mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:03:10 +00:00
commit
a34b240dfc
10 changed files with 18 additions and 19 deletions
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@ -281,7 +281,7 @@ process {
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}
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withName: MALT_RUN {
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}" }
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publishDir = [
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@ -52,6 +52,7 @@ params {
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process {
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withName: MALT_RUN {
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maxForks = 1
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ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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}
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withName: MEGAN_RMA2INFO_TSV {
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maxForks = 1
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@ -46,5 +46,6 @@ params {
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process {
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withName: MALT_RUN {
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maxForks = 1
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ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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}
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}
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@ -45,5 +45,6 @@ params {
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process {
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withName: MALT_RUN {
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maxForks = 1
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ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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}
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}
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@ -37,6 +37,7 @@ params {
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process {
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withName: MALT_RUN {
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maxForks = 1
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ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
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}
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withName: MEGAN_RMA2INFO {
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maxForks = 1
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@ -12,9 +12,9 @@ class WorkflowMain {
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// TODO nf-core: Add Zenodo DOI for pipeline after first release
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//"* The pipeline\n" +
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//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
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"* The nf-core framework\n" +
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" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
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"* Software dependencies\n" +
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'* The nf-core framework\n' +
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' https://doi.org/10.1038/s41587-020-0439-x\n\n' +
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'* Software dependencies\n' +
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" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
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}
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@ -53,15 +53,15 @@ class WorkflowMain {
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System.exit(0)
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}
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// Print parameter summary log to screen
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log.info paramsSummaryLog(workflow, params, log)
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// Validate workflow parameters via the JSON schema
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if (params.validate_params) {
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NfcoreSchema.validateParameters(workflow, params, log)
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}
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// Print parameter summary log to screen
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log.info paramsSummaryLog(workflow, params, log)
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// Check that a -profile or Nextflow config has been provided to run the pipeline
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NfcoreTemplate.checkConfigProvided(workflow, log)
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@ -90,4 +90,5 @@ class WorkflowMain {
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}
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return null
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}
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}
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@ -111,7 +111,7 @@
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},
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"malt/run": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
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},
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"megan/rma2info": {
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"branch": "master",
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8
modules/nf-core/malt/run/main.nf
generated
8
modules/nf-core/malt/run/main.nf
generated
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@ -2,14 +2,13 @@ process MALT_RUN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::malt=0.41" : null)
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conda (params.enable_conda ? "bioconda::malt=0.61" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
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'quay.io/biocontainers/malt:0.41--1' }"
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'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
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'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
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input:
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tuple val(meta), path(fastqs)
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val mode
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path index
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output:
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@ -38,7 +37,6 @@ process MALT_RUN {
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-o . \\
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$args \\
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--inFile ${fastqs.join(' ')} \\
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-m $mode \\
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--index $index/ |&tee ${prefix}-malt-run.log
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cat <<-END_VERSIONS > versions.yml
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4
modules/nf-core/malt/run/meta.yml
generated
4
modules/nf-core/malt/run/meta.yml
generated
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@ -28,10 +28,6 @@ input:
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type: file
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description: Input FASTQ files
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pattern: "*.{fastq.gz,fq.gz}"
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- mode:
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type: string
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description: Program mode
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pattern: "Unknown|BlastN|BlastP|BlastX|Classifier"
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- index:
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type: directory
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description: Index/database directory from malt-build
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@ -97,7 +97,7 @@ workflow PROFILING {
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db: it[2]
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}
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MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
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MALT_RUN ( ch_input_for_malt.reads, ch_input_for_malt.db )
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ch_maltrun_for_megan = MALT_RUN.out.rma6
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.transpose()
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