Optimize bbsplit index handling to avoid large file copies (#9447)

* Optimize bbsplit index handling to avoid large file copies

Replace full directory copy with symlink-based approach: symlink all index
files except summary.txt (which must be copied to apply timestamp fixes).
This significantly reduces I/O overhead while preserving the critical
timestamp correction functionality.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

* Simplify bbsplit index handling implementation

Refactored the bash script sections for index handling to be more concise
and maintainable while preserving all functionality:

- Consolidated directory creation and file operations into single find loops
- Replaced readlink -f with realpath for better macOS compatibility
- Used conditional operators to reduce if/else verbosity
- Inlined variables where appropriate to reduce line count

These changes improve code clarity and cross-platform compatibility
without affecting the underlying logic of file moves, symlink handling,
or timestamp management.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

---------

Co-authored-by: Claude <[email protected]>

Author: pinin4fjords

modules/nf-core/bbmap/bbsplit/main.nf

@@ -68,15 +68,16 @@ process BBMAP_BBSPLIT {
     }
     """
 
-    # If using a pre-built index, copy it to avoid modifying input files in place,
-    # then fix timestamps. When we stage in the index files the time stamps get
-    # disturbed, which bbsplit doesn't like. Fix the time stamps in its summaries.
-    # This needs to be done via Java to match what bbmap does.
+    # If using a pre-built index, create writable structure: symlink all files except
+    # summary.txt (which we copy to modify). When we stage in the index files the time
+    # stamps get disturbed, which bbsplit doesn't like. Fix the time stamps in summaries.
     if [ "$use_index" == "true" ]; then
-        cp -rL input_index index_writable
-
-        for summary_file in \$(find index_writable/ref/genome -name summary.txt); do
-            # Extract the path from summary.txt and update it to point to index_writable
+        find input_index/ref -type f | while read -r f; do
+            target="index_writable/\${f#input_index/}"
+            mkdir -p "\$(dirname "\$target")"
+            [[ \$(basename "\$f") == "summary.txt" ]] && cp "\$f" "\$target" || ln -s "\$(realpath "\$f")" "\$target"
+        done
+        find index_writable/ref/genome -name summary.txt | while read -r summary_file; do
             src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/ref/|index_writable/ref/|')
             mod=\$(echo "System.out.println(java.nio.file.Files.getLastModifiedTime(java.nio.file.Paths.get(\\"\$src\\")).toMillis());" | jshell -J-Djdk.lang.Process.launchMechanism=vfork -)
             sed -e 's|bbsplit_index/ref|index_writable/ref|' -e "s|^last modified.*|last modified\\t\$mod|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
@@ -95,14 +96,11 @@ process BBMAP_BBSPLIT {
         $args 2>| >(tee ${prefix}.log >&2)
 
     # Summary files will have an absolute path that will make the index
-    # impossible to use in other processes- we can fix that
+    # impossible to use in other processes - fix paths and rename atomically
     if [ -d bbsplit_build/ref/genome ]; then
-        for summary_file in \$(find bbsplit_build/ref/genome -name summary.txt); do
-            src=\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit_build|bbsplit_index|')
-            sed "s|^source.*|source\\t\$src|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
+        find bbsplit_build/ref/genome -name summary.txt | while read -r summary_file; do
+            sed "s|^source.*|source\\t\$(grep '^source' "\$summary_file" | cut -f2- -d\$'\\t' | sed 's|.*/bbsplit_build|bbsplit_index|')|" "\$summary_file" > \${summary_file}.tmp && mv \${summary_file}.tmp \${summary_file}
         done
-
-        # Atomically rename the completed index
         mv bbsplit_build bbsplit_index
     fi