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45 lines
1.9 KiB
YAML
45 lines
1.9 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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operation: |
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Set command args to params.umitools_dedup_args
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The program will execute with the following pattern:
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umi_tools dedup --log={SAMPLE_ID}.dedup.log {params.umitools_dedup_args} -I {SAMPLE_ID}.bam -S {SAMPLE_ID}.dedup.bam --output-stats={SAMPLE_ID}
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description: |
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Groups PCR duplicates and de-duplicates 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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- bam:
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type: file array
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description: BAM sequence file and associated BAI index 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, "*SAMPLE_ID.dedup.bam"]
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- dedupBam:
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type: tuple
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description: A tuple of samples id and output bai file
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pattern: [sample_id, "*SAMPLE_ID.dedup.bam.bai"]
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- report:
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type: file
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description: Log file for the umi_tools operation
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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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