update test and README.md

README.md

@@ -31,7 +31,7 @@ On release, automated continuous integration tests run the pipeline on a [full-s
 
 ## Pipeline Summary
 
-1. Basecalling and/or demultiplexing ([`Guppy`](https://nanoporetech.com/nanopore-sequencing-data-analysis) or [`qcat`](https://github.com/nanoporetech/qcat); *optional*)
+1. Basecalling and/or demultiplexing ([`Guppy`](https://nanoporetech.com/nanopore-sequencing-data-analysis), [`demux_fast5`](https://github.com/nanoporetech/ont_fast5_api#demux_fast5) or [`qcat`](https://github.com/nanoporetech/qcat); *optional*)
 2. Sequencing QC ([`pycoQC`](https://github.com/a-slide/pycoQC), [`NanoPlot`](https://github.com/wdecoster/NanoPlot))
 3. Raw read DNA cleaning ([NanoLyse](https://github.com/wdecoster/nanolyse); *optional*)
 4. Raw read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
@@ -88,7 +88,7 @@ An example input samplesheet for performing both basecalling and demultiplexing
 
 nf-core/nanoseq was originally written by [Chelsea Sawyer](https://github.com/csawye01) and [Harshil Patel](https://github.com/drpatelh) from [The Bioinformatics & Biostatistics Group](https://www.crick.ac.uk/research/science-technology-platforms/bioinformatics-and-biostatistics/) for use at [The Francis Crick Institute](https://www.crick.ac.uk/), London. Other primary contributors include [Laura Wratten](https://github.com/lwratten), [Ying Chen](https://github.com/cying111), [Yuk Kei Wan](https://github.com/yuukiiwa) and [Jonathan Goeke](https://github.com/jonathangoeke) from the [Genome Institute of Singapore](https://www.a-star.edu.sg/gis), [Johannes Alneberg](https://github.com/alneberg) and [Franziska Bonath](https://github.com/FranBonath) from [SciLifeLab](https://www.scilifelab.se/), Sweden.
 
-Many thanks to others who have helped out along the way too, including (but not limited to): [@crickbabs](https://github.com/crickbabs), [@AnnaSyme](https://github.com/AnnaSyme).
+Many thanks to others who have helped out along the way too, including (but not limited to): [@crickbabs](https://github.com/crickbabs), [@AnnaSyme](https://github.com/AnnaSyme),[@ekushele](https://github.com/ekushele).
 
 ## Contributions and Support
 

conf/test.config

@@ -15,19 +15,20 @@ params {
   config_profile_description = 'Minimal test dataset to check pipeline function'
 
   // Limit resources so that this can run on GitHub Actions
-  max_cpus            = 2
-  max_memory          = 6.GB
-  max_time            = 12.h
-
-  // Input data to perform both basecalling and demultiplexing
-  input               = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv'
-  protocol            = 'cDNA'
-  flowcell            = 'FLO-MIN106'
-  kit                 = 'SQK-DCS109'
-  barcode_kit         = 'EXP-NBD103'
-  run_nanolyse        = true
-  skip_quantification = true
-
+  max_cpus                 = 2
+  max_memory               = 6.GB
+  max_time                 = 12.h
+
+  // Input data to per     form both basecalling and demultiplexing
+  input                    = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/samplesheet_bc_dx.csv'
+  protocol                 = 'cDNA'
+  flowcell                 = 'FLO-MIN106'
+  kit                      = 'SQK-DCS109'
+  barcode_kit              = 'EXP-NBD103'
+  output_demultiplex_fast5 = true
+  run_nanolyse             = true
+  skip_quantification      = true
+
   // This variable is just for reference and isnt actually required for the tests
   // Files are downloaded and staged using the "GetTestData" process
   input_path          = 'https://raw.githubusercontent.com/nf-core/test-datasets/nanoseq/fast5/barcoded/'