nf-core_modules/software/umi_tools/umi_tools.yml

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