Merge branch 'develop' into 'master'

Develop

See merge request !16

.gitignore

@@ -24,6 +24,120 @@ wheels/
 .installed.cfg
 *.egg
 
+# PyInstaller
+# Created by https://www.gitignore.io/api/r,perl,macos,linux,python,windows
+# Edit at https://www.gitignore.io/?templates=r,perl,macos,linux,python,windows
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Perl ###
+!Build/
+.last_cover_stats
+/META.yml
+/META.json
+/MYMETA.*
+*.o
+*.pm.tdy
+*.bs
+
+# Devel::Cover
+cover_db/
+
+# Devel::NYTProf
+nytprof.out
+
+# Dizt::Zilla
+/.build/
+
+# Module::Build
+_build/
+Build
+Build.bat
+
+# Module::Install
+inc/
+
+# ExtUtils::MakeMaker
+/blib/
+/_eumm/
+/*.gz
+/Makefile
+/Makefile.old
+/MANIFEST.bak
+/pm_to_blib
+/*.zip
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.
@@ -37,6 +151,7 @@ pip-delete-this-directory.txt
 # Unit test / coverage reports
 htmlcov/
 .tox/
+.nox/
 .coverage
 .coverage.*
 .cache
@@ -44,6 +159,7 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -52,6 +168,7 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
+db.sqlite3
 
 # Flask stuff:
 instance/
@@ -69,6 +186,10 @@ target/
 # Jupyter Notebook
 .ipynb_checkpoints
 
+# IPython
+profile_default/
+ipython_config.py
+
 # pyenv
 .python-version
 
@@ -84,6 +205,8 @@ celerybeat-schedule
 env/
 venv/
 ENV/
+env.bak/
+venv.bak/
 
 # Spyder project settings
 .spyderproject
@@ -97,16 +220,94 @@ ENV/
 
 # mypy
 .mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### Python Patch ###
+.venv/
+
+### R ###
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+
+### Windows ###
+# Windows thumbnail cache files
+Thumbs.db
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# End of https://www.gitignore.io/api/r,perl,macos,linux,python,windows
 
 # nextflow analysis folders/files
-/test_data/*.fastq.gz
-/test_data/*.fastq
+/test_data/*
 /workflow/.nextflow/*
 /workflow/work/*
 /workflow/output/*
+/.nextflow/*
+/work/*
+/output/*
 pipeline_trace*.txt*
 .nextflow*.log*
 report.html*
 timeline*.html*
 
 *~
+
+!.gitkeep

.gitlab-ci.yml

 before_script:
   - module load python/3.6.1-2-anaconda
-  - module load nextflow/0.27.6
-  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger_count/*fastq.gz test_data/
+  - module load nextflow/0.31.1_Ignite
+  - mkdir test_data/v2s2r100k
+  - mkdir test_data/v3s2r100k
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v2s2r100k/* test_data/v2s2r100k/
+  - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/* test_data/v3s2r100k/
 
 stages:
   - integration
 
-simple_test:
+simple_cr2v2ref1.2.0:
   stage: integration
   script:
-  - nextflow run workflow/main.nf
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+
+simple_cr2v2ref3.0.0:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '2.1.1'
+
+simple_cr3v2ref3.0.0:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v2s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v2s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'two' --version '3.0.2'
+
+simple_cr3v3ref3.0.0:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --fastq "$CI_PROJECT_DIR/test_data/v3s2r100k/*.fastq.gz" --designFile "$CI_PROJECT_DIR/test_data/v3s2r100k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2'

README.md

@@ -10,4 +10,85 @@ The pipeline uses Nextflow, a bioinformatics workflow tool.
 
 This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.
 
-Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.
\ No newline at end of file
+Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.
+
+To Run:
+-------
+
+* Available parameters:
+  * **--fastq**
+        * path to the fastq location
+        * R1 and R2 only necessary but can include I2
+        * eg: **--fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/\*.fastq.gz'**
+  * **--designFile**
+        * path to design file (csv format) location
+        * column 1 = "Sample"
+        * column 2 = "fastq_R1"
+        * column 3 = "fastq_R2"
+        * can have repeated "Sample" if there are multiole fastq R1/R2 pairs for the samples
+        * eg: **--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/design.csv'**
+    * **--genome**
+        * reference genome
+        * requires workflow/conf/biohpc.config to work
+        * name of available 10x Gemomics premade reference genomes:
+            * *'GRCh38-3.0.0'* = Human GRCh38 release 93
+            * *'GRCh38-1.2.0'* = Human GRCh38 release 84
+            * *'hg19-3.0.0'* = Human GRCh37 (hg19) release 87
+            * *'hg19-1.2.0'* = Human GRCh37 (hg19) release 84
+            * *'mm10-3.0.0'* = Human GRCm38 (mm10) release 93
+            * *'mm10-3.0.0'* = Human GRCm38 (mm10) release 84
+            * *'hg19_and_mm10-3.0.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93
+            * *'hg19_and_mm10-1.2.0'* = Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84
+            * *'ercc92-1.2.0'* = ERCC.92 Spike-In
+        * if --genome is used then --genomeLocationFull is not necessary
+        * eg: **--genome 'GRCh38-3.0.0'**
+    * **--genomeLocationFull**
+        * path to a custom genome
+        * if --genomeLocationFull is used --genome is not necessary and is overwritten
+        * eg. **--genomeLocationFull '/project/apps_database/cellranger/refdata-cellranger-GRCh38-3.0.0'**
+    * **--expectCells**
+        * expected number of cells to be detected
+        * guides cellranger in it's cutoff for background/low quality cells
+        * as a guide it doesn't have to be exact
+        * 0-10000
+        * if --expextedCells is used then --forceCells is not necessary
+        * only used if --forceCells is not entered or set to 0
+        * eg: **--expectCells 10000**
+    * **--forceCells**
+        * forces filtering of the top number of cells matching this parameter
+        * 0-10000
+        * if --forceCells is used then --expectedCells is not necessary and is overwritten
+        * eg: **--forceCells 10000**
+    * **--kitVersion**
+        * the library chemistry version number for the 10x Genomics Gene Expression kit
+        * setting to auto will attempt to autodetect from the detected cycle strategy in the fastq's
+        * version numbers are spelled out
+        * --kitversion is only used if --version (cellranger version) is > 2
+        * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
+        * options:
+            * *'auto'*
+            * *'three'*
+            * *'two'*
+        * eg: **--kitVersion 'three'**'
+    * **--version**
+        * cellranger version
+        * --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
+        * options:
+            * *'3.0.2'*
+            * *'3.0.1'*
+            * *'2.1.1'*
+        * eg: **--version '3.0.2'**'
+    * **--outDir**
+        * optional output directory for run
+        * eg: **--outDir 'test'**
+    * FULL EXAMPLE:
+
+**nextflow main.nf --fastq '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/\*.fastq.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_count/v3s2r100k/design.csv' --genome 'GRCh38-3.0.0' --kitVersion 'three' --version '3.0.2' --outDir 'test'**
+
+* Design example:
+
+| Sample  | fastq_R1                           | fastq_R2                           |
+|---------|------------------------------------|------------------------------------|
+| sample1 | pbmc_1k_v2_S1_L001_R1_001.fastq.gz | pbmc_1k_v2_S1_L001_R2_001.fastq.gz |
+| sample2 | pbmc_1k_v2_S2_L001_R1_001.fastq.gz | pbmc_1k_v2_S2_L001_R2_001.fastq.gz |
+| sample2 | pbmc_1k_v2_S2_L002_R1_001.fastq.gz | pbmc_1k_v2_S2_L002_R2_001.fastq.gz |
\ No newline at end of file

astrocyte_pkg.yml

@@ -41,6 +41,8 @@ documentation_files:
 workflow_modules:
   - 'python/3.6.1-2-anaconda'
   - 'cellranger/2.1.1'
+  - 'cellranger/3.0.1'
+  - 'cellranger/3.0.2'
   - 'bcl2fastq/2.17.1.14'
 
 # A list of parameters used by the workflow, defining how to present them,
@@ -95,11 +97,15 @@ workflow_parameters:
   - id: genome
     type: select
     choices:
-      - [ '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38']
-      - [ '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19)']
-      - [ '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10)']
-      - [ '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19)']
-      - [ '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In']
+      - [ 'GRCh38-3.0.0', 'Human GRCh38 release 93']
+      - [ 'GRCh38-1.2.0', 'Human GRCh38 release 84']
+      - [ 'hg19-3.0.0', 'Human GRCh37 (hg19) release 87']
+      - [ 'hg19-1.2.0', 'Human GRCh37 (hg19) release 84']
+      - [ 'mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93']
+      - [ 'mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84']
+      - [ 'hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93']
+      - [ 'hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
+      - [ 'ercc92-1.2.0', 'ERCC.92 Spike-In']
     required: true
     description: |
       Reference species and genome used for alignment and subsequent analysis.
@@ -122,6 +128,29 @@ workflow_parameters:
     description: |
       Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells.
 
+  - id: kitVersion
+    type: select
+    default: 'auto'
+    choices:
+      - [ 'auto', 'Auto Detect']
+      - [ 'three', '3']
+      - [ 'two', '2']
+    required: true
+    description: |
+      10x single cell gene expression chemistry version (only used in cellranger version 2.x).
+
+  - id: version
+    type: select
+    default: '3.0.2'
+    choices:
+      - [ '3.0.2', '3.0.2']
+      - [ '3.0.1', '3.0.1']
+      - [ '2.1.1', '2.1.1']
+    required: true
+    description: |
+      10x cellranger version.
+
+
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
 # -----------------------------------------------------------------------------

nextflow.config

+profiles {
+  standard {
+    includeConfig 'workflow/conf/biohpc.config'
+  }
+}

test_data/design.csv

-Sample,fastq_R1,fastq_R2
-D17PrPzF_BE,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L001_R1_001.fastq.gz,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L001_R2_001.fastq.gz
-D17PrPzF_BE,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L002_R1_001.fastq.gz,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L002_R2_001.fastq.gz
-D17PrPzF_LE,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_LE_S3_L001_R1_001.fastq.gz,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_LE_S3_L001_R2_001.fastq.gz

workflow/conf/biohpc.config

@@ -7,8 +7,65 @@ process {
     module = ['python/3.6.1-2-anaconda']
     executor = 'local'
   }
-  $count {
+  $count211 {
     module = ['cellranger/2.1.1']
+    memory = '120GB'
+  }
+  $count301 {
+    module = ['cellranger/3.0.1']
+    memory = '120GB'
+  }
+  $count302 {
+    module = ['cellranger/3.0.2']
+    memory = '120GB'
+  }
+}
+
+params {
+  // Reference file paths on BioHPC
+  genomes {
+    'GRCh38-3.0.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'GRCh38-1.2.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'hg19-3.0.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'hg19-1.2.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'mm10-3.0.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'mm10-1.2.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'hg19_and_mm10-3.0.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'hg19_and_mm10-1.2.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+    'ercc92-1.2.0' {
+      loc = '/project/apps_database/cellranger/refdata-cellranger-'
+    }
+  }
+  // Chemistry mapping parameter
+  chemistry {
+    'auto' {
+      param = 'auto'
+    }
+    'one' {
+      param = 'SC3Pv1'
+    }
+   'two' {
+      param = 'SC3Pv2'
+    }
+   'three' {
+      param = 'SC3Pv3'
+    }
   }
 }
 

workflow/main.nf

@@ -6,9 +6,17 @@
 // Define Input variables
 params.fastq = "$baseDir/../test_data/*.fastq.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
+params.genome = 'GRCh38-3.0.0'
+params.genomes = []
+params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
+params.genomeLocationFull = params.genomeLocation+params.genome
 params.expectCells = 10000
 params.forceCells = 0
+params.kitVersion = 'three'
+params.chemistry = []
+params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
+params.version = '3.0.2'
+params.outDir = "$baseDir/output"
 
 // Define regular variables
 designLocation = Channel
@@ -20,14 +28,17 @@ fastqList = Channel
   .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
   .collectFile(name: 'fileList.tsv', newLine: true)
 refLocation = Channel
-  .fromPath(params.genome)
+  .fromPath(params.genomeLocationFull)
   .ifEmpty { exit 1, "referene not found: ${params.genome}" }
 expectCells = params.expectCells
 forceCells = params.forceCells
+chemistryParam = params.chemistryParam
+version = params.version
+outDir = params.outDir
 
 process checkDesignFile {
 
-  publishDir "$baseDir/output", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -36,12 +47,11 @@ process checkDesignFile {
 
   output:
 
-  file("design.csv") into designPaths
+  file("design.checked.csv") into designPaths
 
   script:
 
   """
-  module load python/3.6.1-2-anaconda
   python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
   """
 }
@@ -53,33 +63,117 @@ samples = designPaths
   .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
+
+process count211 {
+  tag "count211-$sample"
+
+  publishDir "$outDir/${task.process}", mode: 'copy'
+
+  input:
+
+  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples211
+  file ref from refLocation211.first()
+  expectCells211
+  forceCells211
+
+  output:
+
+  file("**/outs/**") into outPaths211
+
+  when:
+  version == '2.1.1'
+
+  script:
+  if (forceCells211 == 0){
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
+    	"""
+  } else {
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
+    	"""
+  }
+}
 
-process count {
-  tag "$sample"
+process count301 {
+  tag "count301-$sample"
 
-  publishDir "$baseDir/output", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
-  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples
-  file ref from refLocation.first()
-  expectCells
-  forceCells
+  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples301
+  file ref from refLocation301.first()
+  expectCells301
+  forceCells301
+  chemistryParam301
 
   output:
 
-  file("**/outs/**") into outPaths
+  file("**/outs/**") into outPaths301
+
+  when:
+  version == '3.0.1'
+
+  script:
+  if (forceCells301 == 0){
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
+    	"""
+  } else {
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
+    	"""
+  }
+}
+
+process count302 {
+  tag "count302-$sample"
+
+  publishDir "$outDir/${task.process}", mode: 'copy'
+
+  input:
+
+  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples302
+  file ref from refLocation302.first()
+  expectCells302
+  forceCells302
+  chemistryParam302
+
+  output:
+
+  file("**/outs/**") into outPaths302
+
+  when:
+  version == '3.0.2'
 
   script:
-  if (forceCells == 0){
-    """
-    module load cellranger/2.1.1
-    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
-    """
+  if (forceCells302 == 0){
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
+    	"""
   } else {
-    """
-    module load cellranger/2.1.1
-    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
-    """
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
+    	"""
   }
 }

workflow/scripts/check_design.py

@@ -100,7 +100,7 @@ def main():
     new_design_df = check_design_headers(design_df)
     check_files(design_df, fastq_df)
 
-    new_design_df.to_csv('design.csv', header=True, sep=',', index=False)
+    new_design_df.to_csv('design.checked.csv', header=True, sep=',', index=False)
 
 if __name__ == '__main__':
     main()