From 7cf7adc4ef40755362b18716bef38306f4306cfc Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Tue, 31 Jan 2017 12:22:11 -0600
Subject: [PATCH] yml file updated
---
astrocyte_package.yml | 21 ++++++++-------------
1 file changed, 8 insertions(+), 13 deletions(-)
diff --git a/astrocyte_package.yml b/astrocyte_package.yml
index 6bc210a..2a9f17c 100644
--- a/astrocyte_package.yml
+++ b/astrocyte_package.yml
@@ -17,7 +17,7 @@ title: 'BICF ChIP-seq Analysis Workflow'
# A summary of the workflow package in plain text
description: |
This is a workflow package for the BioHPC/BICF ChIP-seq workflow system.
- It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker MAnorm and HOMER, visualization application.
+ It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker and MEME-ChIP, visualization application.
# -----------------------------------------------------------------------------
# DOCUMENTATION
@@ -76,22 +76,13 @@ workflow_modules:
workflow_parameters:
- - id: bams
- type: files
- required: true
- description: |
- One or more BAM alignments from a ChIP-Seq experiment and a design file with the link between the same name and the sample group. All files will be imported from GreenCenter ChIP-seq peak calling pipeline
- regex: ".*(bam)*"
- min: 1
-
-
- id: design
type: file
required: true
regex: ".*csv"
description: |
A design file listing pairs of sample name and sample group.
- Columns must include: SampleID,SampleName,SampleGroup,FullPathToFqR1,FullPathToFqR2
+ Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller
- id: genome
type: select
@@ -101,9 +92,13 @@ workflow_parameters:
- [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCh38']
required: true
description: |
- Reference genome for alignment
-
+ Reference genome for annotation
+ - id: toppeak
+ type: integer
+ required: true
+ description: |
+ The number of top peaks to use for motif discovery.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
# -----------------------------------------------------------------------------
--
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