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feat: typed parameters #1103

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95c58b9
feat: add typed params block to main.nf
dialvarezs Aug 13, 2026
3f24d66
feat: move parameter defaults out of nextflow.config
dialvarezs Aug 13, 2026
152b9b8
feat: disable typed-param-incompatible linting and CLI typecasting
dialvarezs Aug 13, 2026
309f0c0
fix: defer METABAT2 ext.args evaluation to task time
dialvarezs Aug 13, 2026
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6 changes: 2 additions & 4 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,8 @@ lint:
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/branch.yml
- .github/workflows/linting.yml
nextflow_config:
- config_defaults:
- params.phix_reference
- params.lambda_reference
nextflow_config: false # TODO: Remove when tools supports parameter types
schema_params: false # TODO: Remove when tools supports parameter types
files_exist:
- .github/workflows/linting_comment.yml
nf_core_version: 4.0.3
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858 changes: 428 additions & 430 deletions conf/igenomes.config
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12 changes: 7 additions & 5 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -904,11 +904,13 @@ process {
withName: METABAT2_METABAT2 {
tag = { "${meta.assembler}-${meta.id}" }
ext.prefix = { "${meta.assembler}-MetaBAT2-${meta.id}" }
ext.args = [
params.min_contig_size < 1500 ? "-m 1500" : "-m ${params.min_contig_size}",
"--unbinned",
"--seed ${params.metabat_rng_seed}",
].join(' ').trim()
ext.args = {
[
params.min_contig_size < 1500 ? "-m 1500" : "-m ${params.min_contig_size}",
"--unbinned",
"--seed ${params.metabat_rng_seed}",
].join(' ').trim()
}
publishDir = [
[
path: { "${params.outdir}/GenomeBinning/MetaBAT2/bins/" },
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