Converts a SAM/BAM/CRAM file to FASTA
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
interleave
:boolean
Set true for interleaved fasta files
fasta
*_{1,2}.fasta.gz
Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files.
interleaved
*_interleaved.fasta.gz
Compressed FASTA file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
singleton
*_singleton.fasta.gz
Compressed FASTA file with singleton reads
other
*_other.fasta.gz
Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset
versions_samtools
${task.process}
:string
The process the versions were collected from
samtools
The tool name
samtools version | sed '1!d;s/.* //'
The command used to generate the version of the tool
versions
Tools for dealing with SAM, BAM and CRAM files
