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be85289981
* feat: each output type has dedicated channel replace bgzip with gzip can only zip one at a time * Add condition moving of unbinned files * fix: solution for moving sometimes non-existant files * fix: update meta.yml to add the new channels * fix: remove most of the checksums due to variability * fix: tweaking of output * Update modules/metabat2/metabat2/main.nf Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Fix find commands * Fix find commands Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
69 lines
1.9 KiB
YAML
69 lines
1.9 KiB
YAML
name: metabat2_metabat2
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keywords:
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- sort
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- binning
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- depth
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- bam
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- coverage
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- de novo assembly
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tools:
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- metabat2:
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description: Metagenome binning
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homepage: https://bitbucket.org/berkeleylab/metabat/src/master/
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documentation: https://bitbucket.org/berkeleylab/metabat/src/master/
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tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/
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doi: "10.7717/peerj.7359"
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licence: ['BSD-3-clause-LBNL']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: Fasta file of the assembled contigs
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pattern: "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}"
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- depth:
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type: file
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description: |
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Optional text file listing the coverage per contig pre-generated
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by metabat2_jgisummarizebamcontigdepths
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pattern: "*.txt"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- fasta:
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type: file
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description: Bins created from assembled contigs in fasta file
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pattern: "*.fa.gz"
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- tooshort:
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type: file
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description: Contigs that did not pass length filtering
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pattern: "*.tooShort.fa.gz"
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- lowdepth:
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type: file
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description: Contigs that did not have sufficient depth for binning
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pattern: "*.lowDepth.fa.gz"
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- unbinned:
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type: file
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description: Contigs that pass length and depth filtering but could not be binned
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pattern: "*.unbinned.fa.gz"
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- membership:
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type: file
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description: cluster memberships as a matrix format.
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pattern: "*.tsv.gz"
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authors:
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- "@maxibor"
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- "@jfy133"
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