Remove polyA tail and artificial concatemers
meta
:map
Groovy Map containing sample information e.g. [ id:’test ]
bam
:file
BAM file, cleaned ccs generated by lima
*.bam
primers
fasta file of primers
*.fasta
Groovy Map containing sample information e.g. [ id:‘test’ ]
Set of complete reads (with polyA tail), where the polyA has been trimmed
pbi
*.bam.pbi
Pacbio index file from polyA trimmed reads
*.pbi
consensusreadset
*.consensusreadset.xml
Metadata about read library
*.xml
summary
*.filter_summary.report.json
json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads
*.json
report
*.report.csv
Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name)
*.csv
versions_isoseq
${task.process}
:string
The name of the process
isoseq
The name of the tool
isoseq refine --version | head -n 1 | sed 's/isoseq refine //' | sed 's/ (commit.\+//'
:eval
The expression to obtain the version of the tool
versions
IsoSeq - Scalable De Novo Isoform Discovery
