IsoSeq - Cluster - Cluster trimmed consensus sequences
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
bam
:file
BAM file generated by isoseq refine
*.bam
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.transcripts.bam
BAM file of clustered consensus
pbi
*.transcripts.bam.pbi
Pacbio Index of consensus reads generated by clustering
cluster
*.transcripts.cluster
A two columns (from, to) file describing original read name to new read name
cluster_report
*.transcripts.cluster_report.csv
A table files clusters (transcripts) members (read)
transcriptset
*.transcripts.transcriptset.xml
A metadata xml file which contains full paths to data files
hq_bam
*.transcripts.hq.bam
High quality reads (when —use-qvs is set)
hq_pbi
*.transcripts.hq.bam.pbi
Pacbio index of high quality reads (when —use-qvs is set)
lq_bam
*.transcripts.lq.bam
Low quality reads (when —use-qvs is set)
lq_pbi
*.transcripts.lq.bam.pbi
Pacbio index of low quality reads (when —use-qvs is set)
singletons_bam
*.transcripts.singletons.bam
Unclustered reads (when —singletons is set)
singletons_pbi
*.transcripts.singletons.bam.pbi
Pacbio index of unclustered reads (when —singletons is set)
versions_isoseq
${task.process}
:string
The name of the process
isoseq
The name of the tool
isoseq cluster --version | head -n 1 | sed 's/isoseq cluster //g' | sed 's/ (.*//g'
:eval
The expression to obtain the version of the tool
versions
