diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 57a83b333141e9056fa00b894bc76e43010ee341..8417664465fb8691f52e97960b6acda0b54594c8 100755
--- a/astrocyte_pkg.yml
+++ b/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:
diff --git a/workflow/main.test.nf b/workflow/main.test.nf
deleted file mode 100644
index 581f1777764f5d67b7dc352d17bb9b3e2e350065..0000000000000000000000000000000000000000
--- a/workflow/main.test.nf
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/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
diff --git a/workflow/scripts/check_design.test.py b/workflow/scripts/check_design.test.py
deleted file mode 100755
index e08f08a2573c9a32c88ce3bdbc3860e5bd179446..0000000000000000000000000000000000000000
--- a/workflow/scripts/check_design.test.py
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/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()