Description

Converts a SAM/BAM/CRAM file to FASTA

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

input:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

interleave:boolean

Set true for interleaved fasta files

Output

name:type
description
pattern

fasta

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_{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

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_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

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_singleton.fasta.gz:file

Compressed FASTA file with singleton reads

*_singleton.fasta.gz

other

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

*_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