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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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Original file line number Diff line number Diff line change
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)
- [#470](https://github.com/nf-core/mag/pull/470) - Fix binning preparation from running even when binning was requested to be skipped (reported by @prototaxites, fix by @jfy133)

### `Dependencies`

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20 changes: 13 additions & 7 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 ( !params.skip_binning || params.ancient_dna ) {
BINNING_PREPARATION (
ch_assemblies,
ch_short_reads
)
}

/*
================================================================================
Expand Down Expand Up @@ -686,8 +688,10 @@ workflow MAG {
}
}

ch_versions = ch_versions.mix(BINNING_PREPARATION.out.bowtie2_version.first())
ch_versions = ch_versions.mix(BINNING.out.versions)
if ( !params.skip_binning || params.ancient_dna ) {
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ch_versions = ch_versions.mix(BINNING_PREPARATION.out.bowtie2_version.first())
ch_versions = ch_versions.mix(BINNING.out.versions)
}

/*
* DAS Tool: binning refinement
Expand Down Expand Up @@ -943,7 +947,9 @@ workflow MAG {
}
}

ch_multiqc_files = ch_multiqc_files.mix(BINNING_PREPARATION.out.bowtie2_assembly_multiqc.collect().ifEmpty([]))
if ( !params.skip_binning || params.ancient_dna ) {
ch_multiqc_files = ch_multiqc_files.mix(BINNING_PREPARATION.out.bowtie2_assembly_multiqc.collect().ifEmpty([]))
}

if (!params.skip_binning && !params.skip_prokka){
ch_multiqc_files = ch_multiqc_files.mix(PROKKA.out.txt.collect{it[1]}.ifEmpty([]))
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