
    =hH                     .    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 )FastQCRunnerc	                 B    t         	|   |||||||dddgd dd|       y )Nfastqcz	--threadsz-tTF)loggermanifest_list
input_pathoutput_pathadditional_argsthreadsstepnamesoftware_nameunneeded_argsoutput_typeleafoutput_for_next_stepmode)super__init__)
selfr   r	   r
   r   r   r   r   r   	__class__s
            @/mounts/lovelace/software/shotgun-workflow/dev/modules/fastqc.pyr   zFastQCRunner.__init__   sA    '!#+"&-!& 	 	
    c           	          |D ]7  }| j                   j                  |d   |d   |d   | j                   d d       9 | j                  r|S | j                   S )Nidoutput1output2)r   input1input2r   r   )input_file_listappendr   r   )r   prev_step_fileslines      r   find_input_fileszFastQCRunner.find_input_files   sd    #D  ''4jy/y/"../)  $ 99""'''r   c                    | j                   D ]v  }| j                  d|d    dd| j                   | j                  g}|d   r||d   |d   gz  }n	||d   gz  }| j                  j                  dj                  |             x y )Nz-o r   /z-t r    r    )r!   r   r   r   command_queuer"   join)r   itembase_cmds      r   build_command_queuez FastQCRunner.build_command_queue$   s    ((D""d9o&a(dll^$$$	H H~NN 
 T(^,,%%chhx&89% )r   ) r.   r.      r.   N)__name__
__module____qualname__r   r%   r-   __classcell__)r   s   @r   r   r      s    
"(:r   r   )modules.software_baser   osr    r   r   <module>r7      s    4 	3:% 3:r   