Convert sam files to tsv files
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
bam{:bash}
:file
BAM/CRAM file from alignment
*.{bam,cram}
bai{:bash}
BAI/CRAI file from alignment
*.{bai,crai}
regions_file{:bash}
Optional. Restrict to regions listed in a file
*.{vcf,bed,gtf,gff,vcf.gz,bed.gz,gtf.gz,gff.gz}
meta2{:bash}
Groovy Map containing reference information e.g. [id: ‘reference’]
fasta{:bash}
Reference genome
*.{fasta,fa}
fasta_index{:bash}
Reference genome information for fasta index
*.{fasta.fai,fa.fai}
fasta_dict{:bash}
Reference genome information for fasta dict
*.{.dict}
tsv{:bash}
Groovy Map containing TSV information e.g. [ id:‘test’ ]
*.tsv{:bash}
Output file
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Java utilities for Bioinformatics.
