From 873b64ef5387e3ce92418227ad9a68d2d0152591 Mon Sep 17 00:00:00 2001
From: FrancescoSantini <francesco.santini.bio@gmail.com>
Date: Thu, 22 Aug 2024 13:59:55 +0200
Subject: [PATCH 1/2] fix for precedent commit

---
 etc/settings.yaml.in | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/etc/settings.yaml.in b/etc/settings.yaml.in
index 5e7de0d..4612fcd 100755
--- 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  

From 495ea1e21fa9b88614fa92d452f2a0829cd22ff5 Mon Sep 17 00:00:00 2001
From: FrancescoSantini <francesco.santini.bio@gmail.com>
Date: Fri, 23 Aug 2024 11:19:19 +0200
Subject: [PATCH 2/2] added dynamic resources to check_annotation_files rule

---
 snakefile.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/snakefile.py b/snakefile.py
index b02766f..b21a630 100644
--- 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"