From 021311d951f954fc70bea19d48eb0cfb96445716 Mon Sep 17 00:00:00 2001
From: kdc715 <kedic@LIT-PF3VB193.localdomain>
Date: Tue, 21 Jan 2025 14:47:00 +0100
Subject: [PATCH] fix memory allocation for samtool multithreading rules
---
snakemodules/contigmap.smk | 6 ++++--
snakemodules/crop_remapped.smk | 6 ++++--
snakemodules/crop_unmapped.smk | 6 ++++--
snakemodules/kraken.smk | 6 ++++--
4 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/snakemodules/contigmap.smk b/snakemodules/contigmap.smk
index dc3d8e5..9b88b06 100644
--- a/snakemodules/contigmap.smk
+++ b/snakemodules/contigmap.smk
@@ -96,7 +96,8 @@ rule name_sort_unsorted:
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
@@ -170,7 +171,8 @@ rule coordinate_sort_unsorted:
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools_25G"]["mem"],
+ # mem_mb = resources["samtools_25G"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools_25G"]["time"]
threads:
threads["multi"]["samtools"]
diff --git a/snakemodules/crop_remapped.smk b/snakemodules/crop_remapped.smk
index f05db9c..2a6864b 100644
--- a/snakemodules/crop_remapped.smk
+++ b/snakemodules/crop_remapped.smk
@@ -60,7 +60,8 @@ if config["SICKLE"]=="no":
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
@@ -112,7 +113,8 @@ elif config["SICKLE"]=="yes":
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
diff --git a/snakemodules/crop_unmapped.smk b/snakemodules/crop_unmapped.smk
index 94e79c8..9b04065 100644
--- a/snakemodules/crop_unmapped.smk
+++ b/snakemodules/crop_unmapped.smk
@@ -58,7 +58,8 @@ if config["SICKLE"]=="no":
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
@@ -108,7 +109,8 @@ elif config["SICKLE"]=="yes":
output:
WORK_DIR + "/{sample}/non_ref.bam"
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
diff --git a/snakemodules/kraken.smk b/snakemodules/kraken.smk
index f7814e4..220eb5e 100644
--- a/snakemodules/kraken.smk
+++ b/snakemodules/kraken.smk
@@ -150,7 +150,8 @@ rule samtools_remap_classified_human:
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
@@ -223,7 +224,8 @@ rule remapping_samsort_mates:
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
- mem_mb = resources["samtools"]["mem"],
+ # mem_mb = resources["samtools"]["mem"],
+ mem_mb = lambda wildcards, input, threads, attempt: resources["samtools"]["mem"] * threads,
runtime = resources["samtools"]["time"]
threads:
threads["multi"]["samtools"]
--
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