Merge pull request #59 from molgenis/fix/14-fixModVersions-v1.1.0

Fix #14 Fix module versions (backport)
molgenis · Oct 19, 2020 · 9bec5b4 · 9bec5b4
2 parents e4aaf88 + dabe524
commit 9bec5b4
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Showing 5 changed files with 22 additions and 13 deletions.
diff --git a/pipeline_annotate.sh b/pipeline_annotate.sh
@@ -180,8 +180,8 @@ ops=["self"]
 names=["CAP"]
 EOT
 
-module load vcfanno
-module load HTSlib
+module load "${MOD_VCF_ANNO}"
+module load "${MOD_HTS_LIB}"
 
 VCFANNO_ARGS="-p ${CPU_CORES} ${VCFANNO_PRE_CONF} ${VCFANNO_INPUT}"
 vcfanno ${VCFANNO_ARGS} | bgzip > ${VCFANNO_OUTPUT}
@@ -206,7 +206,7 @@ CAPICE_OUTPUT_VCF="${CAPICE_OUTPUT_DIR}"/vcfanno_bcftools_filter_capice.vcf.gz
 rm -rf "${CAPICE_OUTPUT_DIR}"
 mkdir -p "${CAPICE_OUTPUT_DIR}"
 
-module load BCFtools
+module load "${MOD_BCF_TOOLS}"
 bcftools filter -i 'CAP="."' --threads "${CPU_CORES}" "${BCFTOOLS_FILTER_INPUT}" | bgzip -c > "${BCFTOOLS_FILTER_OUTPUT}"
 module purge
 
@@ -218,14 +218,14 @@ else
 	VCFANNO_ALL_OUTPUT="${CAPICE_OUTPUT_DIR}"/vcfanno_all.vcf.gz
 	echo "calculating CAPICE scores for variants without precomputed score ..."
 
-	module load CADD
+	module load "${MOD_CADD}"
 	# strip headers from input vcf for cadd
 	CADD_INPUT="${CAPICE_OUTPUT_DIR}/input_headerless_$(date +%s).vcf.gz"
 	gunzip -c $CAPICE_INPUT | sed '/^#/d' | bgzip > ${CADD_INPUT}
 	CADD.sh -a -g ${ASSEMBLY} -o ${CAPICE_OUTPUT_DIR}/cadd.tsv.gz -c ${CPU_CORES} -s ${CADD_INPUT}
 	module purge
 
-	module load CAPICE
+	module load "${MOD_CAPICE}"
 	python ${EBROOTCAPICE}/CAPICE_scripts/model_inference.py \
 	--input_path ${CAPICE_OUTPUT_DIR}/cadd.tsv.gz \
 	--model_path ${EBROOTCAPICE}/CAPICE_model/${ASSEMBLY}/xgb_booster.pickle.dat \
@@ -255,8 +255,8 @@ ops=["self"]
 names=["CAP"]
 EOT
 
-	module load vcfanno
-	module load HTSlib
+	module load "${MOD_VCF_ANNO}"
+	module load "${MOD_HTS_LIB}"
 
 	VCFANNO_ARGS="-p ${CPU_CORES} ${VCFANNO_POST_CONF} ${VCFANNO_OUTPUT}"
 	vcfanno ${VCFANNO_ARGS} | bgzip > ${VCFANNO_ALL_OUTPUT}
@@ -274,7 +274,7 @@ VEP_OUTPUT_STATS="${VEP_OUTPUT}"
 rm -rf "${VEP_OUTPUT_DIR}"
 mkdir -p "${VEP_OUTPUT_DIR}"
 
-module load VEP
+module load "${MOD_VEP}"
 VEP_ARGS="\
 --input_file ${VEP_INPUT} --format vcf \
 --output_file ${VEP_OUTPUT} --vcf"

diff --git a/pipeline_filter.sh b/pipeline_filter.sh
@@ -194,7 +194,7 @@ if [ -z "${TMPDIR+x}" ]; then
 	TMPDIR=/tmp
 fi
 
-module load vcf-decision-tree
+module load "${MOD_VCF_DECISION_TREE}"
 java -Djava.io.tmpdir="${TMPDIR}" -XX:ParallelGCThreads=2 -jar "${EBROOTVCFMINDECISIONMINTREE}"/vcf-decision-tree.jar ${DECISION_TREE_ARGS}
 module purge
 
@@ -203,8 +203,8 @@ BCFTOOLS_FILTER_INPUT="${DECISION_TREE_OUTPUT}"
 BCFTOOLS_FILTER_OUTPUT="${OUTPUT}"
 BCFTOOLS_FILTER_ARGS="--threads ${CPU_CORES} ${BCFTOOLS_FILTER_INPUT}"
 
-module load BCFtools
-module load HTSlib
+module load "${MOD_BCF_TOOLS}"
+module load "${MOD_HTS_LIB}"
 if [[ "${BCFTOOLS_FILTER_OUTPUT}" == *.vcf.gz ]]
 then
 	bcftools filter -i'VIPC=="T"' ${BCFTOOLS_FILTER_ARGS} | bgzip -c > "${BCFTOOLS_FILTER_OUTPUT}"

diff --git a/pipeline_preprocess.sh b/pipeline_preprocess.sh
@@ -127,7 +127,7 @@ fi
 
 PREPROCESS_INPUT="${INPUT}"
 
-module load BCFtools
+module load "${MOD_BCF_TOOLS}"
 
 BCFTOOLS_ARGS="\
 norm \

diff --git a/pipeline_report.sh b/pipeline_report.sh
@@ -136,7 +136,7 @@ if [ -z "${TMPDIR+x}" ]; then
 	TMPDIR=/tmp
 fi
 
-module load vcf-report
+module load "${MOD_VCF_REPORT}"
 
 REPORT_ARGS="-i ${INPUT} -o ${OUTPUT}"
 if [ ! -z "${INPUT_PED}" ]; then

diff --git a/utils/header.sh b/utils/header.sh
@@ -1,2 +1,11 @@
 #!/bin/bash
 set -euo pipefail
+
+MOD_BCF_TOOLS="BCFtools/1.10.2-GCCcore-7.3.0"
+MOD_CADD="CADD/v1.4-foss-2018b"
+MOD_CAPICE="CAPICE/v1.3.0-foss-2018b"
+MOD_HTS_LIB="HTSlib/1.10.2-GCCcore-7.3.0"
+MOD_VCF_ANNO="vcfanno/v0.3.2"
+MOD_VCF_DECISION_TREE="vcf-decision-tree/v0.0.1-Java-11-LTS"
+MOD_VCF_REPORT="vcf-report/v1.0.2-Java-11-LTS"
+MOD_VEP="VEP/100.4-foss-2018b-Perl-5.28.0"