start rule for prodigal

tools/prodigal/Snakefile

+"""
+Prodigal manual
+
+Usage:  prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]
+                 [-g tr_table] [-h] [-i input_file] [-m] [-n] [-o output_file]
+                 [-p mode] [-q] [-s start_file] [-t training_file] [-v]
+
+         -a:  Write protein translations to the selected file.
+         -c:  Closed ends.  Do not allow genes to run off edges.
+         -d:  Write nucleotide sequences of genes to the selected file.
+         -f:  Select output format (gbk, gff, or sco).  Default is gbk.
+         -g:  Specify a translation table to use (default 11).
+         -h:  Print help menu and exit.
+         -i:  Specify FASTA/Genbank input file (default reads from stdin).
+         -m:  Treat runs of N as masked sequence; don't build genes across them.
+         -n:  Bypass Shine-Dalgarno trainer and force a full motif scan.
+         -o:  Specify output file (default writes to stdout).
+         -p:  Select procedure (single or meta).  Default is single.
+         -q:  Run quietly (suppress normal stderr output).
+         -s:  Write all potential genes (with scores) to the selected file.
+         -t:  Write a training file (if none exists); otherwise, read and use
+              the specified training file.
+         -v:  Print version number and exit.
+"""
+
+__prodigal_exec_command = config.get(
+    'prodigal', {}
+).get('exec_command', 'prodigal')
+__prodigal_modules = config.get('prodigal', {}).get('modules')
+
+rule prodigal:
+    input:
+        __prodigal_input
+    output:
+        fasta_genes = __prodigal_fasta_genes
+        genes = __prodigal_genes
+    params:
+        exec_command = __prodigal_exec_command,
+        modules = __prodigal_modules
+        options = __prodigal_options
+    run:
+        command = []
+        if params.modules:
+        	command.append("module load {params.modules}")
+        command.append("{params.exec_command} {params.options} -i {input} -d {output.fasta_genes} -o {output.genes}")
+        shell(" && ".join(command))

tools/prodigal/example_usage/Snakefile

+configfile: "config.yaml"
+
+# ==== Snakefile path ====
+__prodigal_rules = config.get("snakefiles", {}).get("prodigal")
+
+__main_output_dir = config.get('output_dir', 'output')
+
+# ==== Main config ====
+SAMPLES = config.get('samples')
+__input_dir = config.get('input_dir', 'data')
+
+# ==== Run prodigal ====
+__prodigal_output_dir = f"{__main_output_dir}/prodigal"
+__prodigal_input = "{dir}/{{sample}}.fa".format(dir=__input_dir, sample="{sample}")
+__prodigal_fasta_genes = "{dir}/{{sample}}.fa".format(dir=__prodigal_output_dir, sample="{sample}")
+__prodigal_genes = "{dir}/{{sample}}.gbk".format(dir=__prodigal_output_dir, sample="{sample}")
+include: __prodigal_rules
+
+rule all:
+    input:
+        fasta_genes = expand("{dir}/{{sample}}.fa".format(dir=__prodigal_output_dir), sample=SAMPLES)
+        genes = expand("{dir}/{{sample}}.gbk".format(dir=__prodigal_output_dir), sample=SAMPLES)

tools/prodigal/example_usage/config.yaml

+snakefiles:
+    prodigal: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/prodigal/Snakefile
+
+input_dir: /some/input/directory
+output_dir: /some/output/directory
+
+samples:
+- test_00000
+- test_00001
+- test_00002
+
+prodigal:
+  exec_command: prodigal
+  modules: prodigal