Merge pull request #312 from TalusBio/feature/bruker_data

Fallback version reporting of zip
bigbio · Oct 24, 2023 · d49a1de · d49a1de
2 parents 8c65409 + fcb2054
commit d49a1de
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,4 +12,9 @@ testing*
 /build/
 results*/
 venv/
+node_modules
+conversion_inputs
+debug_dir
+test_out
+
 lint_log.txt
diff --git a/modules/local/decompress_dotd/main.nf b/modules/local/decompress_dotd/main.nf
@@ -59,7 +59,7 @@ process DECOMPRESS {
 
     tar --help 2>&1 | tee -a ${prefix}_decompression.log
     gunzip --help 2>&1 | tee -a ${prefix}_decompression.log
-    unzip --help 2>&1 | tee -a ${prefix}_decompression.log
+    (unzip --help 2>&1 || zip --help 2>&1) | tee -a ${prefix}_decompression.log
     echo "Unpacking..." | tee -a ${compressed_file.baseName}_decompression.log
 
     extract ${compressed_file} 2>&1 | tee -a ${compressed_file.baseName}_conversion.log
@@ -73,7 +73,7 @@ process DECOMPRESS {
     "${task.process}":
         gunzip: \$(gunzip --help 2>&1 | head -1 | grep -oE "\\d+\\.\\d+(\\.\\d+)?")
         tar: \$(tar --help 2>&1 | head -1 | grep -oE "\\d+\\.\\d+(\\.\\d+)?")
-        unzip: \$(unzip --help | head -2 | tail -1 | grep -oE "\\d+\\.\\d+")
+        unzip: \$((unzip --help 2>&1 || zip --help 2>&1) | head -2 | tail -1 | grep -oE "\\d+\\.\\d+")
     END_VERSIONS
     """
 }