Merge pull request #10 from RoanKanninga/master

small fixes
molgenis · Nov 18, 2024 · 75eb4dd · 75eb4dd
2 parents 051b9f1 + fa69dd6
commit 75eb4dd
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/parameters.csv b/parameters.csv
@@ -11,7 +11,7 @@ gapVersion,GAP/2.8.0
 pythonVersion,Python/3.9.1-${toolChain_min}-bare
 boostVersion,Boost/1.79.0-GCC-11.3.0
 htslibVersion,HTSlib/1.19.1-${toolChain_min}
-RPlusVersion,RPlus/4.2.1-foss-2022a-v22.12.1
+rVersion,R/4.2.2-foss-2022a
 nextflowVersion,nextflow/21.10.6-Java-11-LTS
 bcfToolsVersion,BCFtools/1.19-${toolChain_min}
 javaVersion,Java/11-LTS

diff --git a/protocols_compute/cnv_genotype_call_integration.sh b/protocols_compute/cnv_genotype_call_integration.sh
@@ -27,5 +27,7 @@ ml "${plinkVersion}"
 mkdir -p "${cnvOutDir}.integrated_genotypes_filtered"
 
 plink --bfile 'chr_22_filtered' \
---bmerge "${cnvOutDir}.reweighed_b_dosage.bed" "${cnvOutDir}.reweighed_b_dosage.bim" "${cnvOutDir}.reweighed_b_dosage.fam" \
+--bmerge "${cnvOutDir}.reweighed_b_dosage.bed" \
+"${cnvOutDir}.reweighed_b_dosage.bim" \
+"${cnvOutDir}.reweighed_b_dosage.fam" \
 --make-bed --out "${cnvOutDir}.integrated_genotypes_filtered/chr_22"
diff --git a/protocols_compute/sample_filtering.sh b/protocols_compute/sample_filtering.sh
@@ -2,7 +2,7 @@
 
 #string pgxVersion
 #string plink2Version
-#string RPlusVersion
+#string rVersion
 
 #string sampleListPrefix
 #string concatenatedGenotypesOutputDir
@@ -13,7 +13,7 @@ set -u
 
 module load "${pgxVersion}"
 module load "${plink2Version}"
-module load "${RPlusVersion}"
+module load "${rVersion}"
 #export R_LIBS_USER=${rLibsPath}
 
 sampleListPrefixFolder=$(dirname "${sampleListPrefix}")