Make pipeline to astrocyte standards.

astrocyte_pkg.yml

+#
+# metadata for the  Astrocyte CellRanger mkfastq workflow package
+#
+
+# -----------------------------------------------------------------------------
+# BASIC INFORMATION
+# -----------------------------------------------------------------------------
+
+# A unique identifier for the workflow package, text/underscores only
+name: 'cellranger_mkfastq'
+# Who wrote this?
+author: 'Gervaise Henry and Venkat Malladi'
+# A contact email address for questions
+email: 'bicf@utsouthwestern.edu'
+# A more informative title for the workflow package
+title: 'BICF CellRanger mkfastq Workflow'
+# A summary of the workflow package in plain text
+description: |
+  This is a workflow package for the BICF/Strand Lab CellRanger mkfastq workflow system.
+  It implements 10x CellRanger mkfastq analysis workflow application.
+
+# -----------------------------------------------------------------------------
+# DOCUMENTATION
+# -----------------------------------------------------------------------------
+
+# A list of documentation file in .md format that should be viewable from the
+# web interface. These files are in the 'docs' subdirectory. The first file
+# listed will be used as a documentation index and is index.md by convention
+documentation_files:
+  - ['index.md']
+
+# -----------------------------------------------------------------------------
+# NEXTFLOW WORKFLOW CONFIGURATION
+# -----------------------------------------------------------------------------
+
+# Remember - The workflow file is always named 'workflow/main.nf'
+#            The workflow must publish all final output into $baseDir
+
+# A list of cluster environment modules that this workflow requires to run.
+# Specify versioned module names to ensure reproducability.
+workflow_modules:
+  - 'python/3.6.1-2-anaconda'
+  - 'cellranger/2.1.1'
+  - 'bcl2fastq/2.17.1.14'
+
+# A list of parameters used by the workflow, defining how to present them,
+# options etc in the web interface. For each parameter:
+#
+# REQUIRED INFORMATION
+#  id:         The name of the parameter in the NEXTFLOW workflow
+#  type:       The type of the parameter, one of:
+#                string    - A free-format string
+#                integer   - An integer
+#                real      - A real number
+#                file      - A single file from user data
+#                files     - One or more files from user data
+#                select    - A selection from a list of values
+#  required:    true/false, must the parameter be entered/chosen?
+#  description: A user friendly description of the meaning of the parameter
+#
+# OPTIONAL INFORMATION
+#  default:   A default value for the parameter (optional)
+#  min:       Minium value/characters/files for number/string/files types
+#  max:       Maxumum value/characters/files for number/string/files types
+#  regex:     A regular expression that describes valid entries / filenames
+#
+# SELECT TYPE
+#  choices:   A set of choices presented to the user for the parameter.
+#             Each choice is a pair of value and description, e.g.
+#
+#             choices:
+#               - [ 'myval', 'The first option']
+#               - [ 'myval', 'The second option']
+#
+# NOTE - All parameters are passed to NEXTFLOW as strings... but they
+#        are validated by astrocyte using the information provided above
+
+workflow_parameters:
+
+  - id: bcl
+    type: files
+    required: true
+    description: |
+      One or more input Tarball BCL files from a sequencing of 10x single-cell expereiment .
+    regex: ".*(tar)*"
+
+  - id: design
+    type: file
+    required: true
+    description: |
+      A design file listing lane, sample, corresponding index.
+
+
+# -----------------------------------------------------------------------------
+# SHINY APP CONFIGURATION
+# -----------------------------------------------------------------------------
+
+# Remember - The vizapp is always 'vizapp/server.R' 'vizapp/ui.R'
+#            The workflow must publish all final output into $baseDir
+
+# Name of the R module that the vizapp will run against
+vizapp_r_module: 'R/3.2.1-intel'
+
+# List of any CRAN packages, not provided by the modules, that must be made
+# available to the vizapp
+vizapp_cran_packages:
+  - shiny
+  - shinyFiles
+
+# List of any Bioconductor packages, not provided by the modules,
+# that must be made available to the vizapp
+vizapp_bioc_packages:
+
+vizapp_github_packages:

docs/index.md

+# Astrocyte CellRanger 10x Workflow Package
+
+## Workflow SOP

workflow/conf/biohpc.config

@@ -16,26 +16,6 @@ process {
   }
 }
 
-params {
-  // Reference file paths on BioHPC
-  genomes {
-    'ercc92' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0'
-    }
-    'GRCh38' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
-    }
-    'hg19' {
-	ref = '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0'
-    }
-    'mm10' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0'
-    }
-    'hg19.mm10' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0'
-    }
-  }
-}
 
 trace {
   enabled = true

workflow/main.nf

@@ -6,7 +6,7 @@
 // Define Input variables
 params.bcl = "$baseDir/../test_data/*.tar"
 params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'GRCm38'
+
 
 // Define List of Files
 tarList = Channel.fromPath( params.bcl )
@@ -51,7 +51,7 @@ process untarBCL {
   script:
 
   """
-  
+
   tar -xvf $tar
   """
 }
@@ -60,7 +60,7 @@ process untarBCL {
 process mkfastq {
 
   tag "${bcl.baseName}"
-  publishDir "$baseDir/output/fastq/${bcl.baseName}", mode: 'copy' 
+  publishDir "$baseDir/output/fastq/${bcl.baseName}", mode: 'copy'
 
   input: