Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false, strandedness:‘forward’ ]
meta.strandedness can be use in ext.args to set -p argument
(see ./tests/nextflow.config)
cram
:file
Input cram file
*.{cram}
crai
:file
Index file for cram file
*.{crai}
gff
:file
Feature file with regions of interest
*.{gff,gtf,bed}
fasta
:file
Reference file of cram file
*.{fasta,fa,fna}
fasta_fai
:file
Index file for reference file
*.{fai}
Output
name:type
description
pattern
results
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}
:directory
Qualimap results dir
*/*
versions_qualimap
${task.process}
:string
The name of the process
qualimap
:string
The name of the tool
qualimap -h | sed -n 's/^QualiMap v.//p'
:eval
The expression to obtain the version of the tool
versions_samtools
${task.process}
:string
The name of the process
samtools
:string
The name of the tool
samtools version | sed '1!d;s/.* //'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The name of the process
qualimap
:string
The name of the tool
qualimap -h | sed -n 's/^QualiMap v.//p'
:eval
The expression to obtain the version of the tool
${task.process}
:string
The name of the process
samtools
:string
The name of the tool
samtools version | sed '1!d;s/.* //'
:eval
The expression to obtain the version of the tool
Tools
qualimap
GPL-2.0-only
Qualimap 2 is a platform-independent application written in
Java and R that provides both a Graphical User Interface and
a command-line interface to facilitate the quality control of
alignment sequencing data and its derivatives like feature counts.
