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Fixed metabat input channel #55

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merged 2 commits into from
Jun 29, 2020
Merged

Fixed metabat input channel #55

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a093d4c
Fix metabat input channel
skrakau Jun 28, 2020
7917bd5
Update CHANGELOG
skrakau Jun 28, 2020
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- Added missing parameters to summary
- Updated links to minikraken db
- Fixed kraken2 dp preparation: allow different names for compressed archive file and contained folder as for some minikraken dbs
- Fixed channel joining for multiple samples causing MetaBAT2 error [#32](https://github.com/nf-core/mag/issues/32)

### `Deprecated`

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4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -1019,7 +1019,7 @@ process bowtie2 {
"""
}

assembly_mapping_for_metabat = assembly_mapping_for_metabat.groupTuple(by:[0,1]).join(assembly_all_to_metabat_copy)
assembly_mapping_for_metabat = assembly_mapping_for_metabat.groupTuple(by:[0,1]).join(assembly_all_to_metabat_copy, by:[0,1])

assembly_mapping_for_metabat = assembly_mapping_for_metabat.dump(tag:'assembly_mapping_for_metabat')

Expand All @@ -1029,7 +1029,7 @@ process metabat {
saveAs: {filename -> (filename.indexOf(".bam") == -1 && filename.indexOf(".fastq.gz") == -1) ? "GenomeBinning/$filename" : null}

input:
set val(assembler), val(sample), file(bam), file(index), val(sampleCopy), file(assembly) from assembly_mapping_for_metabat
set val(assembler), val(sample), file(bam), file(index), file(assembly) from assembly_mapping_for_metabat
val(min_size) from params.min_contig_size
val(max_unbinned) from params.max_unbinned_contigs
val(min_length_unbinned) from params.min_length_unbinned_contigs
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