Merge pull request #287 from RoanKanninga/b37_gearshift

B37 gearshift

parameters.csv

@@ -4,44 +4,41 @@ targetedInsertSize,200
 checkStage,module list
 
 ### Tool versions ####
+javaSuffix,Java-8-LTS
+javaVersion,Java/8-LTS
 hpoVersion,90
 gatkJar,gatk-package-4.2.4.2-local.jar
 gavinPlusJar,gavin-plus-1.5.0-RELEASE.jar
 picardJar,picard.jar
 vepDBVersion,92
 vepAssemblyVersion,GRCh37
-bcfToolsVersion,BCFtools/1.14-${toolChain_min}
-bedToolsVersion,BEDTools/2.30.0-${toolChain_min}
+bcfToolsVersion,BCFtools/1.14-${toolChain_max}
+bedToolsVersion,BEDTools/2.30.0-${toolChain_max}
 bwaVersion,BWA/0.7.17-${toolChain_min}
-computeVersion,Molgenis-Compute/v19.01.1-Java-11-LTS
-caddVersion,CADD/v1.4-foss-2018b
+computeVersion,Molgenis-Compute/v19.01.1-${javaSuffix}
+caddVersion,CADD/v1.4-${toolChain_max}
 convadingVersion,1.2.1-${toolChain_min}
-cutadaptVersion,cutadapt/1.13-${toolChain_max}-Python-2.7.10
-fastqcVersion,FastQC/0.11.9-Java-8-LTS
-gatkVersion,GATK/4.2.4.1-Java-8-LTS
-gavinPlusVersion,gavin-plus/1.5.0-Java-11-LTS
-hashdeepVersion,hashdeep/4.4-foss-2015b
-htsLibVersion,HTSlib/1.14-${toolChain_min}
+fastqcVersion,FastQC/0.11.9-${javaSuffix}
+gatkVersion,GATK/4.2.4.1-${javaSuffix}
+gavinPlusVersion,gavin-plus/1.5.0-${javaSuffix}
+hashdeepVersion,hashdeep/4.4-${toolChain_max}
+htsLibVersion,HTSlib/1.14-${toolChain_max}
 iolibVersion,io_lib/1.14.11-${toolChain_min}
-javaVersion,Java/8-LTS
 mantaVersion,manta/1.6.0-${toolChain_min}
-multiQCVersion,multiqc/1.11-${toolChain_min}-Python-3.7.4-bare
-ngsUtilsVersion,ngs-utils/19.03.3-${toolChain_min}
+multiQCVersion,multiqc/1.11-${toolChain_max}
+ngsUtilsVersion,ngs-utils/22.01.1
 perlPlusVersion,PerlPlus/5.30.0-${toolChain_min}-v19.08.1
 plink1Version,PLINK/1.07-x86_64
 plink2Version,plink/1.9-beta6-20190617
 plinkSeqVersion,plinkseq/x86_64-0.10
-picardVersion,picard/2.26.10-Java-11-LTS
-pigzVersion,pigz/2.7-${toolChain_min}
-rVersion,R/3.6.1-${toolChain_max}-bare
+picardVersion,picard/2.26.10-${javaSuffix}
+pigzVersion,pigz/2.7-${toolChain_max}
 sambambaVersion,sambamba/0.7.0
-samtoolsVersion,SAMtools/1.14-${toolChain_min}
+samtoolsVersion,SAMtools/1.14-${toolChain_max}
 seqTkVersion,seqtk/1.3-${toolChain_min}
-snpEffVersion,snpEff/4.3t-Java-11-LTS
+snpEffVersion,snpEff/4.3t-Java-${javaSuffix}
 vcfAnnoVersion,vcfanno/v0.3.3
 vepVersion,VEP/90.5
-verifyBamIDVersion,verifyBamID/1.1.3-${toolChain_min}
-xhmmVersion,xhmm/2016-01-04-cc14e528d909-${toolChain_max}
 
 ##### GENERAL DIRECTORIES #####
 dataDir,${appsDir}/data/

parameters_wingedhelix.csv

@@ -0,0 +1,7 @@
+queue,wh-vcompute
+prmName,prm07
+prmHost,wh-helper.hpc.rug.nl
+root,/
+appsDir,${root}/apps/
+toolChain_max,foss-2018b
+toolChain_min,GCCcore-7.3.0