parameters.hyperchicken.csv

#### ENVIRONMENT VARIABLES ####
queue,atd
workDir,/groups/${groupname}
dataDir,${root}/data
permanentDir,${workDir}/prm03
tmpName,tmp09
root,/apps

## change the tmpDataDir to match your environment
tmpDataDir,${workDir}/${tmpName}
tempDir,${tmpDataDir}/tmp

##### Tools and versions #####
toolchain,foss-2022a
GCCcoreVersion,GCCcore-11.3.0
GCCVersion,GCC-11.3.0
jdkVersion,Java/11-LTS
ngsUtilsVersion,ngs-utils/22.10.1
ngsRNAVersion,NGS_RNA/beta
fastqcVersion,FastQC/0.11.8-Java-11-LTS
samtoolsVersion,SAMtools/1.16.1-${GCCcoreVersion}
bedToolsVersion,BEDTools/2.30.0-${GCCcoreVersion}
BCFtoolsVersion,BCFtools/1.16-${GCCcoreVersion}
sambambaVersion,sambamba/0.7.0
rVersion,R/4.2.1-${toolchain}-bare
rPlusVersion,RPlus/4.2.1-${toolchain}-v23.01.1
picardVersion,picard/2.26.10-Java-8-LTS
htseqVersion,HTSeq/0.11.0-${GCCcoreVersion}-Python-3.10.4
hisatVersion,hisat2/2.1.0-${toolchain}
htsLibVersion,HTSlib/1.16-${GCCcoreVersion}
pythonVersion,Python/3.10.4-${GCCcoreVersion}-bare
python2Version,Python/2.7.16-${GCCcoreVersion}-bare
python2PlusVersion,PythonPlus/2.7.16-foss-2018b-v21.08.1
pythonPlusVersion,PythonPlus/3.10.4-${GCCcoreVersion}-v23.01.1
gatkVersion,GATK/4.1.4.1-Java-8-LTS
multiqcVersion,multiqc_v1.12.sif
starVersion,STAR/2.7.3a-GCC-11.3.0
picardJar,picard.jar
gatkJar,gatk-package-4.1.4.1-local.jar
mergeSamFilesJar,MergeSamFiles
trimGaloreVersion,TrimGalore/0.6.7-${GCCcoreVersion}
cutadaptVersion,cutadapt/4.2-${GCCcoreVersion}-Python-3.10.4-bare
rSeQCVersion,RSeQC/3.0.1-${GCCcoreVersion}-Python-3.10.4
leafcutterVersion,leafcutter/aa12b1e-${GCCcoreVersion}
vipVersion,vip/v3.3.1-${toolchain}
outriderVersion,outrider_latest.sif
regToolsVersion,RegTools/1.0.0-${toolchain}
rMATsVersion,rmats_v4.1.2.sif
sifDir,/apps/data/GAD/singularity/
rnaseqcVersion,${sifDir}/rnaseqc_2.4.2.sif