From ad56b8684212bdf2904f51f0ffa244fc74b59e24 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Mon, 21 Nov 2016 14:40:52 -0600
Subject: [PATCH] update scripts
---
astrocyte_package.yml | 5 +++--
workflow/main.nf | 12 ++++++++++++
2 files changed, 15 insertions(+), 2 deletions(-)
diff --git a/astrocyte_package.yml b/astrocyte_package.yml
index 697e657..9e99a11 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 MEME-CHIP, visualization application.
+ It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker MAnorm and HOMER, visualization application.
# -----------------------------------------------------------------------------
# DOCUMENTATION
@@ -40,6 +40,7 @@ documentation_files:
# Specify versioned module names to ensure reproducability.
workflow_modules:
- 'deeptools/2.3.5'
+ - 'homer/4.7'
# A list of parameters used by the workflow, defining how to present them,
# options etc in the web interface. For each parameter:
#
@@ -86,7 +87,7 @@ workflow_parameters:
- id: design
type: file
required: true
- regex: ".*txt"
+ regex: ".*csv"
description: |
A design file listing pairs of sample name and sample group.
Columns must include: SampleID,SampleName,SampleGroup,FullPathToFqR1,FullPathToFqR2
diff --git a/workflow/main.nf b/workflow/main.nf
index 0c1825b..6588352 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -75,6 +75,18 @@ process peakanno {
"""
}
+//Run deeptools for QC and other plots
+//Since this problem also need all input files, need to build another channel?
+process deeptools {
+ publishDir "$baseDir/output", mode: 'copy'
+ input:
+ file peak_file from input
+ file bam_file from imput
+ output:
+ set
+
+}
+
//Need to do it with more than 1 condition
process diffbind {
publishDir "$baseDir/output", mode: 'copy'
--
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