Merge branch 'revert-8f536aab' into 'develop'

Revert "Merge branch '10-count.features' into 'develop'"

See merge request !30

astrocyte_pkg.yml

@@ -150,16 +150,6 @@ workflow_parameters:
     description: |
       10x cellranger version.
 
-  - id: feature
-    type: select
-    default: 'no'
-    choices:
-      - [ 'no', 'No']
-      - [ 'yes', 'Yes']
-    required: true
-    description: |
-      Additional features to count (only used in cellranger version 3+, ignored otherwise).
-
   - id: astrocyte
     type: select
     choices:

workflow/main.test.nf

-#!/usr/bin/env nextflow
-
-// Path to an input file, or a pattern for multiple inputs
-// Note - $baseDir is the location of this workflow file main.nf
-
-// Define Input variables
-params.fastq = "$baseDir/../test_data/*.fastq.gz"
-params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'GRCh38-3.0.0'
-params.genomes = []
-params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
-params.expectCells = 10000
-params.forceCells = 0
-params.kitVersion = '3'
-params.chemistry = []
-params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
-params.version = '3.0.2'
-params.feature = 'yes'
-params.outDir = "$baseDir/output"
-
-// Define regular variables
-designLocation = Channel
-  .fromPath(params.designFile)
-  .ifEmpty { exit 1, "design file not found: ${params.designFile}" }
-fastqList = Channel
-  .fromPath(params.fastq)
-  .flatten()
-  .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
-  .collectFile(name: 'fileList.tsv', newLine: true)
-refLocation = Channel
-  .fromPath(params.genomeLocation+params.genome)
-  .ifEmpty { exit 1, "referene not found: ${params.genome}" }
-expectCells = params.expectCells
-forceCells = params.forceCells
-chemistryParam = params.chemistryParam
-version = params.version
-feature = params.feature
-featurechk = feature
-outDir = params.outDir
-
-process checkDesignFile {
-
-  publishDir "$outDir/${task.process}", mode: 'copy'
-
-  input:
-
-  file designLocation
-  file fastqList
-  featurechk
-
-  output:
-
-  file("*.checked.csv") into designPaths
-
-  script:
-
-  """
-  python3 $baseDir/scripts/check_design.test.py -d $designLocation -f $fastqList -t "$featurechk"
-  """
-}
-
-// Parse design file
-samples = designPaths
-  .splitCsv (sep: ',', header: true)
-  .map { row -> [ row.Sample, file(row.fastq_R1), file(row.fastq_R2) ] }
-  .groupTuple()
-  //.subscribe { println it }
-
-// Duplicate variables
-samples.into {
-  samples211
-  samples301
-  samples302
-}
-refLocation.into {
-  refLocation211
-  refLocation301
-  refLocation302
-}
-expectCells211 = expectCells
-expectCells301 = expectCells
-expectCells302 = expectCells
-forceCells211 = forceCells
-forceCells301 = forceCells
-forceCells302 = forceCells
-chemistryParam301 = chemistryParam
-chemistryParam302 = chemistryParam
-feature301 = feature
-feature302 = feature

workflow/scripts/check_design.test.py

-#!/usr/bin/env python3
-
-'''Check if design file is correctly formatted and matches files list.'''
-
-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 run QC (tsv format).",
-                        required=True )
-
-    parser.add_argument('-f', '--fastq',
-                        help="File with list of fastq files (tsv format).",
-                        required=True )
-
-    parser.add_argument('-t', '--feature',
-                        help="Additional features to count?",
-                        required=True )
-
-    args = parser.parse_args()
-    return args
-
-
-def check_design_headers_n(design):
-    '''Check if design file conforms to sequencing type.'''
-
-    # Default headers
-    design_template = [
-        'Sample',
-	    'fastq_R1',
-	    'fastq_R2']
-
-    design_headers = list(design.columns.values)
-
-    # Check if headers
-    logger.info("Running header check.")
-
-    missing_headers = set(design_template) - set(design_headers)
-
-    if len(missing_headers) > 0:
-        logger.error('Missing column headers: %s', list(missing_headers))
-        raise Exception("Missing column headers: %s" % list(missing_headers))
-    
-    return design
-
-def check_design_headers_y(design):
-    '''Check if design file conforms to sequencing type.'''
-
-    # Default headers
-    design_template = [
-        'Sample',
-	    'fastq_R1',
-	    'fastq_R2',
-	    'library_type']
-
-    design_headers = list(design.columns.values)
-
-    # Check if headers
-    logger.info("Running header check.")
-
-    missing_headers = set(design_template) - set(design_headers)
-
-    if len(missing_headers) > 0:
-        logger.error('Missing column headers: %s', list(missing_headers))
-        raise Exception("Missing column headers: %s" % list(missing_headers))
-    
-    return design
-
-def check_files(design, fastq):
-    '''Check if design file has the files found.'''
-
-    logger.info("Running file check.")
-
-    files = list(design['fastq_R1']) + list(design['fastq_R2'])
-
-    files_found = fastq['name']
-
-    missing_files = set(files) - set(files_found)
-
-    if len(missing_files) > 0:
-        logger.error('Missing files from design file: %s', list(missing_files))
-        raise Exception("Missing files from design file: %s" %
-            list(missing_files))
-    else:
-        file_dict = fastq.set_index('name').T.to_dict()
-    
-    design['fastq_R1'] = design['fastq_R1'].apply(lambda x: file_dict[x]['path'])
-    design['fastq_R2'] = design['fastq_R2'].apply(lambda x: file_dict[x]['path'])
-
-    return design
-
-
-def main():
-    args = get_args()
-    design = args.design
-
-    # Create a file handler
-    handler = logging.FileHandler('design.log')
-    logger.addHandler(handler)
-
-    # Read files as dataframes
-    design_df = pd.read_csv(args.design, sep=',')
-    fastq_df = pd.read_csv(args.fastq, sep='\t', names=['name', 'path'])
-
-    # Check design file
-    if args.feature == 'no':
-    	new_design_df = check_design_headers_n(design_df)
-    else:
-    	new_design_df = check_design_headers_y(design_df)
-	#new_design_df[['sample']].to_csv('library.checked.csv', header=True, sep=',', index=False)
-
-    check_files(design_df, fastq_df)
-    new_design_df.drop('library_type', 1).to_csv('design.checked.csv', header=True, sep=',', index=False)
-
-
-
-if __name__ == '__main__':
-    main()