added resource request for AWS

BIMSBbioinfo · Aug 21, 2024 · b146852 · b146852
1 parent da6f0d4
commit b146852
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/snakefile.py b/snakefile.py
@@ -256,6 +256,8 @@ def lookup(column, predicate, fields=[]):
     gtf = GTF_FILE
   output: 
     os.path.join(OUTPUT_DIR, 'input_annotation_stats.tsv')
+  resources:
+    mem_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"
 
@@ -417,7 +419,8 @@ def hisat2_file_arguments(args):
   output:
     os.path.join(MAPPED_READS_DIR, 'hisat2', '{sample}_Aligned.sortedByCoord.out.bam')
   resources:
-    mem_mb = config['execution']['rules']['hisat2_map']['memory']
+    mem_mb = config['execution']['rules']['hisat2_map']['memory'],
+    disk_mb=lambda wc, input: max(3 * input.size_mb, config['execution']['rules']['hisat2_map']['disk_mb'])
   params:
     samfile = lambda wildcards: os.path.join(MAPPED_READS_DIR, 'hisat2', "_".join([wildcards.sample, 'Aligned.out.sam'])),
     index_dir = rules.hisat2_index.params.index_directory,