edit runtime

alsmith151 · Oct 16, 2024 · 97f585f · 97f585f
1 parent 1b77ea3
commit 97f585f
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Showing 4 changed files with 5 additions and 5 deletions.
diff --git a/seqnado/workflow/rules/align.smk b/seqnado/workflow/rules/align.smk
@@ -13,7 +13,7 @@ rule align_paired:
         bam=temp("seqnado_output/aligned/raw/{sample}.bam"),
     threads: config["bowtie2"]["threads"]
     resources:
-        runtime=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}h",
+        runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
         mem=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}GB",
     log:
         "seqnado_output/logs/align/{sample}.log",
@@ -34,7 +34,7 @@ rule align_single:
     output:
         bam=temp("seqnado_output/aligned/raw/{sample}.bam"),
     resources:
-        runtime=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}h",
+        runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
         mem=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}GB",
     threads: config["bowtie2"]["threads"]
     log:

diff --git a/seqnado/workflow/rules/peak_call_grouped.smk b/seqnado/workflow/rules/peak_call_grouped.smk
@@ -7,7 +7,7 @@ rule lanceotron_no_input_consensus:
         peaks="seqnado_output/peaks/merged/lanceotron/{group}.bed",
     threads: 8
     resources:
-        runtime=lambda wildcards, attempt: f"{4 * 2 ** (attempt - 1)}h",
+        runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
         mem=lambda wildcards, attempt: f"{10 * 2 ** (attempt - 1)}GB",
     params:
         outdir="seqnado_output/peaks/merged/lanceotron",

diff --git a/seqnado/workflow/rules/qc.smk b/seqnado/workflow/rules/qc.smk
@@ -17,7 +17,7 @@ rule fastqc_raw_paired:
     threads: 1
     resources:
         mem="1.5GB",
-        runtime=lambda wildcards, attempt: f"{1 * 2 ** (attempt - 1)}h",
+        runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
     log:
         "seqnado_output/logs/fastqc_raw/{sample}.log",
     shell:

diff --git a/seqnado/workflow/rules/variant.smk b/seqnado/workflow/rules/variant.smk
@@ -11,7 +11,7 @@ if config["call_snps"]:
             faidx=config["fasta_index"],
         resources:
             mem=lambda wildcards, attempt: f"{10 * 2 ** (attempt -1)}GB",
-            runtime=lambda wildcards, attempt: f"{5 * 2 ** (attempt - 1)}h",
+            runtime=lambda wildcards, attempt: f"{6 * 2 ** (attempt - 1)}h",
         threads: config["bcftools"]["threads"]
         log:
             "seqnado_output/logs/variant/bcftools/bcftools/{sample}.log",