shell:
 '''
 python {extract_barcodes}
     --read1 {{input.R1}}
     --read2 {{input.R2}}
     --outfile {{params.outprefix}}
     {{params.barcodes}}
 '''.format(extract_barcodes = config['extract_barcodes_path'])

shell:
	'''{java}  
	   logdir/{id}.txt  
	   basedir/{input.R1}
	   basedir/{input.R2} 
	   output.vdjca
	   '''.format(java=java_align)

	shell:
               '''{assemble}
	           aligndir/alignments_{id}.vdjca 
		  {output.vdjca_res1}
	       '''.format(assemble=assemble1)

shell:

       '''{assemble}
          assembledir/rescue1_{id}.vdjca 
	  {output.vdjca_res2}
       '''.format(assemble=assemble1)

shell:
      '''{assemble}
         assembledir/rescue2_{id}.vdjca 
	 {output.vdjca_ext}
      '''.format(assemble=assembleEx)

shell:
      '''{assemble}
	 logdir/log_assemble_{id}.txt 
         assembledir/extended_{id}.vdjca
         {output.clns} 
     '''.format(assemble=assemble_f)

shell:

	'''export 
	  exportClones --chains TRA
	  assembledir/{id}.clns  {output.clones_A}
	'''

       shell:

		'''export 
		exportClones --chains TRB
		assembledir  {id}.clns
	        {output.clones_B}
	        ''' 		

shell:

	''' python {parse_log} 
	           -i  logdir  -o logdir
	'''.format(pars_log=confgi['pars_log_path'])

shell:

	''' Rscript {mixcr_qc}
	    {input.a1} 
	    {input.a2} 
        '''

shell:
	'''Rscript {clonetracker} 
	   clonesdir
	   {param}
	   {type}
	'''.format(param=config['pattern'], type= config['chain])