Converts a SAM/BAM/CRAM file to FASTA
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
input
BAM/CRAM/SAM file
*.{bam,cram,sam}
interleave
Set true for interleaved fasta files
versions
File containing software versions
versions.yml
fasta
Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files.
*_{1,2}.fasta.gz
interleaved
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
Compressed FASTA file with singleton reads
*_singleton.fasta.gz
other
Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset
*_other.fasta.gz
Tools for dealing with SAM, BAM and CRAM files
