split single end read groups by length and merge paired end reads
Input
Name (Type)
Description
Pattern
meta (map)
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
bam (file)
Single input BAM file.
*.bam
bai (file)
The BAI file for the input BAM file
*.bai
read_group_settings (file)
TXT file containing the split and merge settings for
each readgroup. Each line consist of one readgroup,
single/double identifier and the maximum cycle number
of the sequencer. e.g. “RG1 single 100”
*.txt
blacklist (file)
blacklist.txt (optional), A txt file with blacklisted read names
that should be ignored and just written to file, each on a new line
*.txt
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
bam (file)
A BAM file with suffix_mergedReads.bam
*_mergedReads.bam
txt (file)
A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz