diff --git a/pipeline_annotate.sh b/pipeline_annotate.sh index a2dfa3a4d..bdcd99879 100644 --- 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 ${VEP_OUTPUT} --vcf" diff --git a/pipeline_filter.sh b/pipeline_filter.sh index d68e32e80..f2d663cf4 100644 --- a/pipeline_filter.sh +++ b/pipeline_filter.sh @@ -194,7 +194,7 @@ if [ -z "${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 index e3eb6b6a2..0b65519f0 100644 --- 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 index ea54c2a73..947b796ed 100644 --- 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 index e5adf607c..6442f8bdd 100644 --- 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" \ No newline at end of file