The module uses bam2fq method from samtools to
convert a SAM, BAM or CRAM file to FASTQ format
Input
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
inputbam (file)
BAM/CRAM/SAM file
*.{bam,cram,sam}
split (boolean)
TRUE/FALSE value to indicate if reads should be separated into
/1, /2 and if present other, or singleton.
Note: choosing TRUE will generate 4 different files.
Choosing FALSE will produce a single file, which will be interleaved in case
the input contains paired reads.
Output
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
versions (file)
File containing software versions
versions.yml
reads (file)
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton)
or a single interleaved .fq.gz file if the user chooses not to split the reads.
