nextflow: add shellPath() bash patch for trace support

Adds missing patch for shellPath() method to use nix store bash
instead of /bin/bash. This is required for trace wrapper execution
when using -with-trace or resource monitoring features.

Without this patch, trace functionality fails with:
  /bin/bash: No such file or directory

Verified with comparison testing of patched vs unpatched versions.
This commit is contained in:
mulatta
2026-02-04 14:06:12 +09:00
parent 82cf89cf54
commit 990ebda331
+1
View File
@@ -41,6 +41,7 @@ stdenv.mkDerivation (finalAttrs: {
# to be reverted for this specific use case.
substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \
--replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \
--replace-fail '? "/bin/bash"' '? "'${bash}'/bin/bash"' \
--replace-fail "if( containerBuilder ) {" "if( containerBuilder ) {
launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")"
'';