update env, temp output, memory usage

snakemake-workflows · Dec 4, 2024 · 4c3c9d7 · 4c3c9d7
1 parent 9ff8128
commit 4c3c9d7
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml
@@ -5,4 +5,4 @@ channels:
 dependencies:
   - varlociraptor >=8.4.13,<8.5
   - vega-lite-cli =5.16
-  - bcftools =1.19
+  - bcftools =1.21
diff --git a/workflow/rules/mapping.smk b/workflow/rules/mapping.smk
@@ -22,7 +22,7 @@ rule map_reads_vg:
         reads=get_map_reads_input,
         index=rules.vg_autoindex.output,
     output:
-        "results/mapped/vg/{sample}.preprocessed.bam",
+        temp("results/mapped/vg/{sample}.preprocessed.bam"),
     log:
         "logs/mapped/vg/{sample}.log",
     benchmark:
@@ -41,7 +41,7 @@ rule fix_mate:
     input:
         "results/mapped/vg/{sample}.preprocessed.bam",
     output:
-        "results/mapped/vg/{sample}.mate_fixed.bam",
+        temp("results/mapped/vg/{sample}.mate_fixed.bam"),
     log:
         "logs/samtools/fix_mate/{sample}.log",
     threads: 8
@@ -57,13 +57,13 @@ rule add_read_group:
     input:
         "results/mapped/vg/{sample}.mate_fixed.bam",
     output:
-        "results/mapped/vg/{sample}.bam",
+        temp("results/mapped/vg/{sample}.bam"),
     log:
         "logs/picard/add_rg/{sample}.log",
     params:
         extra=get_vg_read_group,
     resources:
-        mem_mb=60000,
+        mem_mb=1024,
     wrapper:
         "v2.3.2/bio/picard/addorreplacereadgroups"