diff --git a/CHANGELOG.md b/CHANGELOG.md index aae5dfd..946855e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Previously, `xavier_gui` (with an underscore) was a command in the `ccbrpipeliner` module. - Provide default exome targets for hg38 and mm10, which can be overridden by the optional `--targets` argument. (#102, @kelly-sovacool) - Previously, the `--targets` argument was required with no defaults. +- Increased memory for rules: BWA mem, qualimap, kraken. gatk_contamination is not localrule. (#89, @samarth8392) ## XAVIER 3.0.3 diff --git a/config/cluster.biowulf.json b/config/cluster.biowulf.json index 184b3fa..a647265 100644 --- a/config/cluster.biowulf.json +++ b/config/cluster.biowulf.json @@ -22,13 +22,17 @@ "threads": "2", "time": "4:00:00" }, - + "kraken": { + "mem": "64G" + }, "strelka": { "threads": "16", "time": "16:00:00", "mem": "32G" }, - + "qualimap_bamqc": { + "mem": "32G" + }, "strelka_filter": { "threads": "4", "time": "8:00:00", @@ -57,7 +61,7 @@ "mem": "32G" }, - "merge_somatic_callers": { + "somatic_merge_callers": { "threads": "16", "time": "18:00:00", "mem": "32G" @@ -116,7 +120,7 @@ }, "bwa_mem": { "threads": "24", - "mem": "32G" + "mem": "64G" }, "picard_headers": { "threads": "2", diff --git a/config/cluster.frce.json b/config/cluster.frce.json index 3ddeb16..6c7773d 100644 --- a/config/cluster.frce.json +++ b/config/cluster.frce.json @@ -21,13 +21,17 @@ "threads": "2", "time": "4:00:00" }, - + "kraken": { + "mem": "64G" + }, "strelka": { "threads": "16", "time": "16:00:00", "mem": "32G" }, - + "qualimap_bamqc": { + "mem": "32G" + }, "strelka_filter": { "threads": "4", "time": "8:00:00", @@ -56,7 +60,7 @@ "mem": "32G" }, - "merge_somatic_callers": { + "somatic_merge_callers": { "threads": "16", "time": "18:00:00", "mem": "32G" @@ -115,7 +119,7 @@ }, "bwa_mem": { "threads": "24", - "mem": "32G" + "mem": "64G" }, "picard_headers": { "threads": "2", diff --git a/workflow/rules/somatic_snps.paired.smk b/workflow/rules/somatic_snps.paired.smk index ce8071f..1f5427b 100644 --- a/workflow/rules/somatic_snps.paired.smk +++ b/workflow/rules/somatic_snps.paired.smk @@ -73,7 +73,6 @@ rule pileup_paired: wait """ -localrules: contamination_paired rule contamination_paired: input: tumor = os.path.join(output_somatic_snpindels, "mutect2_out", "pileup_summaries", "{samples}_tumor.pileup.table"), diff --git a/workflow/rules/somatic_snps.tumor_only.smk b/workflow/rules/somatic_snps.tumor_only.smk index 650e3b9..826b07f 100644 --- a/workflow/rules/somatic_snps.tumor_only.smk +++ b/workflow/rules/somatic_snps.tumor_only.smk @@ -67,7 +67,6 @@ rule pileup_single: -O {output.pileup} """ -localrules: contamination_single rule contamination_single: input: pileup = os.path.join(output_somatic_snpindels, "mutect2_out", "pileup_summaries", "{samples}.pileup.table")