Nextflow Registry | nf-core/isoseq/cluster@0.0.0-6c4ed3a

nf-core/isoseq/cluster @ 0.0.0-6c4ed3a

IsoSeq - Cluster - Cluster trimmed consensus sequences

cluster HiFi isoseq Pacbio

Latest version: 0.0.0-6c4ed3a

Total downloads: 3

Source: nf-core/modules

Authors: @sguizard

Maintainers: @sguizard

IsoSeq - Cluster - Cluster trimmed consensus sequences

Add the following snippet to your workflow script to include this module.

include { ISOSEQ_CLUSTER } from 'nf-core/isoseq/cluster'

MIT License

Process

`Name`	`ISOSEQ_CLUSTER`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`bam` file	BAM file generated by isoseq refine `*.bam`

Output 12 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.bam` file	BAM file of clustered consensus `*.transcripts.bam`

#2 pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.bam.pbi` file	Pacbio Index of consensus reads generated by clustering `*.transcripts.bam.pbi`

#3 hq_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.hq.bam` file	High quality reads (when --use-qvs is set) `*.transcripts.hq.bam`

#4 hq_pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.hq.bam.pbi` file	Pacbio index of high quality reads (when --use-qvs is set) `*.transcripts.hq.bam.pbi`

#5 lq_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.lq.bam` file	Low quality reads (when --use-qvs is set) `*.transcripts.lq.bam`

#6 lq_pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.lq.bam.pbi` file	Pacbio index of low quality reads (when --use-qvs is set) `*.transcripts.lq.bam.pbi`

#7 cluster tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.cluster` file	A two columns (from, to) file describing original read name to new read name `*.transcripts.cluster`

#8 versions

`versions.yml` file	File containing software version `versions.yml`

#9 transcriptset tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.transcriptset.xml` file	A metadata xml file which contains full paths to data files `*.transcripts.transcriptset.xml`

#10 cluster_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.cluster_report.csv` file	A table files clusters (transcripts) members (read) `*.transcripts.cluster_report.csv`

#11 singletons_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.transcripts.singletons.bam` file	Unclustered reads (when --singletons is set) `*.transcripts.singletons.bam`

#12 singletons_pbi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]