millironx/taxprofiler
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Merge pull request #255 from nf-core/config-ordering

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Minor clean ups from second release review
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James A. Fellows Yates 2023-03-07 15:29:32 +01:00 committed by GitHub
commit a77517af0d
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8 changed files with 37 additions and 32 deletions
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2
LICENSE
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@ -1,6 +1,6 @@
MIT License
Copyright (c) nf-core community
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
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal

5
assets/multiqc_config.yml
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@ -44,11 +44,6 @@ sp:
fastqc/zip:
fn: "*_fastqc.zip"
#extra_fn_clean_exts:
# - '_fastp'
# - '.pe.settings'
# - '.se.settings'
top_modules:
- "fastqc":
name: "FastQC / Falco (pre-Trimming)"

13
conf/base.config
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@ -60,6 +60,19 @@ process {
withName:CUSTOM_DUMPSOFTWAREVERSIONS {
cache = false
}
withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
}
withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
}
withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
}
withName: MEGAN_RMA2INFO_TSV {
cpus = { check_max( 1 , 'cpus' ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }

33
conf/modules.config
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@ -196,8 +196,8 @@ process {
publishDir = [
path: { "${params.outdir}/bowtie2/build" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_index,
pattern: 'bowtie2'
pattern: 'bowtie2',
enabled: params.save_hostremoval_index
]
}
@ -213,14 +213,14 @@ process {
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_bam,
pattern: '*.bam'
pattern: '*.bam',
enabled: params.save_hostremoval_bam
],
[
path: { "${params.outdir}/bowtie2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped,
pattern: '*.fastq.gz'
pattern: '*.fastq.gz',
enabled: params.save_hostremoval_unmapped
]
]
}
@ -230,8 +230,8 @@ process {
publishDir = [
path: { "${params.outdir}/minimap2/index" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_index,
pattern: '*.mmi'
pattern: '*.mmi',
enabled: params.save_hostremoval_index
]
}
@ -240,8 +240,8 @@ process {
publishDir = [
path: { "${params.outdir}/minimap2/align" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_bam,
pattern: '*.bam'
pattern: '*.bam',
enabled: params.save_hostremoval_bam
]
}
@ -255,8 +255,8 @@ process {
publishDir = [
path: { "${params.outdir}/samtools/bam2fq" },
mode: params.publish_dir_mode,
enabled: params.save_hostremoval_unmapped,
pattern: '*.fq.gz'
pattern: '*.fq.gz',
enabled: params.save_hostremoval_unmapped
]
}
@ -354,7 +354,6 @@ process {
}
withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
publishDir = [
@ -446,17 +445,16 @@ process {
}
withName: CENTRIFUGE_CENTRIFUGE {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt,sam,gz}'
]
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
}
withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [
@ -467,7 +465,6 @@ process {
}
withName: KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE {
errorStrategy = { task.exitStatus in [255,1] ? 'ignore' : 'retry' }
ext.prefix = { "centrifuge_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/centrifuge/" },
@ -477,13 +474,13 @@ process {
}
withName: KAIJU_KAIJU {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.tsv'
]
ext.args = { "${meta.db_params}" }
}
withName: 'KAIJU_KAIJU2TABLE_SINGLE' {

6
modules/local/kraken2_standard_report.nf
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@ -2,10 +2,10 @@ process KRAKEN2_STANDARD_REPORT {
tag "$meta.id"
label 'process_single'
conda "conda-forge::sed=4.8"
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
'biocontainers/biocontainers:v1.2.0_cv2' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(report)

4
modules/local/krona_cleanup.nf
View file

@ -4,8 +4,8 @@ process KRONA_CLEANUP {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"
input:
tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')

2
nextflow.config
View file

@ -300,7 +300,7 @@ dag {
manifest {
name = 'nf-core/taxprofiler'
author = """nf-core community"""
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"""
homePage = 'https://github.com/nf-core/taxprofiler'
description = """Taxonomic classification and profiling of shotgun metagenomic data"""
mainScript = 'main.nf'

4
subworkflows/local/db_check.nf
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@ -63,8 +63,8 @@ def validate_db_rows(LinkedHashMap row){
def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
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(", ")}"
// valid tools specified// TIFNISIH LIST
def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
// valid tools specified
def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
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}"
// detect quotes in params