mem -> mem_mb

metagenome-atlas · Jun 24, 2024 · 515fca2 · 515fca2
1 parent 28d59bd
commit 515fca2
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Showing 5 changed files with 11 additions and 11 deletions.
diff --git a/workflow/rules/annotations.smk b/workflow/rules/annotations.smk
@@ -15,7 +15,7 @@ rule predict_genes:
         "logs/benchmarks/prodigal/{sample}.txt"
     threads: 1
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=1000* config["simplejob_mem"],
         time=config["runtime_simplejob"],
     shell:
         """

diff --git a/workflow/rules/megahit.smk b/workflow/rules/megahit.smk
@@ -75,7 +75,7 @@ rule run_megahit:
         "../envs/megahit.yaml"
     threads: config["assembly_threads"]
     resources:
-        mem=config["assembly_memory"],
+        mem_mb=1000* config["assembly_memory"],
         time=config["runtime_assembly"],
     shell:
         "rm -r {params.outdir} 2> {log} "

diff --git a/workflow/rules/post_assembly.smk b/workflow/rules/post_assembly.smk
@@ -66,7 +66,7 @@ else:
             "../envs/bbmap.yaml"
         threads: 1
         resources:
-            mem=config["simplejob_mem"],
+            mem_mb=1000* config["simplejob_mem"],
             java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
         shell:
             "filterbycoverage.sh "
@@ -94,7 +94,7 @@ rule rename_contigs:
         "../envs/bbmap.yaml"
     threads: config["simplejob_threads"]
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=1000* config["simplejob_mem"],
         time=config["runtime_simplejob"],
     log:
         "logs/assembly/post_process/rename_and_filter_size_{sample}/.log",
@@ -125,7 +125,7 @@ rule calculate_contigs_stats:
         "{sample}/logs/assembly/post_process/contig_stats_{assembly_step}.log",
     threads: 1
     resources:
-        mem=1,
+        mem_mb=1000,
         time=config["runtime_simplejob"],
     shell:
         "stats.sh in={input} format=3 out={output} &> {log}"
@@ -198,7 +198,7 @@ rule pileup_contigs_sample:
         "../envs/bbmap.yaml"
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=1000* config["mem"],
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     shell:
         "pileup.sh "
@@ -223,7 +223,7 @@ rule create_bam_index:
         "../envs/bbmap.yaml"
     threads: 1
     resources:
-        mem=2 * config["simplejob_threads"],
+        mem_mb=2000 * config["simplejob_threads"],
     shell:
         "samtools index {input}"
 

diff --git a/workflow/rules/pre_assembly.smk b/workflow/rules/pre_assembly.smk
@@ -22,7 +22,7 @@ rule init_pre_assembly_processing:
         "../envs/bbmap.yaml"
     threads: config["simplejob_threads"]
     resources:
-        mem=config["simplejob_mem"],
+        mem_mb=1000* config["simplejob_mem"],
         java_mem=int(config["simplejob_mem"] * JAVA_MEM_FRACTION),
     shell:
         " reformat.sh "
@@ -62,7 +62,7 @@ rule error_correction:
     conda:
         "../envs/bbmap.yaml"
     resources:
-        mem=config["mem"],
+        mem_mb=1000* config["mem"],
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     params:
         inputs=lambda wc, input: io_params_for_tadpole(input),
@@ -113,7 +113,7 @@ rule merge_pairs:
         ),
     threads: config["threads"]
     resources:
-        mem=config["mem"],
+        mem_mb=1000* config["mem"],
         java_mem=int(config["mem"] * JAVA_MEM_FRACTION),
     conda:
         "../envs/bbmap.yaml"

diff --git a/workflow/rules/spades.smk b/workflow/rules/spades.smk
@@ -87,7 +87,7 @@ rule run_spades:
         "../envs/spades.yaml"
     threads: config["assembly_threads"]
     resources:
-        mem=config["assembly_memory"],
+        mem_mb=1000* config["assembly_memory"],
         time=config["runtime_assembly"],
     shell:
         # remove pipeline_state file to create all output files again