You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
82 lines
2.3 KiB
YAML
82 lines
2.3 KiB
YAML
name: isoseq3_cluster
|
|
description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
|
|
keywords:
|
|
- cluster
|
|
tools:
|
|
- isoseq3:
|
|
description: IsoSeq3 - Cluster - Cluster trimmed consensus sequences
|
|
homepage: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
|
|
documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
|
|
tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md
|
|
doi: ""
|
|
licence: ['BSD-3-clause-Clear']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test' ]
|
|
- bam:
|
|
type: file
|
|
description: BAM file generated by isoseq3 refine
|
|
pattern: "*.bam"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "versions.yml"
|
|
- bam:
|
|
type: file
|
|
description: BAM file of clustered consensus
|
|
pattern: "*.bam"
|
|
- pbi:
|
|
type: file
|
|
description: Pacbio Index of consensus reads generated by clustering
|
|
pattern: "*.pbi"
|
|
- cluster:
|
|
type: file
|
|
description: A two columns (from, to) file describing original read name to new read name
|
|
pattern: "*.cluster"
|
|
- cluster_report:
|
|
type: file
|
|
description: A table files clusters (transcripts) members (read)
|
|
pattern: "*.cluster_report.csv"
|
|
- transcriptset:
|
|
type: file
|
|
description: A metadata xml file which contains full paths to data files
|
|
pattern: "*.clustered.transcriptset.xml"
|
|
- hq_bam:
|
|
type: file
|
|
description: High quality reads
|
|
pattern: "*.hq.bam"
|
|
- hq_pbi:
|
|
type: file
|
|
description: Pacbio index of high quality reads
|
|
pattern: "*.hq.bam.pbi"
|
|
- lq_bam:
|
|
type: file
|
|
description: Low quality reads
|
|
pattern: "*.lq.bam"
|
|
- lq_pbi:
|
|
type: file
|
|
description: Pacbio index of low quality reads
|
|
pattern: "*.lq.bam.pbi"
|
|
- singletons_bam:
|
|
type: file
|
|
description: Unclustered reads
|
|
pattern: "*.singletons.bam"
|
|
- singletons_pbi:
|
|
type: file
|
|
description: Pacbio index of unclustered reads
|
|
pattern: "*.singletons.bam.pbi"
|
|
|
|
authors:
|
|
- "@sguizard"
|