remove unessessory files

workflow/main.nf

 #!/usr/bin/env nextflow
    params.design="$baseDir/../test_data/samplesheet.csv"
    params.bams = "$baseDir/../test_data/*.bam"
-//   params.bais = "$baseDir/../test_data/*.bai"
    params.peaks = "$baseDir/../test_data/*.broadPeak"
    params.genomepath="/project/shared/bicf_workflow_ref/GRCh37"
-   toppeakcount = 200
+   toppeakcount = -1
    design_file = file(params.design)
    deeptools_design = Channel.fromPath(params.design)
    diffbind_design = Channel.fromPath(params.design)
@@ -17,8 +16,6 @@
    diffbind_bams = Channel.fromPath(params.bams) 
    diffbind_peaks = Channel.fromPath(params.peaks) 
    meme_peaks = Channel.fromPath(params.peaks)
-//   deeptools_bamindex = Channel.fromPath(params.bais)
-//   diffbind_bamindex = Channel.fromPath(params.bais) 
 
 process bamindex {
    publishDir "$baseDir/output/", mode: 'copy'

workflow/scripts/process.py

-#!/usr/bin/python
-# programmer : bbc
-# usage: main function to call all the procedures for chip-seq analysis
-import sys
-import os
-import argparse as ap
-import logging
-import pandas as pd
-import glob
-import subprocess
-from multiprocessing import Pool
-import runDeepTools
-import runMemechip
-logging.basicConfig(level=10)
-
-
-def prepare_argparser():
-  description = "Make wig file for given bed using bam"
-  epilog = "For command line options of each command, type %(prog)% COMMAND -h"
-  argparser = ap.ArgumentParser(description=description, epilog = epilog)
-  argparser.add_argument("-i","--input",dest = "infile",type=str,required=True, help="input design file")
-  argparser.add_argument("-g","--genome",dest = "genome",type=str,required=True, help="genome", default="hg19")
-  argparser.add_argument("--top-peak",dest="toppeak",type=int, default=-1, help = "Only use top peaks for motif call")
-  #argparser.add_argument("-s","--strandtype",dest="stranded",type=str,default="none", choices=["none","reverse","yes"])
-  #argparser.add_argument("-n","--name",dest="trackName",type=str,default="UserTrack",help = "track name for bedgraph header")
-  return(argparser)
-
-def memechip_wrapper(args):
-  #print args  
-  runMemechip.run(*args)
-
-def main():
-  argparser = prepare_argparser()
-  args = argparser.parse_args()
-  #dfile = pd.read_csv(args.infile)
-
-  #for testing, add testing path to all input files
-  test_path = "/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/"
-  designfile = pd.read_csv(args.infile)
-  designfile['Peaks'] = designfile['Peaks'].apply(lambda x: test_path+x)
-  designfile['bamReads'] = designfile['bamReads'].apply(lambda x: test_path+x)
-  designfile['bamControl'] = designfile['bamControl'].apply(lambda x: test_path+x)
-  designfile.to_csv(args.infile+"_new",index=False)
-  dfile = pd.read_csv(args.infile+"_new")
-  #call deeptools
-  runDeepTools.run(args.infile+"_new", args.genome) 
-  #call diffbind
-  this_script = os.path.abspath(__file__).split("/")
-  folder = "/".join(this_script[0:len(this_script)-1])
-  
-  diffbind_command = "Rscript "+folder+"/runDiffBind.R "+args.infile+"_new"
-  #logging.debug(diffbind_command)
-  p = subprocess.Popen(diffbind_command, shell=True)
-  p.communicate()
-  #call chipseeker on original peaks and overlapping peaks
-  chipseeker_command = "Rscript "+folder+"/runChipseeker.R "+",".join(dfile['Peaks'].tolist())+" "+",".join(dfile['SampleID'])
-#BC##  logging.debug(chipseeker_command)
-  p = subprocess.Popen(chipseeker_command, shell=True)
-  p.communicate()
-  overlapping_peaks = glob.glob('*diffbind.bed')
-  overlapping_peak_names = []
-  for pn in overlapping_peaks:
-    overlapping_peak_names.append(pn.split("_diffbind")[0].replace("!","non"))
-  chipseeker_overlap_command = "Rscript "+folder+"/runChipseeker.R "+",".join(overlapping_peaks)+" "+",".join(overlapping_peak_names)
-  p = subprocess.Popen(chipseeker_overlap_command, shell=True)
-  p.communicate()
-  #MEME-chip on all peaks
-  meme_arglist =  zip(dfile['Peaks'].tolist(),[test_path+"hg19.2bit"]*dfile.shape[0],[str(args.toppeak)]*dfile.shape[0],dfile['SampleID'].tolist())
-#BC#  #print meme_arglist
-  work_pool = Pool(min(12,dfile.shape[0]))
-  resultList = work_pool.map(memechip_wrapper, meme_arglist)
-  work_pool.close()
-  work_pool.join()
- 
-
-if __name__=="__main__":
-  main()