Use GALAXY_SLOTS for FragPipe --threads argument.

galaxyproteomics · Jun 29, 2024 · e82739e · e82739e
1 parent 2964cd9
commit e82739e
Showing 1 changed file with 1 addition and 3 deletions.
diff --git a/tools/fragpipe/fragpipe.xml b/tools/fragpipe/fragpipe.xml
@@ -37,7 +37,7 @@
                 --msfragger_key f28c4be2-759b0a11-6c1ea652-1240565a
                 --ionquant_key 47cb2953-b4bf7726-2c96f5fe-8f1013aa
                 --headless
-                --threads $threads
+                --threads \${GALAXY_SLOTS:-8}
                 --ram \$[ \${GALAXY_MEMORY_MB:-8192} / 1024 ]
                 --workflow fp.workflow --manifest fp.manifest
                 --workdir outputs
@@ -77,8 +77,6 @@
             <option value="combined_outputs">FragPipe Combined Outputs</option>
             <option value="concatenated_outputs">TSV Outputs Concatenated</option>
         </param>
-
-        <param argument="--threads" type="integer" value="8" label="Number of threads"/>
     </inputs>
 
     <outputs>