From 97f585ffc9e1c214247e0ce0cb8c150a14965951 Mon Sep 17 00:00:00 2001
From: CChahrour <catherine.chahrour@gmail.com>
Date: Wed, 16 Oct 2024 10:30:49 +0100
Subject: [PATCH] edit runtime

---
 seqnado/workflow/rules/align.smk             | 4 ++--
 seqnado/workflow/rules/peak_call_grouped.smk | 2 +-
 seqnado/workflow/rules/qc.smk                | 2 +-
 seqnado/workflow/rules/variant.smk           | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/seqnado/workflow/rules/align.smk b/seqnado/workflow/rules/align.smk
index 20d74d85..4390cb37 100755
--- 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
index 4e9e99d1..7fe703f4 100755
--- 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
index 2939af3e..cf7acb50 100755
--- 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
index 799cdffa..7aadeece 100755
--- 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",