 438 deletions

4
.github/filters.yml vendored
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@ -309,10 +309,6 @@ tiddit_sv:
- software/tiddit/sv/** - software/tiddit/sv/**
- tests/software/tiddit/sv/** - tests/software/tiddit/sv/**
tool_subtool:
- software/TOOL/SUBTOOL/**
- tests/software/TOOL/SUBTOOL/**
trimgalore: trimgalore:
- software/trimgalore/** - software/trimgalore/**
- tests/software/trimgalore/** - tests/software/trimgalore/**

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@ -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"
}
}
}

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@ -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
"""
}

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@ -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"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

View file

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

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

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