Add in making experiment design files.

workflow/conf/biohpc.config

@@ -31,6 +31,10 @@ process {
     module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2']
     cpus = 32
   }
+  $defineExpDesignFiles {
+    module = ['python/3.6.1-2-anaconda']
+    executor = 'local'
+  }
 }
 
 params {

workflow/main.nf

@@ -164,7 +164,7 @@ process filterReads {
 
 }
 
-// Define channel collecting new design file
+// Define channel collecting dedup reads intp new design file
 dedupDesign = dedupReads
               .map{ sampleId, bam, bai, biosample, factor, treatment, replicate, controlId ->
               "$sampleId\t$bam\t$bai\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
@@ -232,7 +232,7 @@ process crossReads {
 
   output:
 
-  set sampleId, seTagAlign, tagAlign, file('*.cc.qc'), biosample, factor, treatment, replicate, controlId into xcorReads
+  set sampleId, tagAlign, file('*.cc.qc'), biosample, factor, treatment, replicate, controlId into xcorReads
   set file('*.cc.qc'), file('*.cc.plot.pdf') into xcorReadsStats
 
   script:
@@ -249,3 +249,30 @@ process crossReads {
   }
 
 }
+
+// Define channel collecting tagAlign and xcor into design file
+xcorDesign = xcorReads
+              .map{ sampleId, tagAlign, xcor, biosample, factor, treatment, replicate, controlId ->
+              "$sampleId\t$tagAlign\t$xcor\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
+              .collectFile(name:'design_xcor.tsv', seed:"sample_id\ttag_align\txcor\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+
+// Make Experiment design files to be read in for downstream analysis
+process defineExpDesignFiles {
+
+  publishDir "$baseDir/output/design", mode: 'copy'
+
+  input:
+
+  file xcorDesign
+
+  output:
+
+  file '*.tsv' into experimentObjs
+
+  script:
+
+  """
+  python3 $baseDir/scripts/experiment_design.py -d $xcorDesign
+  """
+
+}

workflow/scripts/experiment_design.py

+#!/usr/bin/env python3
+
+'''Generate experiment design files for downstream processing.'''
+
+import argparse
+import logging
+import pandas as pd
+
+EPILOG = '''
+For more details:
+        %(prog)s --help
+'''
+
+# SETTINGS
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+logger.setLevel(logging.INFO)
+
+
+def get_args():
+    '''Define arguments.'''
+    parser = argparse.ArgumentParser(
+        description=__doc__, epilog=EPILOG,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    parser.add_argument('-d', '--design',
+                        help="The design file to make experiemnts (tsv format).",
+                        required=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'''
+
+    logger.info("Running experiment design generation.")
+
+    for experiment, df_experiment in design.groupby('experiment_id'):
+        experiment_file = experiment + '.tsv'
+        new_design.to_csv(experiment_file, header=True, sep='\t', index=False)
+
+
+def main():
+    args = get_args()
+
+    # Create a file handler
+    handler = logging.FileHandler('experiment_generation.log')
+    logger.addHandler(handler)
+
+    # Read files
+    design_file = pd.read_csv(args.design, sep='\t')
+
+    # Update design file for check_controls
+    new_design = update_controls(design_file)
+
+    # write out experiment design files
+    make_experiment_design(new_design)
+
+
+if __name__ == '__main__':
+    main()

workflow/tests/test_experiment_design.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import experiment_design
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/design/'
+
+DESIGN_STRING = """sample_id\ttag_align\txcor\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id
+A_1\tA_1.tagAlign.gz\tA\tLiver\tH3K27ac\tNone\t1\tB_1
+A_2\tA_2.tagAlign.gz\tA\tLiver\tH3K27ac\tNone\t2\tB_2
+B_1\tB_1.tagAlign.gz\tB\tLiver\tInput\tNone\t1\tB_1
+B_2\tB_2.tagAlign.gz\tB\tLiver\tInput\tNone\t2\tB_2
+"""
+
+
+@pytest.fixture
+def design_tag():
+    design_file = StringIO(DESIGN_STRING)
+    design_df = pd.read_csv(design_file, sep="\t")
+    return design_df
+
+
+def test_check_update_controls_tag(design_tag):
+    new_design = experiment_design.update_controls(design_tag)
+    assert new_design.loc[0, 'control_tag_align'] == "B_1.tagAlign.gz"
+
+
+def test_experiment_design_single_end():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.tsv'))
+
+
+def test_experiment_design_paired_end():
+    # Do the same thing for paired end data
+    pass