Fix decision tree issues (regarding FLAG and FILE support) (#597)

* Bump Decision tree module to 4.1.1

* New checksum for decision tree

* bump vip version

* update md5sum for decision tree sif

* bump straglr

* Update straglr md5sum

config/nxf_call_str.config

@@ -2,7 +2,7 @@ includeConfig 'nxf.config'
 
 env {
   CMD_EXPANSIONHUNTER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/expansionhunter-5.0.0.sif ExpansionHunter"
-  CMD_STRAGLR="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/straglr-1.4.4_vip_v2.sif straglr-genotype"
+  CMD_STRAGLR="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/straglr-1.4.4_vip_v3.sif straglr-genotype"
 }
 
 params {

config/nxf_vcf.config

@@ -8,7 +8,7 @@ env {
   CMD_FILTERVEP = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vep-111.0.sif filter_vep"
   CMD_STRANGER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/stranger-0.8.1.sif stranger"
   CMD_VCFREPORT="apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-report-6.0.2.sif"
-  CMD_VCFDECISIONTREE = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-4.0.0.sif"
+  CMD_VCFDECISIONTREE = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-decision-tree-4.1.1.sif"
   CMD_VCFINHERITANCEMATCHER = "apptainer exec --no-mount home --bind \${TMPDIR} ${APPTAINER_CACHEDIR}/vcf-inheritance-matcher-3.1.0.sif"
 
   // workaround for SAMtools https://github.com/samtools/samtools/issues/1366#issuecomment-769170935

install.sh

@@ -82,9 +82,9 @@ download_files() {
   urls+=("7486bd5de526d9888df8eea2d8bdea48" "images/minimap2-2.27.sif")
   urls+=("06ac8a76a307fa42fffd80ab906fd24b" "images/picard-3.1.1.sif")
   urls+=("9a4b685b26744113d3ea0a3904c02706" "images/samtools-1.17-patch1.sif")
-  urls+=("556d7e6b523e282f9920729edc3d0842" "images/straglr-1.4.4_vip_v2.sif")
+  urls+=("8f6e06847776448e004df8b863571109" "images/straglr-1.4.4_vip_v3.sif")
   urls+=("bcc157242cd9b09c66f015c52ef2d61d" "images/stranger-0.8.1.sif")
-  urls+=("4fbbd8642ead7754cb8cc19740e18175" "images/vcf-decision-tree-4.0.0.sif")
+  urls+=("57401e7b835fed2f52fafadc0dd744d4" "images/vcf-decision-tree-4.1.1.sif")
   urls+=("9c4d7b48138f29651cdd45eb8d0cc4b6" "images/vcf-inheritance-matcher-3.1.0.sif")
   urls+=("7f3c5115f68998067a404c922b2e3b15" "images/vcf-report-6.0.2.sif")
   urls+=("7bffc236a7c65b2b2e2e5f7d64beaa87" "images/vep-111.0.sif")

utils/apptainer/build.sh

@@ -93,8 +93,8 @@ main() {
   images+=("picard-3.1.1")
   images+=("samtools-1.17-patch1")
   images+=("stranger-0.8.1")
-  images+=("straglr-1.4.4_vip_v2")
-  images+=("vcf-decision-tree-4.0.0")
+  images+=("straglr-1.4.4_vip_v3")
+  images+=("vcf-decision-tree-4.1.1")
   images+=("vcf-inheritance-matcher-3.1.0")
   images+=("vcf-report-6.0.2")
 

utils/apptainer/def/straglr-1.4.4_vip_v2.def → utils/apptainer/def/straglr-1.4.4_vip_v3.def

@@ -11,8 +11,8 @@ From: sif/build/ubuntu-22.04.sif
     curl -Ls -o /opt/trf/trf "https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64"
     chmod +x /opt/trf/trf
 
-    #3e9fbcb77984617151d4010fee087ea423d998f9 == v1.4.4_vip_v2
-    pip install git+https://github.com/molgenis/straglr.git@3e9fbcb77984617151d4010fee087ea423d998f9#egg=straglr
+    #fef64d4240293df0ddae0a190fb20c5ed9c6c129 == v1.4.4_vip_v3
+    pip install git+https://github.com/molgenis/straglr.git@fef64d4240293df0ddae0a190fb20c5ed9c6c129#egg=straglr
 
     # cleanup
     pip cache purge

utils/apptainer/def/vcf-decision-tree-4.0.0.def → utils/apptainer/def/vcf-decision-tree-4.1.1.def

@@ -7,16 +7,16 @@ From: sif/build/openjdk-17.sif
 
 %post
     version_major=4
-    version_minor=0
-    version_patch=0
+    version_minor=1
+    version_patch=1
 
     # install
     apk update
     apk add --virtual=.build-dependencies curl
 
     mkdir -p /opt/vcf-decision-tree/lib
     curl -Ls -o /opt/vcf-decision-tree/lib/vcf-decision-tree.jar "https://github.com/molgenis/vip-decision-tree/releases/download/v${version_major}.${version_minor}.${version_patch}/vcf-decision-tree.jar"
-    echo "4029e1d488478a1e71214b352ef17b088bbb9ba3eff86036ef5e0fdf60fad33e  /opt/vcf-decision-tree/lib/vcf-decision-tree.jar" | sha256sum -c
+    echo "5c18aa3c302bbc4120c0fae50bca99828f7304837a52d96606bea0133a140780  /opt/vcf-decision-tree/lib/vcf-decision-tree.jar" | sha256sum -c
 
     # cleanup
     apk del .build-dependencies

vip.sh

@@ -7,7 +7,7 @@ SCRIPT_NAME="$(basename "$0")"
 # SCRIPT_DIR is incorrect when vip.sh is submitted as a Slurm job that is submitted as part of another Slurm job
 VIP_DIR="${VIP_DIR:-"${SCRIPT_DIR}"}"
 
-VIP_VERSION="7.7.0"
+VIP_VERSION="7.7.1"
 
 display_version() {
   echo -e "${VIP_VERSION}"