<commit_before>import rnaseq_pipeline.module_helper
module_helper = rnaseq_pipeline.module_helper
import os

def init(param):
   module_helper.checkParameter(param,key='cutadapt_exec',dType=str)
   module_helper.checkParameter(param,key='cutadapt_first_adapter',dType=str)
   if param['paired']:
       module_helper.checkParameter(param,key='cutadapt_second_adapter',dType=str)
   module_helper.checkParameter(param,key='cutadapt_m',dType=str)
   
   
def run_cutadapt(param,infile,outfile,adapter):
    #run the clipper<commit_msg>must have dropped subprocess in all the module moving<commit_after>import rnaseq_pipeline.module_helper
module_helper = rnaseq_pipeline.module_helper
import os
import subprocess

def init(param):
   module_helper.checkParameter(param,key='cutadapt_exec',dType=str)
   module_helper.checkParameter(param,key='cutadapt_first_adapter',dType=str)
   if param['paired']:
       module_helper.checkParameter(param,key='cutadapt_second_adapter',dType=str)
   module_helper.checkParameter(param,key='cutadapt_m',dType=str)
   
   
def run_cutadapt(param,infile,outfile,adapter):
    #run the clipper
{'fraction_non_alphanumeric': 0.10142348754448399, 'fraction_numerical': 0.0, 'mean_word_length': 8.0, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3827324', 'n_tokens_mistral': 378, 'n_tokens_neox': 369, 'n_words': 47}