diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 8417664465fb8691f52e97960b6acda0b54594c8..57a83b333141e9056fa00b894bc76e43010ee341 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -150,6 +150,16 @@ 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
new file mode 100644
index 0000000000000000000000000000000000000000..581f1777764f5d67b7dc352d17bb9b3e2e350065
--- /dev/null
+++ b/workflow/main.test.nf
@@ -0,0 +1,89 @@
+#!/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
new file mode 100755
index 0000000000000000000000000000000000000000..e08f08a2573c9a32c88ce3bdbc3860e5bd179446
--- /dev/null
+++ b/workflow/scripts/check_design.test.py
@@ -0,0 +1,139 @@
+#!/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()