From 1487eaa6439dfd9d1403d004ce3e532b7690b123 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 14 Jun 2018 14:26:50 -0500
Subject: [PATCH] Make pipeline to astrocyte standards.
---
astrocyte_pkg.yml | 114 ++++++++++++++++++++++++++++++++++++
docs/index.md | 3 +
workflow/conf/biohpc.config | 20 -------
workflow/main.nf | 6 +-
4 files changed, 120 insertions(+), 23 deletions(-)
create mode 100644 astrocyte_pkg.yml
create mode 100644 docs/index.md
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
new file mode 100644
index 0000000..c6c16bf
--- /dev/null
+++ b/astrocyte_pkg.yml
@@ -0,0 +1,114 @@
+#
+# 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 $baseDir
+
+# Name of the R module that the vizapp will run against
+vizapp_r_module: 'R/3.2.1-intel'
+
+# List of any CRAN packages, not provided by the modules, that must be made
+# available to the vizapp
+vizapp_cran_packages:
+ - shiny
+ - shinyFiles
+
+# List of any Bioconductor packages, not provided by the modules,
+# that must be made available to the vizapp
+vizapp_bioc_packages:
+
+vizapp_github_packages:
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 0000000..654bef8
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,3 @@
+# Astrocyte CellRanger 10x Workflow Package
+
+## Workflow SOP
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 360f31a..bb45b43 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -16,26 +16,6 @@ process {
}
}
-params {
- // Reference file paths on BioHPC
- genomes {
- 'ercc92' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0'
- }
- 'GRCh38' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
- }
- 'hg19' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0'
- }
- 'mm10' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0'
- }
- 'hg19.mm10' {
- ref = '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0'
- }
- }
-}
trace {
enabled = true
diff --git a/workflow/main.nf b/workflow/main.nf
index 9663e00..18e01b0 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -6,7 +6,7 @@
// Define Input variables
params.bcl = "$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:
--
GitLab