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.
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@@ -41,6 +41,7 @@ stdenv.mkDerivation (finalAttrs: {
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# to be reverted for this specific use case.
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substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \
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--replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \
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--replace-fail '? "/bin/bash"' '? "'${bash}'/bin/bash"' \
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--replace-fail "if( containerBuilder ) {" "if( containerBuilder ) {
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launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")"
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'';
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