add memory increase/cap information to RAM control section

rhysnewell · Sep 5, 2023 · 0a2d7e0 · 0a2d7e0
1 parent 99e6bec
commit 0a2d7e0
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diff --git a/aviary/modules/assembly/assembly.smk b/aviary/modules/assembly/assembly.smk
@@ -452,7 +452,7 @@ rule spades_assembly:
     threads:
         min(config["max_threads"], 64)
     resources:
-        mem_mb = lambda wildcards, attempt: min(int(config["max_memory"])*1024, 512*1024*attempt),
+        mem_mb = lambda wildcards, attempt: min(int(config["max_memory"])*1024, 256*1024*attempt),
         runtime = lambda wildcards, attempt: 72*60 + 24*60*attempt,
     log:
         "logs/spades_assembly.log"

diff --git a/docs/examples.md b/docs/examples.md
@@ -72,4 +72,5 @@ can also be kind of memory intensive when given extra threads.
 
 ### RAM control
 
-When performing assembly, users are required to estimate how much RAM they will need to use via `-m, --max-memory, --max_memory`
+When performing assembly, users are required to estimate how much RAM they will need to use via `-m, --max-memory, --max_memory`.
+With HPC cluster submission (see above), requested job memory is increased with each rerun and capped at `max_memory`.