From 98848d41a3b2abac7a69f64f9f71a02353dcecc2 Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.Fr>
Date: Fri, 15 Mar 2024 11:14:22 +0100
Subject: [PATCH] remove get_threads( function
---
frangiPANe/snakefiles/abyss_merge.smk | 2 +-
frangiPANe/snakefiles/samtools_flagstat.smk | 4 ++--
frangiPANe/snakefiles/samtools_view.smk | 4 ++--
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/frangiPANe/snakefiles/abyss_merge.smk b/frangiPANe/snakefiles/abyss_merge.smk
index e9abc9b..440b5c0 100644
--- a/frangiPANe/snakefiles/abyss_merge.smk
+++ b/frangiPANe/snakefiles/abyss_merge.smk
@@ -30,4 +30,4 @@ rule abyss_merge:
process = subprocess.run(cmd, shell=True, capture_output=True, text=True)
if process.returncode != 0:
- raise ValueError(f"Error executing command: {process.stderr}")
\ No newline at end of file
+ raise ValueError(f"Error executing command: {process.stderr}")
diff --git a/frangiPANe/snakefiles/samtools_flagstat.smk b/frangiPANe/snakefiles/samtools_flagstat.smk
index 9bd0e19..b937719 100644
--- a/frangiPANe/snakefiles/samtools_flagstat.smk
+++ b/frangiPANe/snakefiles/samtools_flagstat.smk
@@ -7,7 +7,7 @@ rule samtools_flagstat:
log:
output = f"{frangipane_obj.path_logs}/stats/flagstat-{{sample_name}}-{{ref_name}}.o",
error = f"{frangipane_obj.path_logs}/stats/flagstat-{{sample_name}}-{{ref_name}}.e"
- threads: get_threads('samtools_flagstat', 1)
+ threads: 1
message:
f"""--------------------
-Running {{rule}}
@@ -28,4 +28,4 @@ rule samtools_flagstat:
"""
cmd="samtools flagstat -@ {threads} {input.bam_file}";
(echo $cmd) > {log.output};
- ($cmd) 1> {output.stat_file} 2> {log.error}"""
\ No newline at end of file
+ ($cmd) 1> {output.stat_file} 2> {log.error}"""
diff --git a/frangiPANe/snakefiles/samtools_view.smk b/frangiPANe/snakefiles/samtools_view.smk
index 28c1518..c86f64b 100644
--- a/frangiPANe/snakefiles/samtools_view.smk
+++ b/frangiPANe/snakefiles/samtools_view.smk
@@ -10,7 +10,7 @@ rule samtools_view:
output = f"{frangipane_obj.path_logs}/samtools_view/{{sample_name}}-{{ref_name}}.o"
params:
other_options = frangipane_obj.get_config_value("PARAMS","samtools_view"),
- threads: get_threads('samtools_view', 1)
+ threads: 1
message:
f"""--------------------
-Running {{rule}}
@@ -37,4 +37,4 @@ rule samtools_view:
cmd2="samtools index -@ {threads} {output.bam_file}";
(echo $cmd2) >> {log.output};
- ($cmd2) 1>> {log.output} 2>> {log.error}"""
\ No newline at end of file
+ ($cmd2) 1>> {log.output} 2>> {log.error}"""
--
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