From 1998065a4293ea51fbbb1b803a61029c0b14a50f Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com>
Date: Mon, 2 Aug 2021 11:04:55 +0200
Subject: [PATCH] update extract of unmapped pairs with samtools
---
tools/samtools/extract_unmapped_pairs/Snakefile | 4 ++--
.../extract_unmapped_pairs/example_usage/Snakefile | 9 +++------
2 files changed, 5 insertions(+), 8 deletions(-)
diff --git a/tools/samtools/extract_unmapped_pairs/Snakefile b/tools/samtools/extract_unmapped_pairs/Snakefile
index 677c4e7..ddc2475 100644
--- a/tools/samtools/extract_unmapped_pairs/Snakefile
+++ b/tools/samtools/extract_unmapped_pairs/Snakefile
@@ -10,8 +10,7 @@ rule extract_unmapped_pairs:
__extract_unmapped_pairs_output
params:
exec_command = __extract_unmapped_pairs_samtools_exec_command,
- modules = __extract_unmapped_pairs_modules,
- options = __extract_unmapped_pairs_options
+ modules = __extract_unmapped_pairs_modules
run:
command = []
if params.modules:
@@ -22,4 +21,5 @@ rule extract_unmapped_pairs:
command.append(
"{params.exec_command} merge -u - {output}.tmps[123].bam | {params.exec_command} sort -n > {output}"
)
+ command.append("rm {output}.tmps[123].bam")
shell(" && ".join(command))
diff --git a/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile b/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile
index e7c4f70..dabd02c 100644
--- a/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile
+++ b/tools/samtools/extract_unmapped_pairs/example_usage/Snakefile
@@ -10,12 +10,9 @@ SAMPLES = config.get('samples')
__input_dir = config.get('input_dir', 'data')
# ==== Extract unmapped pairs ====
-__extract_unmapped_pairs_input = expand(
- "{dir}/{{sample}}.bam".format(dir=__input_dir), sample=SAMPLES
-)
-__extract_unmapped_pairs_output = expand(
- "{dir}/{{sample}}_unmapped.bam".format(dir=__input_dir), sample=SAMPLES
-)
+__extract_unmapped_pairs_output_dir = f"{__main_output_dir}/extract_unmapped_pairs"
+__extract_unmapped_pairs_input = "{dir}/{{sample}}.bam".format(dir=__input_dir, sample="{sample}")
+__extract_unmapped_pairs_output = "{dir}/{{sample}}_unmapped.bam".format(dir=__extract_unmapped_pairs_output_dir, sample="{sample}")
include: __extract_unmapped_pairs_rules
rule all:
--
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