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983ba000c1
* Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
45 lines
1.2 KiB
YAML
45 lines
1.2 KiB
YAML
name: fgbio_callmolecularconsensusreads
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description: Calls consensus sequences from reads with the same unique molecular tag.
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keywords:
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- UMIs
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- consensus sequence
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- bam
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- sam
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tools:
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- fgbio:
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description: Tools for working with genomic and high throughput sequencing data.
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homepage: https://github.com/fulcrumgenomics/fgbio
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documentation: http://fulcrumgenomics.github.io/fgbio/
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licence: ['MIT']
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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, collapse:false ]
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- bam:
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type: file
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description: |
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The input SAM or BAM file.
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pattern: "*.{bam,sam}"
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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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- bam:
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type: file
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description: |
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Output SAM or BAM file to write consensus reads.
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pattern: "*.{bam,sam}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@sruthipsuresh"
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