From deffb1ddcdc6284352c5d3f1e7b038f9e537db56 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@gmail.com>
Date: Tue, 20 Jul 2021 14:36:09 +0200
Subject: [PATCH] start snakemake for samtools view
---
tools/samtools/view/Snakefile | 19 +++++++++++++++++
tools/samtools/view/example_usage/Snakefile | 21 +++++++++++++++++++
tools/samtools/view/example_usage/config.yaml | 15 +++++++++++++
3 files changed, 55 insertions(+)
create mode 100644 tools/samtools/view/Snakefile
create mode 100644 tools/samtools/view/example_usage/Snakefile
create mode 100644 tools/samtools/view/example_usage/config.yaml
diff --git a/tools/samtools/view/Snakefile b/tools/samtools/view/Snakefile
new file mode 100644
index 0000000..7fd8bfb
--- /dev/null
+++ b/tools/samtools/view/Snakefile
@@ -0,0 +1,19 @@
+__samtools_view_exec_command = config.get('samtools_view', {}).get('exec_command', 'samtools view')
+__samtools_view_modules = config.get('samtools_view', {}).get('modules')
+__samtools_view_options = config.get('samtools_view', {}).get('options', "")
+
+rule samtools_view:
+ input:
+ __samtools_view_input
+ output:
+ __samtools_view_output
+ params:
+ exec_command = __samtools_view_exec_command,
+ modules = __samtools_view_modules,
+ options = __samtools_view_options
+ run:
+ command = []
+ if params.modules:
+ command.append("module load {params.modules}")
+ command.append("{params.exec_command} {params.options} {input} > {output}")
+ shell(" && ".join(command))
\ No newline at end of file
diff --git a/tools/samtools/view/example_usage/Snakefile b/tools/samtools/view/example_usage/Snakefile
new file mode 100644
index 0000000..c8212ce
--- /dev/null
+++ b/tools/samtools/view/example_usage/Snakefile
@@ -0,0 +1,21 @@
+configfile: "config.yaml"
+
+# ==== Snakefile path ====
+__samtools_view_rules = config.get("snakefiles", {}).get("samtools_view")
+
+__main_output_dir = config.get('output_dir', 'output')
+
+# ==== Main config ====
+SAMPLES = config.get('samples')
+__input_dir = config.get('input_dir', 'data')
+
+# ==== Samtools view ====
+__samtools_view_input =
+__samtools_view_output =
+
+__samtools_view_input = expand("{dir}/{{sample}}.emapper.seed_orthologs".format(dir=__input_dir), sample=SAMPLES)
+__samtools_view_output = "{dir}/{file_name}".format(dir=__samtools_view_output_dir, file_name=__samtools_view_merged_name)
+include: __samtools_view_rules
+
+rule all:
+ input: "{dir}/{file_name}".format(dir=__samtools_view_output_dir, file_name=__samtools_view_merged_name)
diff --git a/tools/samtools/view/example_usage/config.yaml b/tools/samtools/view/example_usage/config.yaml
new file mode 100644
index 0000000..e31325b
--- /dev/null
+++ b/tools/samtools/view/example_usage/config.yaml
@@ -0,0 +1,15 @@
+snakefiles:
+ samtools_view: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/samtools/view/Snakefile
+
+input_dir: /some/input/directory
+output_dir: /some/output/directory
+
+samples:
+- test_00000
+- test_00001
+- test_00002
+
+samtools_view:
+ exec_command: samtools view
+ modules: samtools
+ options: "-b -f 4"
--
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