Commit bd2e900e authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add rule for strainphlan

parent 6e60eb18
......@@ -2,6 +2,9 @@
This step will reconstruct all species strains found in metaphlan output sam file and store them in a pickle file (*.pkl). Those strains are referred as sample-reconstructed strains.
.. **Note**: output pkl file is written should be written in a individual directory since the script tries
to create and write into a `tmp` dir that leads to error when running sample2markers.py in parallel.
### Help section
```
......
__strainphlan_exec_command = config.get('strainphlan', {}).get('exec_command', 'strainphlan')
__strainphlan_modules = config.get('strainphlan', {}).get('modules')
__strainphlan_options = config.get('strainphlan', {}).get('options', "")
__strainphlan_threads = config.get('strainphlan', {}).get('threads', 1)
rule strainphlan:
input:
__strainphlan_input
output:
__strainphlan_output
params:
exec_command = __strainphlan_exec_command,
modules = __strainphlan_modules,
clade = __strainphlan_clade,
output_dir = __strainphlan_output_dir,
options = __strainphlan_options
threads:
__strainphlan_threads
run:
command = []
if params.modules:
command.append("module load {params.modules}")
command.append("{params.exec_command} -s {input} -n {threads} -c {params.clade} {params.options} -o {params.output_dir}")
shell(" && ".join(command))
input_dir: data
strainphlan:
threads: 4
exec_command: sample2markers.py
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