Commit 234ba95d authored by Jeremy Mathews's avatar Jeremy Mathews

add spaceranger to ymls and mds

parent 54fc41b2
Pipeline #8284 failed with stages
in 13 seconds
......@@ -3,7 +3,7 @@ before_script:
- module load python/3.6.1-2-anaconda
- pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
- module load nextflow/20.01.0
- module load singularity/3.0.2
- module load singularity/3.5.3
- mkdir -p test_data/simple1
- mkdir -p test_data/simple2
- ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/
......
# v3.0.0
**UserFacing**
*
* Add flag to select cellranger vs spaceranger
* Adjust versions to take into account multiple 10x-Ranger softwares
* Remove countDesign process
**Background**
*
* Update scripts to reflect spaceranger or cellranger input
*Known Bugs*
* cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)
......
......@@ -17,7 +17,7 @@ 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.
It implements 10x CellRanger/SpaceRanger mkfastq analysis workflow application.
# -----------------------------------------------------------------------------
# DOCUMENTATION
......@@ -39,7 +39,7 @@ documentation_files:
# A list of cluster environment modules that this workflow requires to run.
# Specify versioned module names to ensure reproducability.
workflow_modules:
- 'singularity/3.0.2'
- 'singularity/3.5.3'
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
......@@ -99,6 +99,16 @@ workflow_parameters:
description: |
Ensure configuraton for astrocyte.
- id: ranger
type: select
choices:
- [ 'CellRanger', 'cellranger' ]
- [ 'SpaceRanger', 'spaceranger' ]
required: true
default: 'CellRanger'
description: |
CellRanger or SpaceRanger 10x data.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
......
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