millironx/taxprofiler
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Merge pull request #214 from nf-core/local-module-template-sync

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Sync local modules with latest template module structure
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James A. Fellows Yates 2023-01-20 14:41:11 +01:00 committed by GitHub
commit d3bad1d720
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4 changed files with 4 additions and 4 deletions
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2
modules/local/ensure_fastq_extension.nf
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@ -2,7 +2,7 @@ process ENSURE_FASTQ_EXTENSION {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::bash=5.0" : null)
conda "conda-forge::bash=5.0
container "${ 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' }"

2
modules/local/kraken2_standard_report.nf
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@ -2,7 +2,7 @@ process KRAKEN2_STANDARD_REPORT {
tag "$meta.id"
label 'process_single'
conda (params.enable_conda ? 'conda-forge::sed=4.8' : null)
conda "conda-forge::sed=4.8"
container "${ 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' }"

2
modules/local/krona_cleanup.nf
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@ -2,7 +2,7 @@ process KRONA_CLEANUP {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
conda "conda-forge::sed=4.7"
container "${ 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' }"

2
workflows/taxprofiler.nf
View file

@ -29,7 +29,7 @@ if ( params.input ) {
if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (!params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"