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Skip binning prep when no binning/aDNA #470

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merged 6 commits into from
Jul 6, 2023
Merged

Skip binning prep when no binning/aDNA #470

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a63cada
Skip binning prep when downstream steps aren't executed
jfy133 Jul 5, 2023
0c37d8e
Update CHANGELOG.md
jfy133 Jul 5, 2023
9a2ee91
Add binning_rpep conditional everywhere
jfy133 Jul 5, 2023
3af800c
Merge branch 'skip-binning-prep' of github.com:nf-core/mag into skip-…
jfy133 Jul 5, 2023
c60a9d0
Add final skippbinning condition
jfy133 Jul 5, 2023
54869cf
Fix channel mixing
jfy133 Jul 6, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -31,6 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#439](https://github.com/nf-core/mag/pull/445) - Fix bug in assembly input (by @prototaxites)
- [#447](https://github.com/nf-core/mag/pull/447) - Remove `default: None` from parameter schema (by @drpatelh)
- [#449](https://github.com/nf-core/mag/pull/447) - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133)
- [#XXX](https://github.com/nf-core/mag/pull/447) - Fix binning preparation from running even when binning was requested to be skipped (reported by @prototaxites, fix by @jfy133)
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### `Dependencies`

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10 changes: 6 additions & 4 deletions workflows/mag.nf
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Expand Up @@ -617,10 +617,12 @@ workflow MAG {
ch_busco_summary = Channel.empty()
ch_checkm_summary = Channel.empty()

BINNING_PREPARATION (
ch_assemblies,
ch_short_reads
)
if ( !skip_binning || params.ancient_dna ) {
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BINNING_PREPARATION (
ch_assemblies,
ch_short_reads
)
}

/*
================================================================================
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