design process and deeptools works for main

workflow/main.nf

@@ -4,7 +4,7 @@
 // params.bams="$baseDir/../test/*.bam"
    params.testpath="/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/"
    params.design="/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/samplesheet.csv"
-   params.genome="/project/shared/bicf_workflow_ref/GRCh37/"
+   params.genebed="/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/genome/hg19/gene.bed"
 
 // design_file = file(params.design)
 // bams=file(params.bams)
@@ -13,22 +13,72 @@
 //geneset = file("$params.genome/gsea_gmt/$params.geneset")
 
 
-
-process run_chipseq_analysis {
-//   publishDir "$baseDir/output", mode: 'copy'
+process processdesign {
+   publishDir "$baseDir/output/", mode: 'copy'
 //   input:
 //   file design_file from input
+//   file annotation Tdx
+   output:
+     file "new_design" into deeptools_design
+//     file "new_design" into diffbind_design
+
+     script:
+     """
+     module load python/2.7.x-anaconda
+     source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+     python $baseDir/scripts/preprocessDesign.py -i ${params.design} 
+"""
+}
+
+process run_deeptools {
+//   publishDir "$baseDir/output", mode: 'copy'
+   input:
+     file deeptools_design_file from deeptools_design
 //   file annotation Tdx
    output:
      stdout result
      script:
      """
      module load python/2.7.x-anaconda
-     module load meme/4.11.1-gcc-openmpi
      source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
      module load deeptools/2.3.5 
-     module load meme/4.11.1-gcc-openmpi     
-     python $baseDir/scripts/process.py -i ${params.design} -g hg19 --top-peak 200
+     python $baseDir/scripts/runDeepTools.py -i $deeptools_design_file -g ${params.genebed}
+"""
+}
+
+
+process run_diffbind {
+//   publishDir "$baseDir/output", mode: 'copy'
+   input:
+     file diffbind_design_file from diffbind_design
+//   file annotation Tdx
+   output:
+     file "*_diffbind.bed" into diffpeaks_chipseeker
+     file "*_diffbind.bed" into diffpeaks_meme
+
+     script:
+     """
+     module load python/2.7.x-anaconda
+     source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+     Rscript $baseDir/scripts/runDiffBind.R -i $diffbind_design_file
 """
 }
 
+//process run_chipseeker {
+////   publishDir "$baseDir/output", mode: 'copy'
+//   input:
+//     file diffbind_design_file from diffbind_design
+////   file annotation Tdx
+//   output:
+//     file "*_diffbind.bed" into diffpeaks_chipseeker
+//     file "*_diffbind.bed" into diffpeaks_meme
+//
+//     script:
+//     """
+//     module load python/2.7.x-anaconda
+//     source activate /project/shared/bicf_workflow_ref/chipseq_bchen4/
+//     Rscript $baseDir/scripts/runDiffBind.R -i $diffbind_design_file
+//"""
+//}
+
+

workflow/scripts/runDeepTools.py

@@ -47,7 +47,7 @@ def bam2bw_wrapper(command):
 
 def run_signal(files, labels, genome):
   #compute matrix and draw profile and heatmap
-  gene_bed = "/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/genome/"+genome+"/gene.bed"
+  gene_bed = genome#"/project/BICF/BICF_Core/bchen4/chipseq_analysis/test/genome/"+genome+"/gene.bed"
   bw_commands = []
   for f in files:
     bw_commands.append("bamCoverage -bs 10 -b "+f+" -o "+f.replace("bam","bw"))