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44 lines
1.6 KiB
YAML
44 lines
1.6 KiB
YAML
name: umi_tools
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version: 1.0
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description: Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
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keywords:
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- UMI
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- RMT
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- Barcode
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tools:
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- umi_tools:
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description: |
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Tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes.
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homepage: https://github.com/CGATOxford/UMI-tools
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documentation: https://umi-tools.readthedocs.io/en/latest/
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processes:
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- dedup:
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opperation: |
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Set command args to params.umitools_dedup_args
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The program will execute with the following pattern: umi_tools dedeup ARGS -I $bam -S SAMPLE_ID.dedup.bam --output-stats=SAMPLE_ID
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description: |
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Groups PCR duplicates and deduplicates reads to yield one read per group.
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Use this when you want to remove the PCR duplicates prior to any downstream analysis.
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input:
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- sample_id:
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type: string
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description: Sample identifier
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- bai:
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type: file
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description: BAM file index
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- bam:
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type: file
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description: BAM sequence file
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output:
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- dedupBam:
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type: tuple
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description: A tuple of samples id and output bam file
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pattern: *SAMPLE_ID.dedup.bam
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- report:
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type: file
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description: Log file for the umi_tools opperation
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pattern: *SAMPLE_ID.dedup.log
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authors:
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- @candiceh08
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- @chris-cheshire
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