mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 21:53:09 +00:00
Start working on adding adapterremoval
This commit is contained in:
parent
323883bd3e
commit
c4c93bd59d
7 changed files with 281 additions and 14 deletions
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@ -3,6 +3,9 @@
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"homePage": "https://github.com/nf-core/taxprofiler",
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"repos": {
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"nf-core/modules": {
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"adapterremoval": {
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"git_sha": "f0800157544a82ae222931764483331a81812012"
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},
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"cat/fastq": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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@ -32,4 +35,4 @@
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}
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}
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}
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}
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}
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70
modules/nf-core/modules/adapterremoval/main.nf
generated
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70
modules/nf-core/modules/adapterremoval/main.nf
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@ -0,0 +1,70 @@
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process ADAPTERREMOVAL {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::adapterremoval=2.3.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' :
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'quay.io/biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }"
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input:
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tuple val(meta), path(reads)
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path(adapterlist)
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output:
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tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated
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tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded
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tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated
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tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated
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tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed
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tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated
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tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
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tuple val(meta), path('*.log') , emit: log
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def list = adapterlist ? "--adapter-list ${adapterlist}" : ""
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prefix = task.ext.prefix ?: "${meta.id}"
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if (meta.single_end) {
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"""
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AdapterRemoval \\
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--file1 $reads \\
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$args \\
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$adapterlist \\
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--basename ${prefix} \\
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--threads ${task.cpus} \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--gzip
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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END_VERSIONS
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"""
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} else {
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"""
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AdapterRemoval \\
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--file1 ${reads[0]} \\
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--file2 ${reads[1]} \\
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$args \\
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$adapterlist \\
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--basename ${prefix} \\
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--threads $task.cpus \\
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--settings ${prefix}.log \\
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--seed 42 \\
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--gzip
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
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END_VERSIONS
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"""
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}
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}
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90
modules/nf-core/modules/adapterremoval/meta.yml
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90
modules/nf-core/modules/adapterremoval/meta.yml
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name: adapterremoval
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description: Trim sequencing adapters and collapse overlapping reads
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keywords:
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- trimming
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- adapters
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- merging
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- fastq
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tools:
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- adapterremoval:
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description: The AdapterRemoval v2 tool for merging and clipping reads.
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homepage: https://github.com/MikkelSchubert/adapterremoval
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documentation: https://adapterremoval.readthedocs.io
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licence: ["GPL v3"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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- adapterlist:
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type: file
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description: Optional text file containing list of adapters to look for for removal
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with one adapter per line. Otherwise will look for default adapters (see
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AdapterRemoval man page), or can be modified to remove user-specified
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adapters via ext.args.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- singles_truncated:
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type: file
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description: |
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Adapter trimmed FastQ files of either single-end reads, or singleton
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'orphaned' reads from merging of paired-end data (i.e., one of the pair
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was lost due to filtering thresholds).
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pattern: "*.truncated.gz"
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- discarded:
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type: file
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description: |
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Adapter trimmed FastQ files of reads that did not pass filtering
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thresholds.
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pattern: "*.discarded.gz"
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- pair1_truncated:
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type: file
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description: |
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Adapter trimmed R1 FastQ files of paired-end reads that did not merge
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with their respective R2 pair due to long templates. The respective pair
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is stored in 'pair2_truncated'.
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pattern: "*.pair1.truncated.gz"
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- pair2_truncated:
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type: file
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description: |
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Adapter trimmed R2 FastQ files of paired-end reads that did not merge
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with their respective R1 pair due to long templates. The respective pair
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is stored in 'pair1_truncated'.
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pattern: "*.pair2.truncated.gz"
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- collapsed:
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type: file
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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respective R1 pair but were not trimmed.
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pattern: "*.collapsed.gz"
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- collapsed_truncated:
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type: file
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description: |
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Collapsed FastQ of paired-end reads that successfully merged with their
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respective R1 pair and were trimmed of adapter due to sufficient overlap.
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pattern: "*.collapsed.truncated.gz"
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- log:
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type: file
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description: AdapterRemoval log file
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@maxibor"
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- "@jfy133"
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@ -10,7 +10,10 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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"description": "Method used to save pipeline results to output directory.",
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"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
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"fa_icon": "fas fa-copy",
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"hidden": true
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},
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"email_on_fail": {
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},
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp"
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"default": "fastp",
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"enum": [
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"fastp",
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"adapterremoval"
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]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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},
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"shortread_clipmerge_adapter1": {
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"type": "string",
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"default": null
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"default": "None"
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},
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"shortread_clipmerge_adapter2": {
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"type": "string",
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"default": null
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"default": "None"
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},
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"shortread_clipmerge_minlength": {
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"type": "integer",
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"default": 15
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}
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}
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}
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}
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91
subworkflows/local/shortread_adapterremoval.nf
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91
subworkflows/local/shortread_adapterremoval.nf
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/*
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Process short raw reads with AdapterRemoval
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*/
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_SINGLE } from '../../modules/nf-core/modules/adapterremoval/main'
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include { ADAPTERREMOVAL as ADAPTERREMOVAL_PAIRED } from '../../modules/nf-core/modules/adapterremoval/main'
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include { CAT_FASTQ } from '../../modules/nf-core/modules/cat/fastq/main'
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workflow SHORTREAD_ADAPTERREMOVAL {
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take:
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reads // [[meta], [reads]]
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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ch_input_for_adapterremoval = reads
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.dump(tag: "pre_adapterremoval_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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ADAPTERREMOVAL_SINGLE ( ch_input_for_adapterremoval.single, [] )
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ADAPTERREMOVAL_PAIRED ( ch_input_for_adapterremoval.paired, [] )
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if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
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ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
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.mix(
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ADAPTERREMOVAL_PAIRED.out.collapsed_truncated,
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ADAPTERREMOVAL_PAIRED.out.singles_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair1_truncated,
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ADAPTERREMOVAL_PAIRED.out.pair2_truncated
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)
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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}
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.groupTuple(by: 0)
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ch_adapterremoval_reads_prepped_pe = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
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ch_adapterremoval_for_cat = ADAPTERREMOVAL_PAIRED.out.collapsed
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.mix( ADAPTERREMOVAL_PAIRED.out.collapsed_truncated )
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.map {
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meta, reads ->
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def meta_new = meta.clone()
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meta_new['single_end'] = 1
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[ meta_new, reads ]
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}
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.groupTuple(by: 0)
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ch_adapterremoval_reads_prepped_pe = CAT_FASTQ ( ch_adapterremoval_for_cat ).reads
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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} else {
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ch_adapterremoval_reads_prepped_pe = ADAPTERREMOVAL_PAIRED.out.pair1_truncated
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.join( ADAPTERREMOVAL_PAIRED.out.pair2_truncated )
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.dump(tag: "pre-group")
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.groupTuple(by: 0)
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.dump(tag: "post-group")
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.map { meta, pair1, pair2 ->
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[ meta, [ pair1, pair2 ].flatten() ]
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}
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.dump(tag: "post-map")
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ch_adapterremoval_reads_prepped = ch_adapterremoval_reads_prepped_pe
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.mix( ADAPTERREMOVAL_SINGLE.out.singles_truncated )
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}
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ch_processed_reads = ch_adapterremoval_reads_prepped
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_SINGLE.out.versions.first() )
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ch_versions = ch_versions.mix( ADAPTERREMOVAL_PAIRED.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix( ADAPTERREMOVAL_PAIRED.out.log.collect{it[1]}, ADAPTERREMOVAL_SINGLE.out.log.collect{it[1]} )
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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ch_multiqc_files = Channel.empty()
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ch_input_for_fastp = reads
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.dump(tag: "pre-fastp_branch")
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.branch{
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single: it[0]['single_end'] == true
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paired: it[0]['single_end'] == false
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}
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ch_input_for_fastp.single.dump(tag: "input_fastp_single")
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ch_input_for_fastp.paired.dump(tag: "input_fastp_paired")
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FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
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// Last parameter here turns on merging of PE data
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FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
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ch_versions = ch_versions.mix(FASTP_SINGLE.out.versions.first())
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ch_versions = ch_versions.mix(FASTP_PAIRED.out.versions.first())
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ch_processed_reads = ch_fastp_reads_prepped.dump(tag: "ch_fastp_reads_prepped")
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ch_processed_reads = ch_fastp_reads_prepped
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_SINGLE.out.json.collect{it[1]} )
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ch_multiqc_files = ch_multiqc_files.mix( FASTP_PAIRED.out.json.collect{it[1]} )
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ch_multiqc_files.dump(tag: "preprocessing_fastp_mqc_final")
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emit:
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reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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include { SHORTREAD_FASTP } from './shortread_fastp'
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include { SHORTREAD_ADAPTERREMOVAL } from './shortread_adapterremoval'
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include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
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workflow SHORTREAD_PREPROCESSING {
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ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
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ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
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} else if ( params.shortread_clipmerge_tool == "adapterremoval" ) {
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ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads ).reads
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ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )
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} else {
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ch_processed_reads = reads
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}
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