m2 location funcotator

broadinstitute · Apr 8, 2022 · 957c907 · 957c907
1 parent 69861d4
commit 957c907
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Showing 3 changed files with 3 additions and 22 deletions.
diff --git a/.github/actions/install-cromwell/action.yml b/.github/actions/install-cromwell/action.yml
@@ -16,23 +16,4 @@ runs:
       run: |
         wget -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/cromwell-${{ inputs.CROMWELL_VERSION }}.jar;
         wget -O $WOMTOOL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ inputs.CROMWELL_VERSION }}/womtool-${{ inputs.CROMWELL_VERSION }}.jar;
-      shell: bash
-
-
-
-
-
-
-#
-#installCromwell:
-#  runs-on: ubuntu-latest
-#  name: Cromwell Local Setup
-#  steps:
-#    - name: Set Cromwell env variables
-#      run: |
-#        echo "CROMWELL_JAR=${HOME}/cromwell-${{ env.inputs.CROMWELL_VERSION }}.jar" >> $GITHUB_ENV;
-#        echo "WOMTOOL_JAR=${HOME}/womtool-${{ env.inputs.CROMWELL_VERSION }}.jar" >> $GITHUB_ENV;
-#    - name: Download Cromwell and Womtools
-#      run: |
-#        wget -O $CROMWELL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ env.inputs.CROMWELL_VERSION }}/cromwell-${{ env.inputs.CROMWELL_VERSION }}.jar;
-#        wget -O $WOMTOOL_JAR https://github.com/broadinstitute/cromwell/releases/download/${{ env.inputs.CROMWELL_VERSION }}/womtool-${{ env.inputs.CROMWELL_VERSION }}.jar;
+      shell: bash
diff --git a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -l
-##set -e
+set -e
 
 MODE=$1
 # We split up the test into CASE in COHORT to reduce overall test runtime

diff --git a/scripts/m2_cromwell_tests/test_m2_wdl_multi.json b/scripts/m2_cromwell_tests/test_m2_wdl_multi.json
@@ -5,7 +5,7 @@
   "Mutect2_Multi.ref_fai": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta.fai",
   "Mutect2_Multi.ref_dict": "/home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.dict",
   "Mutect2_Multi.pair_list": "/home/runner/work/gatk/gatk/scripts/m2_cromwell_tests/pair_list",
-  "Mutect2_Multi.funco_data_sources_tar_gz": "/home/runner/work/gatk/gatk/build/broadinstitute/small_ds_pik3ca.tar.gz",
+  "Mutect2_Multi.funco_data_sources_tar_gz": "/home/runner/work/gatk/gatk/small_ds_pik3ca.tar.gz",
   "Mutect2_Multi.funco_reference_version": "hg19",
   "Mutect2_Multi.scatter_count": 2,
   "Mutect2_Multi.run_orientation_bias_mixture_model_filter": true,