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https://github.com/MillironX/taxprofiler.git
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Merge pull request #255 from nf-core/config-ordering
Minor clean ups from second release review
This commit is contained in:
commit
a77517af0d
8 changed files with 37 additions and 32 deletions
2
LICENSE
2
LICENSE
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@ -1,6 +1,6 @@
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MIT License
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Copyright (c) nf-core community
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Copyright (c) James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lauri Mesilaakso, Thomas A. Christensen II, Jianhong Ou, Mahwash Jamy, Maxime Borry, Rafal Stepien, Tanja Normark
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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@ -44,11 +44,6 @@ sp:
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fastqc/zip:
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fn: "*_fastqc.zip"
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#extra_fn_clean_exts:
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# - '_fastp'
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# - '.pe.settings'
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# - '.se.settings'
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top_modules:
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- "fastqc":
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name: "FastQC / Falco (pre-Trimming)"
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@ -60,6 +60,19 @@ process {
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withName:CUSTOM_DUMPSOFTWAREVERSIONS {
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cache = false
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}
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
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errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
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}
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withName: MEGAN_RMA2INFO_TSV {
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cpus = { check_max( 1 , 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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@ -196,8 +196,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: 'bowtie2'
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pattern: 'bowtie2',
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enabled: params.save_hostremoval_index
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]
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}
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@ -213,14 +213,14 @@ process {
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_bam,
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pattern: '*.bam'
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pattern: '*.bam',
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enabled: params.save_hostremoval_bam
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],
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[
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path: { "${params.outdir}/bowtie2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fastq.gz'
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pattern: '*.fastq.gz',
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enabled: params.save_hostremoval_unmapped
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]
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]
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}
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@ -230,8 +230,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/minimap2/index" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_index,
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pattern: '*.mmi'
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pattern: '*.mmi',
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enabled: params.save_hostremoval_index
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]
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}
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@ -240,8 +240,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/minimap2/align" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_bam,
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pattern: '*.bam'
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pattern: '*.bam',
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enabled: params.save_hostremoval_bam
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]
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}
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@ -255,8 +255,8 @@ process {
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publishDir = [
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path: { "${params.outdir}/samtools/bam2fq" },
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mode: params.publish_dir_mode,
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enabled: params.save_hostremoval_unmapped,
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pattern: '*.fq.gz'
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pattern: '*.fq.gz',
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enabled: params.save_hostremoval_unmapped
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]
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}
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@ -354,7 +354,6 @@ process {
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}
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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@ -446,17 +445,16 @@ process {
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}
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withName: CENTRIFUGE_CENTRIFUGE {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.{txt,sam,gz}'
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]
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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}
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withName: CENTRIFUGE_KREPORT {
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
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publishDir = [
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@ -467,7 +465,6 @@ process {
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}
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withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
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errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
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ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
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publishDir = [
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path: { "${params.outdir}/centrifuge/" },
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@ -477,13 +474,13 @@ process {
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}
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withName: KAIJU_KAIJU {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
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publishDir = [
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path: { "${params.outdir}/kaiju/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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pattern: '*.tsv'
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]
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ext.args = { "${meta.db_params}" }
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}
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withName: 'KAIJU_KAIJU2TABLE_SINGLE' {
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@ -2,10 +2,10 @@ process KRAKEN2_STANDARD_REPORT {
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tag "$meta.id"
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label 'process_single'
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conda "conda-forge::sed=4.8"
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conda "conda-forge::sed=4.7"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
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'biocontainers/biocontainers:v1.2.0_cv2' }"
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'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
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'ubuntu:20.04' }"
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input:
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tuple val(meta), path(report)
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@ -4,8 +4,8 @@ process KRONA_CLEANUP {
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conda "conda-forge::sed=4.7"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
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'biocontainers/biocontainers:v1.2.0_cv1' }"
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'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
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'ubuntu:20.04' }"
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input:
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tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
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@ -300,7 +300,7 @@ dag {
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manifest {
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name = 'nf-core/taxprofiler'
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author = """nf-core community"""
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author = """James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lauri Mesilaakso, Thomas A. Christensen II, Jianhong Ou, Mahwash Jamy, Maxime Borry, Rafal Stepien, Tanja Normark"""
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homePage = 'https://github.com/nf-core/taxprofiler'
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description = """Taxonomic classification and profiling of shotgun metagenomic data"""
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mainScript = 'main.nf'
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@ -63,8 +63,8 @@ def validate_db_rows(LinkedHashMap row){
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def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
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if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
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// valid tools specified// TIFNISIH LIST
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def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
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// valid tools specified
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def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
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if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
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// detect quotes in params
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