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Merge pull request #214 from nf-core/local-module-template-sync
Sync local modules with latest template module structure
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commit
d3bad1d720
4 changed files with 4 additions and 4 deletions
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@ -2,7 +2,7 @@ process ENSURE_FASTQ_EXTENSION {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::bash=5.0" : null)
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conda "conda-forge::bash=5.0
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container "${ 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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@ -2,7 +2,7 @@ process KRAKEN2_STANDARD_REPORT {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? 'conda-forge::sed=4.8' : null)
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conda "conda-forge::sed=4.8"
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container "${ 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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@ -2,7 +2,7 @@ process KRONA_CLEANUP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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conda "conda-forge::sed=4.7"
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container "${ 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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@ -29,7 +29,7 @@ if ( params.input ) {
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if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
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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."
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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."
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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"
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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'"
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