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add chopper, porechop, and savont
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Lines changed: 941 additions & 67 deletions

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‎conf/modules.config‎

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@@ -41,6 +41,20 @@ process {
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]
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}
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withName: PORECHOP_ABI {
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ext.prefix = { "${meta.id}.porechop_abi" }
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publishDir = [
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path: { "${params.outdir}/porechop_abi" },
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mode: params.publish_dir_mode,
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pattern: "*.log"
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]
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}
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withName: CHOPPER {
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ext.args2 = "-q 16"
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ext.prefix = { "${meta.id}.chopper" }
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}
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withName: CUTADAPT_BASIC {
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ext.args = { [
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"--minimum-length 1",
@@ -93,6 +107,31 @@ process {
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]
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}
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withName: SAVONT_ASV {
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ext.args = { "$params.savont_options" }
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publishDir = [
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[
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path: { params.sample_inference == "pooled" ? "${params.outdir}/savont" : "${params.outdir}/savont/per-sample" },
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mode: params.publish_dir_mode,
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pattern: "*{_feature-table.tsv,_final_asvs.fasta,_savont.log}"
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],
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[
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path: { "${params.outdir}/savont/intermediate/${meta.id}" },
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mode: params.publish_dir_mode,
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enabled: params.save_intermediates
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]
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]
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}
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withName: SAVONT_EXPORT {
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publishDir =
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[
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path: { "${params.outdir}/savont" },
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mode: params.publish_dir_mode,
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pattern: "*{_feature-table.tsv,_final_asvs.fasta,_savont.log}"
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]
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}
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withName: CUTADAPT_TAXONOMY {
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ext.args = { "--discard-untrimmed --minimum-length 1 -g ${meta.fw_primer}...${meta.rv_primer_revcomp}" }
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ext.outformat = "fasta"

‎conf/test_savont.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Nextflow config file for running minimal tests
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Defines input files and everything required to run a fast and simple pipeline test.
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Use as follows:
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nextflow run nf-core/ampliseq -profile test_savont,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/
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process {
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resourceLimits = [
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cpus: 4,
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memory: '15.GB',
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time: '1.h'
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]
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}
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params {
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config_profile_name = 'Test profile'
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config_profile_description = 'Minimal test dataset to check pipeline function with Savont'
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// Input data
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input = "samplesheet_nanopore.tsv" //input = params.pipelines_testdata_base_path + "ampliseq/samplesheets/samplesheet_nanopore.tsv" // TODO
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metadata = "metadata_nanopore.tsv" //metadata = params.pipelines_testdata_base_path + "ampliseq/samplesheets/metadata_nanopore.tsv" // TODO
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nanopore = true
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skip_cutadapt = true
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sample_inference = "pooled"
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// ASV postprocessing
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filter_ssu = "bac"
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min_len_asv = 1000
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// Clean up - not needed
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min_samples = 2
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// taxonomic classification
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dada_ref_taxonomy = "gtdb=R07-RS207"
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// reduce runtime
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skip_alpha_rarefaction = true
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skip_diversity_indices = true
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// Compare to expected
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expected_sequences = "expected_sequences_abundances/D6305-D6311_ZymoBIOMICS.STD.refseq.v2.ssrRNAs.unique.fasta"
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expected_sequences_mismatches = 10
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expected_abundances = "expected_sequences_abundances/D6305-D6311_ZymoBIOMICS.STD.refseq.v2.ssrRNAs.unique.abundance.tsv"
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// restrict ANCOM analysis to higher taxonomic levels
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tax_agglom_max = 3
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// Test ANCOMBC2
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ancombc2 = true
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}

‎modules.json‎

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"https://github.com/nf-core/modules.git": {
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"modules": {
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"nf-core": {
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"chopper": {
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"branch": "master",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"clustalo/align": {
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"branch": "master",
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"git_sha": "ad65d06c959cff1da9e94c4a972deaf7430931fa",
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"git_sha": "145b0a6fb5e6b56bccd9a030a1baf75b207ac250",
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"installed_by": ["modules"]
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},
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"porechop/abi": {
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"branch": "master",
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"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
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"installed_by": ["modules"]
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},
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"seqtk/subseq": {
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"branch": "master",
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"git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33",

‎modules/local/savont_asv.nf‎

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process SAVONT_ASV {
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tag "$meta.id"
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label 'process_medium'
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label 'process_long'
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conda "bioconda::savont=0.6.1c"
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container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/savont:0.6.1c--hec9b1f2_0' :
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'biocontainers/savont:0.6.1c--hec9b1f2_0' }"
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input:
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tuple val(meta), path(reads), val(sample_string)
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output:
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path("*_feature-table.tsv") , emit: asv
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path("*_final_asvs.fasta") , emit: fasta
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path("*_final_clusters.tsv"), emit: clusters
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path("savont_asv_*/temp/*") , emit: temp
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tuple val(meta), path("savont_asv_*"), emit: output_folder
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path("*_savont.log") , emit: log
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tuple val("${task.process}"), val('savont'), eval("savont --version 2>&1 | cut -d ' ' -f 2"), topic: versions, emit: versions_savont
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script:
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def prefix = task.ext.prefix ?: "$meta.id"
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def args = task.ext.args ?: ''
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def reads_cmd = reads instanceof List ? "--pooled-samples ${reads.join(' ')}" : "${reads}"
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"""
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savont asv \\
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-t $task.cpus \\
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$args \\
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-o savont_asv_${prefix} \\
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$reads_cmd
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# adjust the naming of the samples:
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sed '1s/.*/${sample_string}/' savont_asv_${prefix}/feature-table.tsv > ${prefix}_feature-table.tsv
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# copy other files to include the prefix
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cp savont_asv_${prefix}/final_asvs.fasta ${prefix}_final_asvs.fasta
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cp savont_asv_${prefix}/final_clusters.tsv ${prefix}_final_clusters.tsv
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cp savont_asv_${prefix}/savont_*.log ${prefix}_savont.log
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"""
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}

‎modules/local/savont_export.nf‎

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process SAVONT_EXPORT {
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tag "$prefix"
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label 'process_low'
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conda "bioconda::savont=0.6.1c"
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container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/savont:0.6.1c--hec9b1f2_0' :
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'biocontainers/savont:0.6.1c--hec9b1f2_0' }"
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input:
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tuple val(prefix), path(output_folders), val(sample_string)
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output:
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path("*_feature-table.tsv") , emit: asv
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path("*_final_asvs.fasta") , emit: fasta
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path("*_savont.log") , emit: log
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tuple val("${task.process}"), val('savont'), eval("savont --version 2>&1 | cut -d ' ' -f 2"), topic: versions, emit: versions_savont
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script:
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def args = task.ext.args ?: ''
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def folders = "${output_folders.join(' ')}"
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"""
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savont export \\
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-i $folders \\
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-o savont_export \\
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--relabel $sample_string
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# copy other files to include the prefix
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cp savont_export/merged_feature_table.tsv ${prefix}_feature-table.tsv
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cp savont_export/merged_rep_seqs.fasta ${prefix}_final_asvs.fasta
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cp savont_export/savont_*.log ${prefix}_savont.log
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"""
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}

‎modules/nf-core/chopper/environment.yml‎

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‎modules/nf-core/chopper/main.nf‎

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‎modules/nf-core/chopper/meta.yml‎

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