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:false ]
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
bam
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_mergedReads.bam:file
A BAM file with suffix_mergedReads.bam
*_mergedReads.bam
txt
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.txt.gz:file
A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz
*.txt.gz
versions
versions.yml:file
File containing software versions
versions.yml
Tools
atlas
GPL v3
ATLAS, a suite of methods to accurately genotype and estimate genetic diversity
