Merge pull request #149 from FrancescoSantini/resmem

dynamic requirements for some rules
BIMSBbioinfo · Aug 23, 2024 · 463013e · 463013e
2 parents 0957d26 + 495ea1e
commit 463013e
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/etc/settings.yaml.in b/etc/settings.yaml.in
@@ -118,6 +118,7 @@ execution:
     hisat2_map:
       threads: 2
       memory: 8000
+      disk_mb: 7000
     index_bam:
       threads: 2
       memory: 500
@@ -135,7 +136,7 @@ execution:
       memory: 6000
     check_annotation_files: 
       threads: 1
-      memory: 16000
+      memory: 6000
     report1:
       threads: 1
       memory: 4000  

diff --git a/snakefile.py b/snakefile.py
@@ -257,7 +257,7 @@ def lookup(column, predicate, fields=[]):
   output: 
     os.path.join(OUTPUT_DIR, 'input_annotation_stats.tsv')
   resources:
-    mem_mb = config['execution']['rules']['check_annotation_files']['memory']
+    mem_mb = lambda wc, input: max(1.5 * input.size_mb, config['execution']['rules']['check_annotation_files']['memory'])
   log: os.path.join(LOG_DIR, 'check_annotation_files.log')
   shell: "{RSCRIPT_EXEC} {SCRIPTS_DIR}/validate_input_annotation.R {input.gtf} {input.cdna} {input.dna} {OUTPUT_DIR} >> {log} 2>&1"