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:file
Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files.
*_{1,2}.fasta.gz
interleaved
*_interleaved.fasta.gz:file
Compressed FASTA file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
*_interleaved.fasta.gz
singleton
*_singleton.fasta.gz:file
Compressed FASTA file with singleton reads
*_singleton.fasta.gz
other
*_other.fasta.gz:file
Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset
*_other.fasta.gz
versions
versions.yml:file
File containing software versions
versions.yml
Tools for dealing with SAM, BAM and CRAM files
