
     i\                     .    d dl mZ d dlZ G d de      Zy)    )WorkflowRunnerBaseNc                   ,     e Zd Zd fd	Zd Zd Z xZS )PMDtoolsRunnerc	                 @    t         	|   |||||||dg ddd|       y )Nz	runpmd.py)z-iz--inputz-oz--outputbamF)loggermanifest_list
input_pathoutput_pathadditional_argsthreadsstepnamesoftware_nameunneeded_argsoutput_typeshellmode)super__init__)
selfr   r	   r
   r   r   r   r   r   	__class__s
            >/mounts/lovelace/software/hts-workflow/dev/modules/pmdtools.pyr   zPMDtoolsRunner.__init__   s9    '!#+%= 	 	
    c                 b    | j                   j                  d d d d d d       | j                  r|S y )N)idinput1input2output1output2)input_file_listappendleaf)r   prev_step_filess     r   find_input_fileszPMDtoolsRunner.find_input_files   s<    ##%
 	 99""r   c                    | j                   d| j                   d| j                   d| j                   | j                   g}| j
                  j                  |        | j                  j                  dj                  |             y )Nz
--threads z--input z	--output  )
r   r   r
   r   r   r   infocommand_queuer!   join)r   cmds     r   build_command_queuez"PMDtoolsRunner.build_command_queue#   s~    't'((()*##$
 	C5"!!#((3-0r   )    N)__name__
__module____qualname__r   r$   r+   __classcell__)r   s   @r   r   r      s    
 
1r   r   )modules.software_baser   osr    r   r   <module>r5      s    4 	)1' )1r   