From 572abb00b3b2e1e6c61e02b1ad1b31bd65d03f70 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 15 Mar 2021 13:16:43 +0100 Subject: [PATCH] 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 | 4 - software/TOOL/SUBTOOL/functions.nf | 59 ------------ software/TOOL/SUBTOOL/main.nf | 90 ------------------- software/TOOL/SUBTOOL/meta.yml | 72 --------------- software/bandage/image/main.nf | 2 +- software/bcftools/consensus/main.nf | 2 +- software/bcftools/filter/main.nf | 2 +- software/bcftools/isec/main.nf | 2 +- software/bcftools/merge/main.nf | 2 +- software/bcftools/mpileup/main.nf | 2 +- software/bcftools/stats/main.nf | 2 +- software/bedtools/complement/main.nf | 2 +- software/bedtools/genomecov/main.nf | 2 +- software/bedtools/getfasta/main.nf | 2 +- software/bedtools/intersect/main.nf | 2 +- software/bedtools/maskfasta/main.nf | 2 +- software/bedtools/merge/main.nf | 2 +- software/bedtools/slop/main.nf | 2 +- software/bedtools/sort/main.nf | 2 +- software/bismark/deduplicate/main.nf | 2 +- software/bismark/genome_preparation/main.nf | 2 +- software/blast/blastn/main.nf | 2 +- software/blast/makeblastdb/main.nf | 2 +- software/bowtie/align/main.nf | 2 +- software/bowtie/build/main.nf | 2 +- software/bowtie2/align/main.nf | 2 +- software/bowtie2/build/main.nf | 2 +- software/bwa/index/main.nf | 2 +- software/bwa/mem/main.nf | 2 +- software/bwamem2/index/main.nf | 2 +- software/bwamem2/mem/main.nf | 2 +- software/bwameth/align/main.nf | 2 +- software/bwameth/index/main.nf | 2 +- software/cat/fastq/main.nf | 2 +- software/cutadapt/main.nf | 2 +- software/deeptools/computematrix/main.nf | 2 +- software/deeptools/plotfingerprint/main.nf | 2 +- software/deeptools/plotheatmap/main.nf | 2 +- software/deeptools/plotprofile/main.nf | 2 +- software/dsh/filterbed/main.nf | 2 +- software/dsh/splitbed/main.nf | 2 +- software/fastp/main.nf | 2 +- software/fastqc/main.nf | 2 +- software/gatk4/bedtointervallist/main.nf | 4 +- .../gatk4/createsequencedictionary/main.nf | 2 +- software/gatk4/mergevcfs/main.nf | 4 +- software/gatk4/revertsam/main.nf | 4 +- software/gatk4/samtofastq/main.nf | 4 +- software/gatk4/splitncigarreads/main.nf | 4 +- software/gffread/main.nf | 2 +- software/gunzip/main.nf | 2 +- software/hisat2/align/main.nf | 2 +- software/hisat2/build/main.nf | 2 +- software/hisat2/extractsplicesites/main.nf | 1 + software/homer/annotatepeaks/main.nf | 2 +- software/ivar/consensus/main.nf | 2 +- software/ivar/trim/main.nf | 2 +- software/ivar/variants/main.nf | 2 +- software/macs2/callpeak/main.nf | 2 +- software/methyldackel/extract/main.nf | 2 +- software/methyldackel/mbias/main.nf | 2 +- software/minimap2/align/main.nf | 2 +- software/mosdepth/main.nf | 2 +- software/multiqc/main.nf | 2 +- software/pangolin/main.nf | 2 +- software/phantompeakqualtools/main.nf | 2 +- .../picard/collectmultiplemetrics/main.nf | 2 +- software/picard/markduplicates/main.nf | 2 +- software/picard/mergesamfiles/main.nf | 2 +- software/preseq/lcextrap/main.nf | 2 +- software/qualimap/bamqc/main.nf | 2 +- software/qualimap/rnaseq/main.nf | 2 +- software/quast/main.nf | 2 +- software/rsem/calculateexpression/main.nf | 2 +- software/rsem/preparereference/main.nf | 2 +- software/rseqc/bamstat/main.nf | 2 +- software/rseqc/inferexperiment/main.nf | 2 +- software/rseqc/innerdistance/main.nf | 2 +- software/rseqc/junctionannotation/main.nf | 2 +- software/rseqc/junctionsaturation/main.nf | 2 +- software/rseqc/readdistribution/main.nf | 2 +- software/rseqc/readduplication/main.nf | 2 +- software/salmon/index/main.nf | 2 +- software/salmon/quant/main.nf | 2 +- software/samtools/faidx/main.nf | 3 +- software/samtools/flagstat/main.nf | 3 +- software/samtools/idxstats/main.nf | 3 +- software/samtools/index/main.nf | 3 +- software/samtools/mpileup/main.nf | 2 +- software/samtools/sort/main.nf | 2 +- software/samtools/stats/main.nf | 3 +- software/samtools/view/main.nf | 2 +- software/seacr/callpeak/main.nf | 2 +- software/seqkit/split2/main.nf | 2 +- software/seqwish/induce/main.nf | 2 +- software/sortmerna/main.nf | 2 +- software/star/align/main.nf | 2 +- software/star/genomegenerate/main.nf | 2 +- software/stringtie/main.nf | 2 +- software/subread/featurecounts/main.nf | 2 +- software/tabix/bgzip/main.nf | 2 +- software/tabix/tabix/main.nf | 2 +- software/tiddit/sv/main.nf | 2 +- software/trimgalore/main.nf | 2 +- software/ucsc/bedgraphtobigwig/main.nf | 2 +- software/umitools/dedup/main.nf | 2 +- software/umitools/extract/main.nf | 2 +- software/untar/main.nf | 2 +- tests/software/TOOL/SUBTOOL/main.nf | 13 --- tests/software/TOOL/SUBTOOL/test.yml | 8 -- tests/software/bismark/deduplicate/test.yml | 1 - tests/software/bwameth/align/test.yml | 3 +- tests/software/qualimap/bamqc/test.yml | 24 ----- tests/software/seqkit/split2/main.nf | 18 ++-- tests/software/seqkit/split2/test.yml | 90 +++++++++---------- 115 files changed, 166 insertions(+), 438 deletions(-) delete mode 100644 software/TOOL/SUBTOOL/functions.nf delete mode 100644 software/TOOL/SUBTOOL/main.nf delete mode 100644 software/TOOL/SUBTOOL/meta.yml delete mode 100644 tests/software/TOOL/SUBTOOL/main.nf delete mode 100644 tests/software/TOOL/SUBTOOL/test.yml diff --git a/.github/filters.yml b/.github/filters.yml index b960d2b3..81b118c0 100644 --- a/.github/filters.yml +++ b/.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/** diff --git a/software/TOOL/SUBTOOL/functions.nf b/software/TOOL/SUBTOOL/functions.nf deleted file mode 100644 index d25eea86..00000000 --- a/software/TOOL/SUBTOOL/functions.nf +++ /dev/null @@ -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" - } - } -} diff --git a/software/TOOL/SUBTOOL/main.nf b/software/TOOL/SUBTOOL/main.nf deleted file mode 100644 index 8619655c..00000000 --- a/software/TOOL/SUBTOOL/main.nf +++ /dev/null @@ -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.*\$//' > ${software}.version.txt - """ -} diff --git a/software/TOOL/SUBTOOL/meta.yml b/software/TOOL/SUBTOOL/meta.yml deleted file mode 100644 index 111c30da..00000000 --- a/software/TOOL/SUBTOOL/meta.yml +++ /dev/null @@ -1,72 +0,0 @@ -## TODO nf-core: Please delete all of these TODO statements once the file has been curated -## TODO nf-core: Change the name of "tool_subtool" below -name: tool_subtool -## TODO nf-core: Add a description and keywords -description: Sort SAM/BAM/CRAM file -keywords: - - sort - - bam - - sam - - cram -tools: - ## TODO nf-core: Change the name of the tool below - - samtools: - ## TODO nf-core: Add a description and other details for the software below - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: http://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 -## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below -params: - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - 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" diff --git a/software/bandage/image/main.nf b/software/bandage/image/main.nf index 7f311746..f4547f21 100644 --- a/software/bandage/image/main.nf +++ b/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 "${meta.id}" diff --git a/software/bcftools/consensus/main.nf b/software/bcftools/consensus/main.nf index 2a15136c..213655fa 100644 --- a/software/bcftools/consensus/main.nf +++ b/software/bcftools/consensus/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BCFTOOLS_CONSENSUS { tag "$meta.id" diff --git a/software/bcftools/filter/main.nf b/software/bcftools/filter/main.nf index b8d658dc..070b3e99 100644 --- a/software/bcftools/filter/main.nf +++ b/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 "$meta.id" diff --git a/software/bcftools/isec/main.nf b/software/bcftools/isec/main.nf index e5a15072..b7be2fe4 100644 --- a/software/bcftools/isec/main.nf +++ b/software/bcftools/isec/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BCFTOOLS_ISEC { tag "$meta.id" diff --git a/software/bcftools/merge/main.nf b/software/bcftools/merge/main.nf index 57bffb5b..52ca4513 100644 --- a/software/bcftools/merge/main.nf +++ b/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 "$meta.id" diff --git a/software/bcftools/mpileup/main.nf b/software/bcftools/mpileup/main.nf index 413a2cc5..f09630dc 100644 --- a/software/bcftools/mpileup/main.nf +++ b/software/bcftools/mpileup/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BCFTOOLS_MPILEUP { tag "$meta.id" diff --git a/software/bcftools/stats/main.nf b/software/bcftools/stats/main.nf index ace1d86b..fd36495f 100644 --- a/software/bcftools/stats/main.nf +++ b/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 "$meta.id" diff --git a/software/bedtools/complement/main.nf b/software/bedtools/complement/main.nf index b3433ed7..ab9f1008 100644 --- a/software/bedtools/complement/main.nf +++ b/software/bedtools/complement/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BEDTOOLS_COMPLEMENT { tag "$meta.id" diff --git a/software/bedtools/genomecov/main.nf b/software/bedtools/genomecov/main.nf index 75c0586d..1244e130 100644 --- a/software/bedtools/genomecov/main.nf +++ b/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 "$meta.id" diff --git a/software/bedtools/getfasta/main.nf b/software/bedtools/getfasta/main.nf index a0218ee7..1818b37c 100644 --- a/software/bedtools/getfasta/main.nf +++ b/software/bedtools/getfasta/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BEDTOOLS_GETFASTA { tag "$bed" diff --git a/software/bedtools/intersect/main.nf b/software/bedtools/intersect/main.nf index b45f08af..d779972d 100644 --- a/software/bedtools/intersect/main.nf +++ b/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 "$meta.id" diff --git a/software/bedtools/maskfasta/main.nf b/software/bedtools/maskfasta/main.nf index ccd93df7..6afef67f 100644 --- a/software/bedtools/maskfasta/main.nf +++ b/software/bedtools/maskfasta/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BEDTOOLS_MASKFASTA { tag "$meta.id" diff --git a/software/bedtools/merge/main.nf b/software/bedtools/merge/main.nf index 307873ce..3b668c13 100644 --- a/software/bedtools/merge/main.nf +++ b/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 "$meta.id" diff --git a/software/bedtools/slop/main.nf b/software/bedtools/slop/main.nf index a2e7844e..dc783efa 100644 --- a/software/bedtools/slop/main.nf +++ b/software/bedtools/slop/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BEDTOOLS_SLOP { tag "$meta.id" diff --git a/software/bedtools/sort/main.nf b/software/bedtools/sort/main.nf index bd9e75e7..a3d0321f 100644 --- a/software/bedtools/sort/main.nf +++ b/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 "$meta.id" diff --git a/software/bismark/deduplicate/main.nf b/software/bismark/deduplicate/main.nf index b7727cbe..c75b868c 100644 --- a/software/bismark/deduplicate/main.nf +++ b/software/bismark/deduplicate/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BISMARK_DEDUPLICATE { tag "$meta.id" diff --git a/software/bismark/genome_preparation/main.nf b/software/bismark/genome_preparation/main.nf index 5a265508..8c98de15 100644 --- a/software/bismark/genome_preparation/main.nf +++ b/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 "$fasta" diff --git a/software/blast/blastn/main.nf b/software/blast/blastn/main.nf index ec02f609..cb4beb89 100644 --- a/software/blast/blastn/main.nf +++ b/software/blast/blastn/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BLAST_BLASTN { tag "$meta.id" diff --git a/software/blast/makeblastdb/main.nf b/software/blast/makeblastdb/main.nf index c79b99da..75266990 100644 --- a/software/blast/makeblastdb/main.nf +++ b/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 "$fasta" diff --git a/software/bowtie/align/main.nf b/software/bowtie/align/main.nf index 05371f12..2197dffc 100644 --- a/software/bowtie/align/main.nf +++ b/software/bowtie/align/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BOWTIE_ALIGN { tag "$meta.id" diff --git a/software/bowtie/build/main.nf b/software/bowtie/build/main.nf index 4dd20b85..4acb7e2c 100644 --- a/software/bowtie/build/main.nf +++ b/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 "$fasta" diff --git a/software/bowtie2/align/main.nf b/software/bowtie2/align/main.nf index 4c018aa9..846589e6 100644 --- a/software/bowtie2/align/main.nf +++ b/software/bowtie2/align/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BOWTIE2_ALIGN { tag "$meta.id" diff --git a/software/bowtie2/build/main.nf b/software/bowtie2/build/main.nf index b2ff6fb8..56dca466 100644 --- a/software/bowtie2/build/main.nf +++ b/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 "$fasta" diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf index 915c6623..69737dfb 100644 --- a/software/bwa/index/main.nf +++ b/software/bwa/index/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BWA_INDEX { tag "$fasta" diff --git a/software/bwa/mem/main.nf b/software/bwa/mem/main.nf index d2652b62..be6d8977 100644 --- a/software/bwa/mem/main.nf +++ b/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 "$meta.id" diff --git a/software/bwamem2/index/main.nf b/software/bwamem2/index/main.nf index 52f1ac71..2de37358 100644 --- a/software/bwamem2/index/main.nf +++ b/software/bwamem2/index/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BWAMEM2_INDEX { tag "$fasta" diff --git a/software/bwamem2/mem/main.nf b/software/bwamem2/mem/main.nf index 85b24520..afe15e76 100644 --- a/software/bwamem2/mem/main.nf +++ b/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 "$meta.id" diff --git a/software/bwameth/align/main.nf b/software/bwameth/align/main.nf index 4660e13a..c7ef15ed 100644 --- a/software/bwameth/align/main.nf +++ b/software/bwameth/align/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process BWAMETH_ALIGN { tag "$meta.id" diff --git a/software/bwameth/index/main.nf b/software/bwameth/index/main.nf index 1468e15c..d51c579f 100644 --- a/software/bwameth/index/main.nf +++ b/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 "$fasta" diff --git a/software/cat/fastq/main.nf b/software/cat/fastq/main.nf index 1ea520ca..b3f01af9 100644 --- a/software/cat/fastq/main.nf +++ b/software/cat/fastq/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process CAT_FASTQ { tag "$meta.id" diff --git a/software/cutadapt/main.nf b/software/cutadapt/main.nf index f06f6e58..05ef8842 100644 --- a/software/cutadapt/main.nf +++ b/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 "$meta.id" diff --git a/software/deeptools/computematrix/main.nf b/software/deeptools/computematrix/main.nf index 18f9c248..4c61b9e0 100644 --- a/software/deeptools/computematrix/main.nf +++ b/software/deeptools/computematrix/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process DEEPTOOLS_COMPUTEMATRIX { tag "$meta.id" diff --git a/software/deeptools/plotfingerprint/main.nf b/software/deeptools/plotfingerprint/main.nf index c3d4c33b..25d185e2 100644 --- a/software/deeptools/plotfingerprint/main.nf +++ b/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 "$meta.id" diff --git a/software/deeptools/plotheatmap/main.nf b/software/deeptools/plotheatmap/main.nf index 624b4b9e..e59fcd05 100644 --- a/software/deeptools/plotheatmap/main.nf +++ b/software/deeptools/plotheatmap/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process DEEPTOOLS_PLOTHEATMAP { tag "$meta.id" diff --git a/software/deeptools/plotprofile/main.nf b/software/deeptools/plotprofile/main.nf index d4326434..8b7cae1b 100644 --- a/software/deeptools/plotprofile/main.nf +++ b/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 "$meta.id" diff --git a/software/dsh/filterbed/main.nf b/software/dsh/filterbed/main.nf index 7de7a8e3..056f673e 100644 --- a/software/dsh/filterbed/main.nf +++ b/software/dsh/filterbed/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process DSH_FILTERBED { tag "${meta.id}" diff --git a/software/dsh/splitbed/main.nf b/software/dsh/splitbed/main.nf index 9925b252..a81299fb 100644 --- a/software/dsh/splitbed/main.nf +++ b/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 "${meta.id}" diff --git a/software/fastp/main.nf b/software/fastp/main.nf index a9d048cf..d192c725 100644 --- a/software/fastp/main.nf +++ b/software/fastp/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process FASTP { tag "$meta.id" diff --git a/software/fastqc/main.nf b/software/fastqc/main.nf index cce410a0..4e847876 100644 --- a/software/fastqc/main.nf +++ b/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 "$meta.id" diff --git a/software/gatk4/bedtointervallist/main.nf b/software/gatk4/bedtointervallist/main.nf index 85fb8372..b10254d1 100644 --- a/software/gatk4/bedtointervallist/main.nf +++ b/software/gatk4/bedtointervallist/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process GATK4_BEDTOINTERVALLIST { tag "$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 { diff --git a/software/gatk4/createsequencedictionary/main.nf b/software/gatk4/createsequencedictionary/main.nf index edae4658..c67e2cbf 100644 --- a/software/gatk4/createsequencedictionary/main.nf +++ b/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 "$fasta" diff --git a/software/gatk4/mergevcfs/main.nf b/software/gatk4/mergevcfs/main.nf index a22ca6f6..913c56e3 100644 --- a/software/gatk4/mergevcfs/main.nf +++ b/software/gatk4/mergevcfs/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process GATK4_MERGEVCFS { tag "$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 { diff --git a/software/gatk4/revertsam/main.nf b/software/gatk4/revertsam/main.nf index b303623b..150ccf60 100644 --- a/software/gatk4/revertsam/main.nf +++ b/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 "$meta.id" @@ -11,7 +11,7 @@ process GATK4_REVERTSAM { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null) + conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0' } else { diff --git a/software/gatk4/samtofastq/main.nf b/software/gatk4/samtofastq/main.nf index 04164f3f..ff4e7016 100644 --- a/software/gatk4/samtofastq/main.nf +++ b/software/gatk4/samtofastq/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process GATK4_SAMTOFASTQ { tag "$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 { diff --git a/software/gatk4/splitncigarreads/main.nf b/software/gatk4/splitncigarreads/main.nf index 0d7e0aa7..dd80e934 100644 --- a/software/gatk4/splitncigarreads/main.nf +++ b/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 "$meta.id" @@ -11,7 +11,7 @@ process GATK4_SPLITNCIGARREADS { mode: params.publish_dir_mode, saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } - conda (params.enable_conda ? 'bioconda::gatk4:4.1.9.0' : null) + conda (params.enable_conda ? 'bioconda::gatk4=4.1.9.0' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container 'https://depot.galaxyproject.org/singularity/gatk4:4.1.9.0--py39_0' } else { diff --git a/software/gffread/main.nf b/software/gffread/main.nf index 3d81a125..d0a4e02f 100644 --- a/software/gffread/main.nf +++ b/software/gffread/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process GFFREAD { tag "$gff" diff --git a/software/gunzip/main.nf b/software/gunzip/main.nf index 20f6467d..d3159aa2 100644 --- a/software/gunzip/main.nf +++ b/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" diff --git a/software/hisat2/align/main.nf b/software/hisat2/align/main.nf index 4af22d6d..fc04da27 100644 --- a/software/hisat2/align/main.nf +++ b/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' diff --git a/software/hisat2/build/main.nf b/software/hisat2/build/main.nf index c703fd48..f1c83f99 100644 --- a/software/hisat2/build/main.nf +++ b/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' diff --git a/software/hisat2/extractsplicesites/main.nf b/software/hisat2/extractsplicesites/main.nf index 2ff846a3..96327efc 100644 --- a/software/hisat2/extractsplicesites/main.nf +++ b/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' diff --git a/software/homer/annotatepeaks/main.nf b/software/homer/annotatepeaks/main.nf index 1e03eb64..9b3b1910 100644 --- a/software/homer/annotatepeaks/main.nf +++ b/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' diff --git a/software/ivar/consensus/main.nf b/software/ivar/consensus/main.nf index b36a1c50..63cadf43 100644 --- a/software/ivar/consensus/main.nf +++ b/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" diff --git a/software/ivar/trim/main.nf b/software/ivar/trim/main.nf index cc7e5928..4c1c5fbd 100644 --- a/software/ivar/trim/main.nf +++ b/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 "$meta.id" diff --git a/software/ivar/variants/main.nf b/software/ivar/variants/main.nf index 1f940d67..85ad9463 100644 --- a/software/ivar/variants/main.nf +++ b/software/ivar/variants/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process IVAR_VARIANTS { tag "$meta.id" diff --git a/software/macs2/callpeak/main.nf b/software/macs2/callpeak/main.nf index de518669..49b3a055 100644 --- a/software/macs2/callpeak/main.nf +++ b/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 "$meta.id" diff --git a/software/methyldackel/extract/main.nf b/software/methyldackel/extract/main.nf index b8b2d156..a8ae868c 100644 --- a/software/methyldackel/extract/main.nf +++ b/software/methyldackel/extract/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process METHYLDACKEL_EXTRACT { tag "$meta.id" diff --git a/software/methyldackel/mbias/main.nf b/software/methyldackel/mbias/main.nf index 1d3b3f3b..3e432719 100644 --- a/software/methyldackel/mbias/main.nf +++ b/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 "$meta.id" diff --git a/software/minimap2/align/main.nf b/software/minimap2/align/main.nf index 18a71a9d..27418c4f 100644 --- a/software/minimap2/align/main.nf +++ b/software/minimap2/align/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process MINIMAP2_ALIGN { tag "$meta.id" diff --git a/software/mosdepth/main.nf b/software/mosdepth/main.nf index cce90848..f41927ef 100644 --- a/software/mosdepth/main.nf +++ b/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 "$meta.id" diff --git a/software/multiqc/main.nf b/software/multiqc/main.nf index ff1175fc..a92e533a 100644 --- a/software/multiqc/main.nf +++ b/software/multiqc/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process MULTIQC { label 'process_medium' diff --git a/software/pangolin/main.nf b/software/pangolin/main.nf index 23227eb9..10127052 100644 --- a/software/pangolin/main.nf +++ b/software/pangolin/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process PANGOLIN { tag "$meta.id" diff --git a/software/phantompeakqualtools/main.nf b/software/phantompeakqualtools/main.nf index 19a7c388..addff05b 100644 --- a/software/phantompeakqualtools/main.nf +++ b/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' diff --git a/software/picard/collectmultiplemetrics/main.nf b/software/picard/collectmultiplemetrics/main.nf index a4eb4e5f..2ab53207 100644 --- a/software/picard/collectmultiplemetrics/main.nf +++ b/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 "$meta.id" diff --git a/software/picard/markduplicates/main.nf b/software/picard/markduplicates/main.nf index 958f4502..da4853e1 100644 --- a/software/picard/markduplicates/main.nf +++ b/software/picard/markduplicates/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process PICARD_MARKDUPLICATES { tag "$meta.id" diff --git a/software/picard/mergesamfiles/main.nf b/software/picard/mergesamfiles/main.nf index 400fecde..bfd5d3ab 100644 --- a/software/picard/mergesamfiles/main.nf +++ b/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 "$meta.id" diff --git a/software/preseq/lcextrap/main.nf b/software/preseq/lcextrap/main.nf index 7be82eb8..601e5375 100644 --- a/software/preseq/lcextrap/main.nf +++ b/software/preseq/lcextrap/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process PRESEQ_LCEXTRAP { tag "$meta.id" diff --git a/software/qualimap/bamqc/main.nf b/software/qualimap/bamqc/main.nf index a1426d93..4a9a8355 100644 --- a/software/qualimap/bamqc/main.nf +++ b/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 "$meta.id" diff --git a/software/qualimap/rnaseq/main.nf b/software/qualimap/rnaseq/main.nf index c649bb50..c2487486 100644 --- a/software/qualimap/rnaseq/main.nf +++ b/software/qualimap/rnaseq/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process QUALIMAP_RNASEQ { tag "$meta.id" diff --git a/software/quast/main.nf b/software/quast/main.nf index 4d5ed531..aa8d7d90 100644 --- a/software/quast/main.nf +++ b/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' diff --git a/software/rsem/calculateexpression/main.nf b/software/rsem/calculateexpression/main.nf index 6f8c54a0..79ba2bd3 100644 --- a/software/rsem/calculateexpression/main.nf +++ b/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 "$meta.id" diff --git a/software/rsem/preparereference/main.nf b/software/rsem/preparereference/main.nf index d82e4270..4f963f4d 100644 --- a/software/rsem/preparereference/main.nf +++ b/software/rsem/preparereference/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process RSEM_PREPAREREFERENCE { tag "$fasta" diff --git a/software/rseqc/bamstat/main.nf b/software/rseqc/bamstat/main.nf index 1ee570e7..9b5df52f 100644 --- a/software/rseqc/bamstat/main.nf +++ b/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 "$meta.id" diff --git a/software/rseqc/inferexperiment/main.nf b/software/rseqc/inferexperiment/main.nf index 834a01a5..fb9bf76f 100644 --- a/software/rseqc/inferexperiment/main.nf +++ b/software/rseqc/inferexperiment/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process RSEQC_INFEREXPERIMENT { tag "$meta.id" diff --git a/software/rseqc/innerdistance/main.nf b/software/rseqc/innerdistance/main.nf index df6d1fd1..e7966694 100644 --- a/software/rseqc/innerdistance/main.nf +++ b/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 "$meta.id" diff --git a/software/rseqc/junctionannotation/main.nf b/software/rseqc/junctionannotation/main.nf index 9d39ccc8..4c50d774 100644 --- a/software/rseqc/junctionannotation/main.nf +++ b/software/rseqc/junctionannotation/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process RSEQC_JUNCTIONANNOTATION { tag "$meta.id" diff --git a/software/rseqc/junctionsaturation/main.nf b/software/rseqc/junctionsaturation/main.nf index b11cdad8..d119cdd9 100644 --- a/software/rseqc/junctionsaturation/main.nf +++ b/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 "$meta.id" diff --git a/software/rseqc/readdistribution/main.nf b/software/rseqc/readdistribution/main.nf index 6782c40b..c715dbcf 100644 --- a/software/rseqc/readdistribution/main.nf +++ b/software/rseqc/readdistribution/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process RSEQC_READDISTRIBUTION { tag "$meta.id" diff --git a/software/rseqc/readduplication/main.nf b/software/rseqc/readduplication/main.nf index 1d0d99fd..32ed2fcc 100644 --- a/software/rseqc/readduplication/main.nf +++ b/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 "$meta.id" diff --git a/software/salmon/index/main.nf b/software/salmon/index/main.nf index 0b335aa9..763a4147 100644 --- a/software/salmon/index/main.nf +++ b/software/salmon/index/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process SALMON_INDEX { tag "$transcript_fasta" diff --git a/software/salmon/quant/main.nf b/software/salmon/quant/main.nf index 716f13da..cbb1734c 100644 --- a/software/salmon/quant/main.nf +++ b/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 "$meta.id" diff --git a/software/samtools/faidx/main.nf b/software/samtools/faidx/main.nf index 9f0dda34..340c1d12 100644 --- a/software/samtools/faidx/main.nf +++ b/software/samtools/faidx/main.nf @@ -1,7 +1,8 @@ // Import generic module functions -include { saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] +options = initOptions(params.options) process SAMTOOLS_FAIDX { tag "$fasta" diff --git a/software/samtools/flagstat/main.nf b/software/samtools/flagstat/main.nf index 9b663ee7..863be3d8 100644 --- a/software/samtools/flagstat/main.nf +++ b/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 "$meta.id" diff --git a/software/samtools/idxstats/main.nf b/software/samtools/idxstats/main.nf index 26ff4075..99fa9853 100644 --- a/software/samtools/idxstats/main.nf +++ b/software/samtools/idxstats/main.nf @@ -1,7 +1,8 @@ // Import generic module functions -include { saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] +options = initOptions(params.options) process SAMTOOLS_IDXSTATS { tag "$meta.id" diff --git a/software/samtools/index/main.nf b/software/samtools/index/main.nf index 5dd631da..b4fd1347 100644 --- a/software/samtools/index/main.nf +++ b/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 "$meta.id" diff --git a/software/samtools/mpileup/main.nf b/software/samtools/mpileup/main.nf index 662588fd..ca83f498 100644 --- a/software/samtools/mpileup/main.nf +++ b/software/samtools/mpileup/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process SAMTOOLS_MPILEUP { tag "$meta.id" diff --git a/software/samtools/sort/main.nf b/software/samtools/sort/main.nf index 2b95b1d5..9bb4e21e 100644 --- a/software/samtools/sort/main.nf +++ b/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 "$meta.id" diff --git a/software/samtools/stats/main.nf b/software/samtools/stats/main.nf index d8d1d020..c16fbe88 100644 --- a/software/samtools/stats/main.nf +++ b/software/samtools/stats/main.nf @@ -1,7 +1,8 @@ // Import generic module functions -include { saveFiles; getSoftwareName } from './functions' +include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] +options = initOptions(params.options) process SAMTOOLS_STATS { tag "$meta.id" diff --git a/software/samtools/view/main.nf b/software/samtools/view/main.nf index 968fcc4c..befaf5a6 100644 --- a/software/samtools/view/main.nf +++ b/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 "$meta.id" diff --git a/software/seacr/callpeak/main.nf b/software/seacr/callpeak/main.nf index 3d67a058..977702f3 100644 --- a/software/seacr/callpeak/main.nf +++ b/software/seacr/callpeak/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) def VERSION = '1.3' diff --git a/software/seqkit/split2/main.nf b/software/seqkit/split2/main.nf index c2fa888d..31c154c6 100644 --- a/software/seqkit/split2/main.nf +++ b/software/seqkit/split2/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process SEQKIT_SPLIT2 { tag "$meta.id" diff --git a/software/seqwish/induce/main.nf b/software/seqwish/induce/main.nf index 592058ab..99d6fd9f 100644 --- a/software/seqwish/induce/main.nf +++ b/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' diff --git a/software/sortmerna/main.nf b/software/sortmerna/main.nf index ac1ce074..7ce96d4a 100644 --- a/software/sortmerna/main.nf +++ b/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 "$meta.id" diff --git a/software/star/align/main.nf b/software/star/align/main.nf index 3c317ad1..b885a48d 100644 --- a/software/star/align/main.nf +++ b/software/star/align/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process STAR_ALIGN { tag "$meta.id" diff --git a/software/star/genomegenerate/main.nf b/software/star/genomegenerate/main.nf index e9aa1234..7ca662d6 100644 --- a/software/star/genomegenerate/main.nf +++ b/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 "$fasta" diff --git a/software/stringtie/main.nf b/software/stringtie/main.nf index 4412d531..6870ef42 100644 --- a/software/stringtie/main.nf +++ b/software/stringtie/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process STRINGTIE { tag "$meta.id" diff --git a/software/subread/featurecounts/main.nf b/software/subread/featurecounts/main.nf index d9780ea5..053cb68b 100644 --- a/software/subread/featurecounts/main.nf +++ b/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 "$meta.id" diff --git a/software/tabix/bgzip/main.nf b/software/tabix/bgzip/main.nf index 80d4159c..5aefbc75 100644 --- a/software/tabix/bgzip/main.nf +++ b/software/tabix/bgzip/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process TABIX_BGZIP { tag "$meta.id" diff --git a/software/tabix/tabix/main.nf b/software/tabix/tabix/main.nf index 0416a00d..65381562 100644 --- a/software/tabix/tabix/main.nf +++ b/software/tabix/tabix/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process TABIX_TABIX { tag "$meta.id" diff --git a/software/tiddit/sv/main.nf b/software/tiddit/sv/main.nf index f8ea3e74..417b5561 100644 --- a/software/tiddit/sv/main.nf +++ b/software/tiddit/sv/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process TIDDIT_SV { tag "$meta.id" diff --git a/software/trimgalore/main.nf b/software/trimgalore/main.nf index 79cc7456..0fc163f3 100644 --- a/software/trimgalore/main.nf +++ b/software/trimgalore/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process TRIMGALORE { tag "$meta.id" diff --git a/software/ucsc/bedgraphtobigwig/main.nf b/software/ucsc/bedgraphtobigwig/main.nf index 10300280..8936362b 100644 --- a/software/ucsc/bedgraphtobigwig/main.nf +++ b/software/ucsc/bedgraphtobigwig/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) def VERSION = '377' diff --git a/software/umitools/dedup/main.nf b/software/umitools/dedup/main.nf index 9df37494..f4ec3e2c 100644 --- a/software/umitools/dedup/main.nf +++ b/software/umitools/dedup/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process UMITOOLS_DEDUP { tag "$meta.id" diff --git a/software/umitools/extract/main.nf b/software/umitools/extract/main.nf index 89f78b9b..0fe02711 100644 --- a/software/umitools/extract/main.nf +++ b/software/umitools/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 UMITOOLS_EXTRACT { tag "$meta.id" diff --git a/software/untar/main.nf b/software/untar/main.nf index 8912fb0b..e1594263 100644 --- a/software/untar/main.nf +++ b/software/untar/main.nf @@ -2,7 +2,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions' params.options = [:] -def options = initOptions(params.options) +options = initOptions(params.options) process UNTAR { tag "$archive" diff --git a/tests/software/TOOL/SUBTOOL/main.nf b/tests/software/TOOL/SUBTOOL/main.nf deleted file mode 100644 index 8a34a384..00000000 --- a/tests/software/TOOL/SUBTOOL/main.nf +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { TOOL_SUBTOOL } from '../../../../software/TOOL/SUBTOOL/main.nf' addParams( options: [:] ) - -workflow test_tool_subtool { - def input = [] - input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] - - TOOL_SUBTOOL ( input ) -} \ No newline at end of file diff --git a/tests/software/TOOL/SUBTOOL/test.yml b/tests/software/TOOL/SUBTOOL/test.yml deleted file mode 100644 index 35d9b3c7..00000000 --- a/tests/software/TOOL/SUBTOOL/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: tool subtool - command: nextflow run ./tests/software/TOOL/SUBTOOL -entry test_tool_subtool -c tests/config/nextflow.config - tags: - - tool - - tool_subtool - files: - - path: output/tool/test.bam - md5sum: e667c7caad0bc4b7ac383fd023c654fc \ No newline at end of file diff --git a/tests/software/bismark/deduplicate/test.yml b/tests/software/bismark/deduplicate/test.yml index dae657b2..ed6f7440 100644 --- a/tests/software/bismark/deduplicate/test.yml +++ b/tests/software/bismark/deduplicate/test.yml @@ -5,6 +5,5 @@ - bismark_deduplicate files: - path: output/bismark/test_methylated_paired_end.deduplicated.bam - md5sum: 850eb64ac788c72db9d6c29072b0aa53 - path: output/bismark/test_methylated_paired_end.deduplication_report.txt md5sum: 3876d694f10c58f47e380ba8476a356b diff --git a/tests/software/bwameth/align/test.yml b/tests/software/bwameth/align/test.yml index cf1d2d6c..ceb1bcf0 100644 --- a/tests/software/bwameth/align/test.yml +++ b/tests/software/bwameth/align/test.yml @@ -5,7 +5,6 @@ - bwameth_align files: - path: output/test_single_end/test.bam - md5sum: df75d1d633105d77039634de5cf00c1a - name: Run bwameth paired-end test workflow command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config @@ -14,4 +13,4 @@ - bwameth_align files: - path: output/test_paired_end/test.bam - md5sum: e359417da97fe092160834091a7fdc0e + diff --git a/tests/software/qualimap/bamqc/test.yml b/tests/software/qualimap/bamqc/test.yml index a7d0f5ff..edc010dd 100644 --- a/tests/software/qualimap/bamqc/test.yml +++ b/tests/software/qualimap/bamqc/test.yml @@ -18,19 +18,12 @@ - path: ./output/qualimap/test/css/searchtools.js md5sum: d550841adeedc8ed47c40ee607620937 - path: ./output/qualimap/test/css/up.png - md5sum: ecc373278454cc8ecc12d6ca69e55b36 - path: ./output/qualimap/test/css/file.png - md5sum: 6587e59c55e626744eb6fc11129d99a7 - path: ./output/qualimap/test/css/up-pressed.png - md5sum: 8ea9bd109342f87fee97943b479c6f7e - path: ./output/qualimap/test/css/down.png - md5sum: f6f3c819cc7ca27d7fd3347e5e7ffe0f - path: ./output/qualimap/test/css/minus.png - md5sum: 8d572395aa95c89584a09813ada4dfa1 - path: ./output/qualimap/test/css/bgtop.png - md5sum: 626a50532dc6e5adbdd968746ef318e8 - path: ./output/qualimap/test/css/comment.png - md5sum: 882e40f3d6a16c6ed35659b105251525 - path: ./output/qualimap/test/css/basic.css md5sum: 25b2823342c0604924a2870eeb4e7e94 - path: ./output/qualimap/test/css/report.css @@ -38,19 +31,15 @@ - path: ./output/qualimap/test/css/pygments.css md5sum: d625a0adb949f181bd0d3f1432b0fa7f - path: ./output/qualimap/test/css/comment-close.png - md5sum: 2635dda49c823e8122d4d11ed385f33d - path: ./output/qualimap/test/css/doctools.js md5sum: 5ff571aa60e63f69c1890283e240ff8d - path: ./output/qualimap/test/css/comment-bright.png - md5sum: 0c850bb4920b581bf5e5dba5fa493a64 - path: ./output/qualimap/test/css/qualimap_logo_small.png - md5sum: 7526f145a97be4682fd59e27dda4f71b - path: ./output/qualimap/test/css/websupport.js md5sum: 9e61e1e8a7433c56bd7e5a615affcf85 - path: ./output/qualimap/test/css/agogo.css md5sum: bd757b1a7ce6fdc0288ba148680f4583 - path: ./output/qualimap/test/css/bgfooter.png - md5sum: ed01bb040346e4623cc87de331ddb4e1 - path: ./output/qualimap/test/css/jquery.js md5sum: 10092eee563dec2dca82b77d2cf5a1ae - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt @@ -78,28 +67,15 @@ - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt md5sum: e199f6930d4bda5f9e871cb5c628a69a - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png - md5sum: 9308f15e347723353405de7acae5f12a - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png - md5sum: 56dc44b1d46f89af2203bd95cdcfe988 - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png - md5sum: 1f1e4be86f50ac20a893fadf2e5a2eb2 - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png - md5sum: 63963c9deab015707bc38576c7e5be7f - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png - md5sum: d2d344fd1cc656eda5fe4edba829ec7c - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png - md5sum: 9d23cab54617567e75b7deac49f0d87c - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png - md5sum: a23cf8d16c74101a29091a3fdde22c80 - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png - md5sum: 2914588916e54d9ff832f99390b3543c - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png - md5sum: daa71b1206e65845ce00eecf1731c2b8 - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png - md5sum: feb622e5e03d3ff10a1a3cf374e3e927 - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png - md5sum: 8cd9d9364e597b3a8034c9e0ca1251a7 - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png - md5sum: 0067996b78bd410cda8295025964c581 - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png - md5sum: 781e8befa89c7d957318cef465bf5e64 diff --git a/tests/software/seqkit/split2/main.nf b/tests/software/seqkit/split2/main.nf index af926bb0..bc9e7b79 100644 --- a/tests/software/seqkit/split2/main.nf +++ b/tests/software/seqkit/split2/main.nf @@ -2,14 +2,14 @@ nextflow.enable.dsl = 2 -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 26K'] ) -include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 200' ] ) +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 8K'] ) +include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 50' ] ) include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-part 3'] ) workflow test_seqkit_split2_single_end_length { def input = [] input = [ [ id:'test', single_end:true ], // meta map - file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ] + file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] SEQKIT_SPLIT2_LENGTH ( input ) } @@ -17,7 +17,7 @@ workflow test_seqkit_split2_single_end_length { workflow test_seqkit_split2_single_end_size { def input = [] input = [ [ id:'test', single_end:true ], // meta map - file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ] + file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] SEQKIT_SPLIT2_SIZE ( input ) } @@ -25,7 +25,7 @@ workflow test_seqkit_split2_single_end_size { workflow test_seqkit_split2_single_end_part { def input = [] input = [ [ id:'test', single_end:true ], // meta map - file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ] + file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] SEQKIT_SPLIT2_PART ( input ) } @@ -33,7 +33,7 @@ workflow test_seqkit_split2_single_end_part { workflow test_seqkit_split2_paired_end_length { def input = [] input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ] + file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_[1-2].fastq.gz", checkIfExists: true) ] SEQKIT_SPLIT2_LENGTH ( input ) } @@ -41,7 +41,7 @@ workflow test_seqkit_split2_paired_end_length { workflow test_seqkit_split2_paired_end_size { def input = [] input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ] + file("${launchDir}//tests/data/genomics/sarscov2/fastq/test_[1-2].fastq.gz", checkIfExists: true) ] SEQKIT_SPLIT2_SIZE ( input ) } @@ -49,7 +49,7 @@ workflow test_seqkit_split2_paired_end_size { workflow test_seqkit_split2_paired_end_part { def input = [] input = [ [ id:'test', single_end:false ], // meta map - file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ] + file("${launchDir}//tests/data/genomics/sarscov2/fastq/test_[1-2].fastq.gz", checkIfExists: true) ] SEQKIT_SPLIT2_PART ( input ) -} \ No newline at end of file +} diff --git a/tests/software/seqkit/split2/test.yml b/tests/software/seqkit/split2/test.yml index 1e5a0353..269f0ea1 100644 --- a/tests/software/seqkit/split2/test.yml +++ b/tests/software/seqkit/split2/test.yml @@ -6,10 +6,10 @@ - seqkit_split2_single_end - length files: - - path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz - md5sum: fb45cfec0d0d37f85abe81a0d299137e - - path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz - md5sum: 0dfb5284ee0bb7e1b77b57dc1bd16311 + - path: output/seqkit/test.split/test_1.part_001.fastq.gz + md5sum: 6f7d58ba35c254c0817fe9a7c69862e4 + - path: output/seqkit/test.split/test_1.part_002.fastq.gz + md5sum: cf38c51506e45380fe25abdd1bd5ccc6 - name: seqkit split2 single-end size @@ -20,12 +20,10 @@ - seqkit_split2_single_end - size files: - - path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz - md5sum: e76ac276819eb862c0a931755a220b50 - - path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz - md5sum: 79eb15ff1aac645308fab188915f9edf - - path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz - md5sum: f01fa62d34012a2e9cc48972dfe8c14c + - path: output/seqkit/test.split/test_1.part_001.fastq.gz + md5sum: bf835e685d597fc1ab5e5ac7dd689619 + - path: output/seqkit/test.split/test_1.part_002.fastq.gz + md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54 - name: seqkit split2 single-end part command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config @@ -35,12 +33,12 @@ - seqkit_split2_single_end - part files: - - path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz - md5sum: c394bc973e1f0f9bda835e4a7610d2e1 - - path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz - md5sum: 152e4470b8caeed1fc1c0326f34aa4e6 - - path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz - md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d + - path: output/seqkit/test.split/test_1.part_001.fastq.gz + md5sum: fa25951435471238d5567fd2cae31f55 + - path: output/seqkit/test.split/test_1.part_002.fastq.gz + md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a + - path: output/seqkit/test.split/test_1.part_003.fastq.gz + md5sum: 8bc86ba83a611c54f592f4eae19b680f - name: seqkit split2 paired-end length command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config @@ -50,14 +48,14 @@ - seqkit_split2_paired_end - length files: - - path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz - md5sum: fb45cfec0d0d37f85abe81a0d299137e - - path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz - md5sum: 0dfb5284ee0bb7e1b77b57dc1bd16311 - - path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz - md5sum: 4e9704a4a0f4bcab4900b6fcd9323d8a - - path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz - md5sum: da93241d0cfa84d4b806e1e102c16977 + - path: output/seqkit/test.split/test_1.part_001.fastq.gz + md5sum: 6f7d58ba35c254c0817fe9a7c69862e4 + - path: output/seqkit/test.split/test_1.part_002.fastq.gz + md5sum: cf38c51506e45380fe25abdd1bd5ccc6 + - path: output/seqkit/test.split/test_2.part_001.fastq.gz + md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4 + - path: output/seqkit/test.split/test_2.part_002.fastq.gz + md5sum: 927097c6ac7522199a9e016333181a8e - name: seqkit split2 paired-end size command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config @@ -67,18 +65,14 @@ - seqkit_split2_paired_end - size files: - - path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz - md5sum: e76ac276819eb862c0a931755a220b50 - - path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz - md5sum: 79eb15ff1aac645308fab188915f9edf - - path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz - md5sum: f01fa62d34012a2e9cc48972dfe8c14c - - path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz - md5sum: 357bfa5b981f34d87f682aebcf5e46fe - - path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz - md5sum: f48f3389d2870f4934139a901e5c4bb2 - - path: output/seqkit/test.split/SRR396636_R2.part_003.fastq.gz - md5sum: d161aa05bac2f7d1823da0479949512b + - path: output/seqkit/test.split/test_1.part_001.fastq.gz + md5sum: bf835e685d597fc1ab5e5ac7dd689619 + - path: output/seqkit/test.split/test_1.part_002.fastq.gz + md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54 + - path: output/seqkit/test.split/test_2.part_001.fastq.gz + md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba + - path: output/seqkit/test.split/test_2.part_002.fastq.gz + md5sum: 8796c3f327b1094244bfcdb36d536526 - name: seqkit split2 paired-end part command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config @@ -88,15 +82,15 @@ - seqkit_split2_paired_end - part files: - - path: output/seqkit/test.split/SRR396636_R1.part_001.fastq.gz - md5sum: c394bc973e1f0f9bda835e4a7610d2e1 - - path: output/seqkit/test.split/SRR396636_R1.part_002.fastq.gz - md5sum: 152e4470b8caeed1fc1c0326f34aa4e6 - - path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz - md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d - - path: output/seqkit/test.split/SRR396636_R2.part_001.fastq.gz - md5sum: 228aff8f1e56050967476fcad164a4fc - - path: output/seqkit/test.split/SRR396636_R2.part_002.fastq.gz - md5sum: 41047f3df10126c0df7f8e9bfd752b83 - - path: output/seqkit/test.split/SRR396636_R1.part_003.fastq.gz - md5sum: 6d8a9f6ed0f4eadbb8b1c560bfea384d \ No newline at end of file + - path: output/seqkit/test.split/test_1.part_001.fastq.gz + md5sum: fa25951435471238d5567fd2cae31f55 + - path: output/seqkit/test.split/test_1.part_002.fastq.gz + md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a + - path: output/seqkit/test.split/test_1.part_003.fastq.gz + md5sum: 8bc86ba83a611c54f592f4eae19b680f + - path: output/seqkit/test.split/test_2.part_001.fastq.gz + md5sum: f0055c99cd193fd97466b3cde9dd1b8f + - path: output/seqkit/test.split/test_2.part_002.fastq.gz + md5sum: 8a90df768201785f7a7cd5dbb41e846a + - path: output/seqkit/test.split/test_2.part_003.fastq.gz + md5sum: 890b90083e8e1606bd13ba34149cedd7