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Merge pull request #174 from nf-core/malt-update

Update MALT
This commit is contained in:
James A. Fellows Yates 2022-12-01 13:58:30 +01:00 committed by GitHub
commit a34b240dfc
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10 changed files with 18 additions and 19 deletions

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@ -281,7 +281,7 @@ process {
}
withName: MALT_RUN {
ext.args = { "${meta.db_params}" }
ext.args = { "${meta.db_params} -m ${params.malt_mode}" }
// one run with multiple samples, so fix ID to just db name to ensure clean log name
ext.prefix = { "${meta.db_name}" }
publishDir = [

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@ -52,6 +52,7 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: MEGAN_RMA2INFO_TSV {
maxForks = 1

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@ -46,5 +46,6 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
}

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@ -45,5 +45,6 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
}

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@ -37,6 +37,7 @@ params {
process {
withName: MALT_RUN {
maxForks = 1
ext.args = { "-m ${params.malt_mode} -J-Xmx12G" }
}
withName: MEGAN_RMA2INFO {
maxForks = 1

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@ -12,9 +12,9 @@ class WorkflowMain {
// TODO nf-core: Add Zenodo DOI for pipeline after first release
//"* The pipeline\n" +
//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
"* The nf-core framework\n" +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" +
"* Software dependencies\n" +
'* The nf-core framework\n' +
' https://doi.org/10.1038/s41587-020-0439-x\n\n' +
'* Software dependencies\n' +
" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
}
@ -53,15 +53,15 @@ class WorkflowMain {
System.exit(0)
}
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
// Validate workflow parameters via the JSON schema
if (params.validate_params) {
NfcoreSchema.validateParameters(workflow, params, log)
}
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
// Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log)
@ -90,4 +90,5 @@ class WorkflowMain {
}
return null
}
}

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@ -111,7 +111,7 @@
},
"malt/run": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "6d9712f03ec2de8264a50ee4541a617e1e063b51"
},
"megan/rma2info": {
"branch": "master",

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@ -2,14 +2,13 @@ process MALT_RUN {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::malt=0.41" : null)
conda (params.enable_conda ? "bioconda::malt=0.61" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
'quay.io/biocontainers/malt:0.41--1' }"
'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' :
'quay.io/biocontainers/malt:0.61--hdfd78af_0' }"
input:
tuple val(meta), path(fastqs)
val mode
path index
output:
@ -38,7 +37,6 @@ process MALT_RUN {
-o . \\
$args \\
--inFile ${fastqs.join(' ')} \\
-m $mode \\
--index $index/ |&tee ${prefix}-malt-run.log
cat <<-END_VERSIONS > versions.yml

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@ -28,10 +28,6 @@ input:
type: file
description: Input FASTQ files
pattern: "*.{fastq.gz,fq.gz}"
- mode:
type: string
description: Program mode
pattern: "Unknown|BlastN|BlastP|BlastX|Classifier"
- index:
type: directory
description: Index/database directory from malt-build

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@ -97,7 +97,7 @@ workflow PROFILING {
db: it[2]
}
MALT_RUN ( ch_input_for_malt.reads, params.malt_mode, ch_input_for_malt.db )
MALT_RUN ( ch_input_for_malt.reads, ch_input_for_malt.db )
ch_maltrun_for_megan = MALT_RUN.out.rma6
.transpose()