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Always run in METASPADES --meta mode #705

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merged 3 commits into from
Oct 25, 2024
Merged

Always run in METASPADES --meta mode #705

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38d3f3c
Always run in --meta mode
jfy133 Oct 25, 2024
e974653
Update conf/modules.config
jfy133 Oct 25, 2024
723e621
Update conf/modules.config
jfy133 Oct 25, 2024
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4 changes: 2 additions & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -263,13 +263,13 @@ process {
}

withName: METASPADES {
ext.args = params.spades_options ?: '--meta'
ext.args = params.spades_options ? params.spades_options + '--meta' : '--meta'
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ext.prefix = { "SPAdes-${meta.id}" }
publishDir = [path: { "${params.outdir}/Assembly/SPAdes" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
}

withName: METASPADESHYBRID {
ext.args = params.spades_options ?: '--meta'
ext.args = params.spades_options ? params.spades_options + '--meta' : '--meta'
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ext.prefix = { "SPAdesHybrid-${meta.id}" }
publishDir = [path: { "${params.outdir}/Assembly/SPAdesHybrid" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
}
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4 changes: 2 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -551,8 +551,8 @@
},
"spades_options": {
"type": "string",
"description": "Additional custom options for SPAdes and SPAdesHybrid. You must also specify `--meta` to run SPAdes in metagenomic mode if customising these options!",
"help_text": "An example is adjusting k-mers (\"-k 21,33,55,77\") or adding [advanced options](https://github.com/ablab/spades#advanced-options). But not -t, -m, -o or --out-prefix, because these are already in use. Must be used like this: --spades_options \"-k 21,33,55,77\")"
"description": "Additional custom options for SPAdes and SPAdesHybrid. Do not specify `--meta` as this will be added for you!",
"help_text": "An example is adjusting k-mers (\"-k 21,33,55,77\") or adding [advanced options](https://github.com/ablab/spades#advanced-options). But not --meta, -t, -m, -o or --out-prefix, because these are already in use. Must be used like this: --spades_options \"-k 21,33,55,77\")"
},
"megahit_options": {
"type": "string",
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