From 51eba5426c76bb941add399ddb0dc061e11642a2 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Thu, 26 Aug 2021 10:46:12 +0000
Subject: [PATCH] Add temp directories for ALFA
---
workflow/Snakefile | 36 ++++++++++++++++++++++++++++++++----
1 file changed, 32 insertions(+), 4 deletions(-)
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 2714fd7..9c939d0 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -1508,7 +1508,17 @@ rule generate_alfa_index:
"{organism}",
"{index_size}",
"ALFA",
- "sorted_genes.unstranded.ALFA_index")
+ "sorted_genes.unstranded.ALFA_index"),
+ temp_dir = temp(
+ directory(
+ os.path.join(
+ config["alfa_indexes"],
+ "{organism}",
+ "{index_size}",
+ "ALFA_temp",
+ )
+ )
+ )
params:
cluster_log_path = config["cluster_log_dir"],
@@ -1540,9 +1550,11 @@ rule generate_alfa_index:
current_rule + "_{organism}_{index_size}.log")
shell:
- "(alfa -a {input.gtf} \
+ "(mkdir -p {output.temp_dir}; \
+ alfa -a {input.gtf} \
-g {params.genome_index} \
--chr_len {input.chr_len} \
+ --temp_dir {output.temp_dir} \
-p {threads} \
-o {params.out_dir} \
{params.additional_params}) \
@@ -1610,7 +1622,18 @@ rule alfa_qc:
"{sample}",
"ALFA",
"{renamed_unique}",
- "{sample}.ALFA_feature_counts.tsv")
+ "{sample}.ALFA_feature_counts.tsv"),
+ temp_dir = temp(
+ directory(
+ os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "ALFA",
+ "{renamed_unique}",
+ "ALFA_temp")
+ )
+ )
params:
cluster_log_path = config["cluster_log_dir"],
@@ -1631,6 +1654,9 @@ rule alfa_qc:
'libtype',
search_id='index',
search_value=wildcards.sample),"alfa"),
+ temp_dir = lambda wildcards, output:
+ os.path.abspath(
+ os.path.dirname(output.temp_dir)),
additional_params = parse_rule_config(
rule_config,
current_rule=current_rule,
@@ -1655,11 +1681,13 @@ rule alfa_qc:
current_rule + ".{renamed_unique}.log")
shell:
- "(cd {params.out_dir}; \
+ "(mkdir -p {output.temp_dir};\
+ cd {params.out_dir}; \
alfa \
-g {params.genome_index} \
--bedgraph {params.plus} {params.minus} {params.name} \
-s {params.alfa_orientation} \
+ --temp_dir {params.temp_dir} \
{params.additional_params}) \
&> {log}"
--
GitLab