start snakemake for samtools view

tools/samtools/view/Snakefile

+__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

tools/samtools/view/example_usage/Snakefile

+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)

tools/samtools/view/example_usage/config.yaml

+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"