endorS.py calculates endogenous DNA from samtools flagstat files and print to screen
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
stats_raw
:file
output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed
stats_qualityfiltered
:file
output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d
stats_deduplicated
:file
output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads
Output
name:type
description
pattern
json
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*_mqc.json
:file
file with the endogenous DNA calculation tailored for multiQC
*_mqc.json
versions_endorspy
${task.process}
:string
The name of the process
endorspy
:string
The name of the tool
endorspy --version 2>&1 | sed 's/^endorS.py //'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
endorspy
:string
The name of the tool
endorspy --version 2>&1 | sed 's/^endorS.py //'
:eval
The expression to obtain the version of the tool
Tools
endorspy
GPL v3
endorS.py calculates percent on target and/or clonality from samtools flagstat files and print to screen
