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Improve condition so SPLIT_FASTQ skipped if only concoct selected as … #667

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Sep 12, 2024
Merged

Improve condition so SPLIT_FASTQ skipped if only concoct selected as … #667

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Improve condition so SPLIT_FASTQ skipped if only concoct selected as …
jfy133 Sep 11, 2024
9fc4153
Update subworkflows/local/binning.nf
jfy133 Sep 12, 2024
fcdb518
Update subworkflows/local/binning.nf
jfy133 Sep 12, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)

### `Dependencies`

| Tool | Previous version | New version |
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12 changes: 7 additions & 5 deletions subworkflows/local/binning.nf
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Expand Up @@ -94,18 +94,20 @@ workflow BINNING {
bams: [ meta, bams, bais ]
}

FASTA_BINNING_CONCOCT ( ch_concoct_input )
FASTA_BINNING_CONCOCT ( ch_concoct_input.bins, ch_concoct_input.bams )
ch_final_bins_for_gunzip = ch_final_bins_for_gunzip.mix( FASTA_BINNING_CONCOCT.out.bins.transpose() )
ch_binning_results_gzipped_final = ch_binning_results_gzipped_final.mix( FASTA_BINNING_CONCOCT.out.bins )
ch_versions = ch_versions.mix(FASTA_BINNING_CONCOCT.out.versions)
}

// decide which unbinned fasta files to further filter, depending on which binners selected
// NOTE: CONCOCT does not produce 'unbins' itself, therefore not included here.
if ( !params.skip_metabat2 & params.skip_maxbin2 ) {
if ( !params.skip_metabat2 && params.skip_maxbin2 ) {
ch_input_splitfasta = METABAT2_METABAT2.out.unbinned
} else if ( params.skip_metabat2 & !params.skip_maxbin2 ) {
} else if ( params.skip_metabat2 && !params.skip_maxbin2 ) {
ch_input_splitfasta = MAXBIN2.out.unbinned_fasta
} else if ( params.skip_metabat2 && params.skip_maxbin2 ) {
ch_input_splitfasta = Channel.empty()
} else {
ch_input_splitfasta = METABAT2_METABAT2.out.unbinned.mix(MAXBIN2.out.unbinned_fasta)
}
Expand All @@ -116,11 +118,11 @@ workflow BINNING {
ch_split_fasta_results_transposed = SPLIT_FASTA.out.unbinned.transpose()
ch_versions = ch_versions.mix(SPLIT_FASTA.out.versions)

GUNZIP_BINS ( ch_final_bins_for_gunzip )
GUNZIP_BINS ( ch_final_bins_for_gunzip.dump(tag: 'final_bins') )
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ch_binning_results_gunzipped = GUNZIP_BINS.out.gunzip
.groupTuple(by: 0)

GUNZIP_UNBINS ( ch_split_fasta_results_transposed )
GUNZIP_UNBINS ( ch_split_fasta_results_transposed.dump(tag: 'final_unbins') )
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ch_splitfasta_results_gunzipped = GUNZIP_UNBINS.out.gunzip
.groupTuple(by: 0)

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