Fixing issues with google life sciences test

Signed-off-by: jorgee <[email protected]>
nextflow-io · Oct 9, 2024 · fb770bb · fb770bb
1 parent dce2f98
commit fb770bb
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/...ins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy b/...ins/nf-google/src/main/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelper.groovy
@@ -365,7 +365,7 @@ class GoogleLifeSciencesHelper {
         final remoteTaskDir = getRemoteTaskDir(workDir)
         def result = 'set -x; '
         result += "trap 'err=\$?; exec 1>&2; gsutil -m -q cp -R $localTaskDir/${TaskRun.CMD_LOG} ${remoteTaskDir}/${TaskRun.CMD_LOG} || true; [[ \$err -gt 0 || \$GOOGLE_LAST_EXIT_STATUS -gt 0 || \$NXF_DEBUG -gt 0 ]] && { ls -lah $localTaskDir || true; gsutil -m -q cp -R /google/ ${remoteTaskDir}; } || rm -rf $localTaskDir; exit \$err' EXIT; "
-        result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage; } >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
+        result += "{ cd $localTaskDir; bash ${TaskRun.CMD_RUN} nxf_unstage; bash ${TaskRun.CMD_RUN} nxf_unstage_std_files;} >> $localTaskDir/${TaskRun.CMD_LOG} 2>&1"
         return result
     }
 

diff --git a/...nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy b/...nf-google/src/test/nextflow/cloud/google/lifesciences/GoogleLifeSciencesHelperTest.groovy
@@ -548,7 +548,7 @@ class GoogleLifeSciencesHelperTest extends GoogleSpecification {
         def unstage = helper.getUnstagingScript(dir)
         then:
         unstage ==
-                'set -x; trap \'err=$?; exec 1>&2; gsutil -m -q cp -R /work/dir/.command.log gs://my-bucket/work/dir/.command.log || true; [[ $err -gt 0 || $GOOGLE_LAST_EXIT_STATUS -gt 0 || $NXF_DEBUG -gt 0 ]] && { ls -lah /work/dir || true; gsutil -m -q cp -R /google/ gs://my-bucket/work/dir; } || rm -rf /work/dir; exit $err\' EXIT; { cd /work/dir; bash .command.run nxf_unstage; } >> /work/dir/.command.log 2>&1'
+                'set -x; trap \'err=$?; exec 1>&2; gsutil -m -q cp -R /work/dir/.command.log gs://my-bucket/work/dir/.command.log || true; [[ $err -gt 0 || $GOOGLE_LAST_EXIT_STATUS -gt 0 || $NXF_DEBUG -gt 0 ]] && { ls -lah /work/dir || true; gsutil -m -q cp -R /google/ gs://my-bucket/work/dir; } || rm -rf /work/dir; exit $err\' EXIT; { cd /work/dir; bash .command.run nxf_unstage; bash .command.run nxf_unstage_std_files;} >> /work/dir/.command.log 2>&1'
     }
 
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