From 06e80ae5752aed8e0b0710cbf7fa505e8debc2d0 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Mon, 19 Oct 2020 15:24:52 +0200
Subject: [PATCH] use onsuccess to properly remove index dirs
---
Snakefile | 10 ++++++----
workflow/rules/paired_end.snakefile.smk | 8 +++++++-
workflow/rules/single_end.snakefile.smk | 9 ++++++++-
3 files changed, 21 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index 1648e97..d7dd8fb 100644
--- a/Snakefile
+++ b/Snakefile
@@ -38,6 +38,12 @@ if cluster_config:
include: os.path.join("workflow", "rules", "paired_end.snakefile.smk")
include: os.path.join("workflow", "rules", "single_end.snakefile.smk")
+onsuccess:
+ print("Workflow finished, no error.")
+ os.system("rm -rv " + config['kallisto_indexes'])
+ os.system("rm -rv " + config['salmon_indexes'])
+ os.system("rm -rv " + config['alfa_indexes'])
+
rule finish:
"""
Rule for collecting outputs
@@ -195,8 +201,6 @@ rule create_index_star:
"STAR_index",
"chrName.txt")
- shadow: "full"
-
params:
output_dir = os.path.join(
config['star_indexes'],
@@ -386,8 +390,6 @@ rule create_index_kallisto:
"{organism}",
"kallisto.idx")
- shadow: "full"
-
params:
output_dir = os.path.join(
config['kallisto_indexes'],
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index f06d4dc..a756856 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -401,7 +401,13 @@ rule pe_genome_quantification_kallisto:
"samples",
"{sample}",
"quant_kallisto",
- "{sample}.pe.kallisto.pseudo.sam")
+ "{sample}.pe.kallisto.pseudo.sam"),
+ abundances = os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "quant_kallisto",
+ "abundance.h5")
shadow: "full"
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 565bc01..a1c62e4 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -343,7 +343,14 @@ rule genome_quantification_kallisto:
"samples",
"{sample}",
"quant_kallisto",
- "{sample}.se.kallisto.pseudo.sam")
+ "{sample}.se.kallisto.pseudo.sam"),
+ abundances = os.path.join(
+ config["output_dir"],
+ "samples",
+ "{sample}",
+ "quant_kallisto",
+ "abundance.h5")
+
shadow: "full"
--
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