 A wrapper for biobambam2 bamtofastq tool. See the [dockstore-biobambam2](https://github.com/cancerit/dockstore-biobambam2) website for more information about this wrapper. For queries relating to the underlying software see [biobambam2](https://github.com/gt1/biobambam2). __Minimum Dockstore Version__: 1.2.3 Usage at time of writing: ``` biobambam2 is distributed under version 3 of the GNU General Public License. Key=Value pairs: F= : matched pairs first mates (file name, NO path) F2= : matched pairs second mates (file name, NO path) S= : single end (file name, NO path) O= : unmatched pairs first mates (file name, NO path) O2= : unmatched pairs second mates (file name, NO path) collate= : collate pairs combs= : print some counts after collation based processing filename= : input filename (default: read file from standard input) inputformat= : input format: cram, bam or sam reference= : name of reference FastA in case of inputformat=cram ranges= : input ranges (bam and cram input only, default: read complete file) exclude= : exclude alignments matching any of the given flags disablevalidation= : disable validation of input data colhlog= : base 2 logarithm of hash table size used for collation colsbs= : size of hash table overflow list in bytes gz= : compress output streams in gzip format (default: 0) level= : compression setting if gz=1 (-1=zlib default,0=uncompressed,1=fast,9=best) fasta= : output FastA instead of FastQ inputbuffersize= : size of input buffer outputperreadgroup= : split output per read group (for collate=1 only) outputperreadgroupsuffixF= : suffix for F category when outputperreadgroup=1 (.gz not added when gz=1) outputperreadgroupsuffixF2= : suffix for F2 category when outputperreadgroup=1 (.gz not added when gz=1) outputperreadgroupsuffixO= : suffix for O category when outputperreadgroup=1 (.gz not added when gz=1) outputperreadgroupsuffixO2= : suffix for O2 category when outputperreadgroup=1 (.gz not added when gz=1) outputperreadgroupsuffixS= : suffix for S category when outputperreadgroup=1 (.gz not added when gz=1) tryoq= : use OQ field instead of quality field if present (collate={0,1} only) split= : split named output files into chunks of this amount of reads (0: do not split) splitprefix= : file name prefix if collate=0 and split>0 (NO path elements) tags= : list of aux tags to be copied (default: do not copy any aux fields) outputperreadgrouprgsm= : add read group field SM ahead of read group id when outputperreadgroup=1 (for collate=1 only) outputperreadgroupprefix= : prefix added in front of file names if outputperreadgroup=1 (for collate=1 only) (NO path elements) Alignment flags: PAIRED,PROPER_PAIR,UNMAP,MUNMAP,REVERSE,MREVERSE,READ1,READ2,SECONDARY,QCFAIL,DUP,SUPPLEMENTARY ``` Some options are not available within the wrapper: ``` outputdir=<> : directory for output if outputperreadgroup=1 (default: current directory) T= : temporary file name ``` All option names have been maintained in the CWL mapping. NOTE: Please ensure you use file extensions that match the following so that outputs are captured: * For FASTQ: * `.fq` * `.fq.gz` * For FASTA: * `.fa` * `.fa.gz`
This is a companion discussion topic for the original entry at https://dockstore.org/containers/quay.io/wtsicgp/dockstore-biobambam2/bamtofastq