readCounter function from HMMcopy utilities, used to generate read in windows
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM/CRAM file
*.{bam,cram}
bai
BAM/CRAM index file
*.{bai}
meta2
fasta
Genome fasta file. Required when using a CRAM file.
wig
*.wig
A wig file with the number of reads lying within each window in each chromosome
versions_hmmcopy
${task.process}
:string
The name of the process
hmmcopy
The name of the tool
0.1.1
The expression to obtain the version of the tool
versions_samtools
samtools
samtools version | sed '1!d;s/.* //'
:eval
versions
C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
