parameters.fender.csv

#### ENVIRONMENT VARIABLES ####
queue,atd
workDir,/groups/${groupname}/
dataDir,${root}/data/
tmpName,tmp10
root,/apps/
tempDir,${workDir}/${tmpName}/tmp/
permanentDir,${workDir}/prm10
toolchain,foss-2018b
GCCcoreVersion,GCCcore-11.3.0

##### Tools and versions #####
jdkVersion,Java/11-LTS
ngsUtilsVersion,ngs-utils/22.10.1
ngsRNAVersion,NGS_RNA/beta
fastqcVersion,FastQC/0.11.8-Java-11-LTS
samtoolsVersion,SAMtools/1.9-${GCCcoreVersion}
bedToolsVersion,BEDTools/2.28.0-${GCCcoreVersion}
sambambaVersion,sambamba/0.7.0
rVersion,R/3.6.1-${toolchain}-bare
RDepBundle,RPlus/3.6.1-${toolchain}-v21.10.1
picardVersion,picard/2.20.5-Java-11-LTS
htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.7.4
hisatVersion,hisat2/2.1.0-${toolchain}
htsLibVersion,HTSlib/1.11-${GCCcoreVersion}
pythonVersion,Python/3.7.4-${GCCcoreVersion}-bare
python2Version,Python/2.7.16-${GCCcoreVersion}-bare
python2PlusVersion,PythonPlus/2.7.16-${toolchain}-v20.12.1
pythonPlusVersion,PythonPlus/3.7.4-${toolchain}-v20.02.1
gatkVersion,GATK/4.1.4.1-Java-8-LTS
multiqcVersion,multiqc_v1.12.sif
starVersion,STAR/2.7.3a-${toolchain}
picardJar,picard.jar
gatkJar,gatk-package-4.1.4.1-local.jar
mergeSamFilesJar,MergeSamFiles
trimGaloreVersion,TrimGalore/0.4.5-${GCCcoreVersion}-Python-3.7.4-bare
cutadaptVersion,cutadapt/2.6-${GCCcoreVersion}-Python-3.7.4-bare
rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.7.4
leafcutterVersion,leafcutter/aa12b1e-${toolchain}
vipVersion,vip/v3.3.1-${toolchain}
outriderVersion,outrider_latest.sif
rMATsVersion,rmats_v4.1.2.sif
sifDir,/apps/data/GAD/singularity/
rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif