Merge pull request wtsi-npg#783 from mgcam/branch_propagation_in_ci

Correct propagation of the CI target branch.

.github/workflows/run-tests.yml

@@ -13,8 +13,8 @@ jobs:
     env:
       PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
       NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
-      WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
-      WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF}
+      WSI_NPG_GITHUB_URL: https://github.com/wtsi-npg
+      WSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
 
 
     strategy:

Changes

@@ -41,6 +41,8 @@ LIST OF CHANGES
    'analysis'). The duplicate runfolder in 'incoming' is disregarded'.
  - DRAGEN samplesheet generation - limit analysis to human samples only.
  - Fixed incorrect string comparison in the npg_move_runfolder script.
+ - Ensure that pull requests to the master branch source dependencies from
+   master branches (devel branch was hardcoded).
 
 release 97.0.2
  - pin DBD::mysql to 4.050 to keep temp support for old mysql clients

scripts/install_wsi_dependencies.sh

@@ -21,9 +21,10 @@ for repo in "$@" ; do
     cd "/tmp/${repo}.git"
 
     # Shift off master to appropriate branch (if possible)
+    echo "Want to switch to branch $WSI_NPG_BUILD_BRANCH"
     git ls-remote --heads --exit-code origin "$WSI_NPG_BUILD_BRANCH" && \
-	    git pull origin "$WSI_NPG_BUILD_BRANCH" && \
-	    echo "Switched to branch $WSI_NPG_BUILD_BRANCH"
+      git pull origin "$WSI_NPG_BUILD_BRANCH" && \
+      echo "Switched to branch $WSI_NPG_BUILD_BRANCH"
     repos="$repos /tmp/${repo}.git"
 done