Fix Pool and Pseudoreps

workflow/main.nf

@@ -403,21 +403,26 @@ xcorDesign = xcorReads
 // Make Experiment design files to be read in for downstream analysis
 process defineExpDesignFiles {
 
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "${outDir}/design", mode: 'copy'
 
   input:
-
-  file xcorDesign
+    file xcorDesign
 
   output:
-
-  file '*.tsv' into experimentObjs mode flatten
+    file '*.tsv' into experimentObjs mode flatten
 
   script:
-
-  """
-  python3 $baseDir/scripts/experiment_design.py -d $xcorDesign -a
-  """
+    if (params.astrocyte == true) {
+      """
+      module load python/3.6.1-2-anaconda
+      python3 ${baseDir}/scripts/experiment_design.py -d ${xcorDesign}
+      """
+    }
+    else {
+      """
+      python3 ${baseDir}/scripts/experiment_design.py -d ${xcorDesign}
+      """
+    }
 
 }
 
@@ -427,28 +432,41 @@ process poolAndPsuedoReads {
 
 
   tag "${experimentObjs.baseName}"
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "${outDir}/design", mode: 'copy'
 
   input:
-
-  file experimentObjs
+    file experimentObjs
 
   output:
-
-  file '*.tsv' into experimentPoolObjs
+    file '*.tsv' into experimentPoolObjs
 
   script:
-
-  if (pairedEnd) {
-    """
-    python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -p -a
-    """
-  }
-  else {
-    """
-    python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -a
-    """
-  }
+    if (params.astrocyte == true) {
+      if (pairedEnd) {
+        """
+        module load python/3.6.1-2-anaconda
+        python3 ${baseDir}/scripts/pool_and_psuedoreplicate.py -d ${experimentObjs} -p
+        """
+      }
+      else {
+        """
+        module load python/3.6.1-2-anaconda
+        python3 ${baseDir}/scripts/pool_and_psuedoreplicate.py -d ${experimentObjs}
+        """
+      }
+    }
+    else {
+      if (pairedEnd) {
+        """
+        python3 ${baseDir}/scripts/pool_and_psuedoreplicate.py -d ${experimentObjs} -p
+        """
+      }
+      else {
+        """
+        python3 ${baseDir}/scripts/pool_and_psuedoreplicate.py -d ${experimentObjs}
+        """
+      }
+    }
 
 }
 

workflow/scripts/experiment_design.py

@@ -30,33 +30,10 @@ def get_args():
                         help="The design file to make experiemnts (tsv format).",
                         required=True)
 
-    parser.add_argument('-a', '--atac',
-                        help="True/False if ATAC-seq or ChIP-seq.",
-                        default=False,
-                        action='store_true')
-
     args = parser.parse_args()
     return args
 
 
-def update_controls(design):
-    '''Update design file to append controls list.'''
-
-    logger.info("Running control file update.")
-
-    file_dict = design[['sample_id', 'tag_align']] \
-                .set_index('sample_id').T.to_dict()
-
-    design['control_tag_align'] = design['control_id'] \
-                                .apply(lambda x: file_dict[x]['tag_align'])
-
-    logger.info("Removing rows that are there own control.")
-
-    design = design[design['control_id'] != design['sample_id']]
-
-    return design
-
-
 def make_experiment_design(design):
     '''Make design file by grouping for each experiment'''
 
@@ -70,7 +47,6 @@ def make_experiment_design(design):
 def main():
     args = get_args()
     design = args.design
-    atac = args.atac
 
     # Create a file handler
     handler = logging.FileHandler('experiment_generation.log')
@@ -79,14 +55,8 @@ def main():
     # Read files as dataframes
     design_df = pd.read_csv(design, sep='\t')
 
-    # Update design file for check_controls
-    if not atac:
-        new_design_df = update_controls(design_df)
-    else:
-        new_design_df = design_df
-
     # write out experiment design files
-    make_experiment_design(new_design_df)
+    make_experiment_design(design_df)
 
 
 if __name__ == '__main__':

workflow/scripts/pool_and_psuedoreplicate.py

@@ -43,11 +43,6 @@ def get_args():
                         help="Cutoff ratio used for choosing controls.",
                         default=1.2)
 
-    parser.add_argument('-a', '--atac',
-                        help="True/False if ATAC-seq or ChIP-seq.",
-                        default=False,
-                        action='store_true')
-
     args = parser.parse_args()
     return args
 
@@ -146,7 +141,6 @@ def main():
     paired = args.paired
     design = args.design
     cutoff_ratio = args.cutoff
-    atac = args.atac
 
     # Create a file handler
     handler = logging.FileHandler('experiment_generation.log')