From 2e1df2693b88aab9c3b229d7028af6d332aaa485 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 7 Jan 2020 09:57:51 -0600
Subject: [PATCH] Fix documentationn for choosing only fastq files.
---
astrocyte_pkg.yml | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index ded1127..afd00cb 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -19,7 +19,7 @@ description: |
This is a workflow package for the BioHPC/BICF RNASeq workflow system.
It implements differential expression analysis, gene set enrichment analysis,
gene fusion analysis and variant identification using RNASeq data.
-
+
# -----------------------------------------------------------------------------
# DOCUMENTATION
@@ -88,7 +88,7 @@ workflow_parameters:
type: files
required: true
description: |
- One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group
+ One or more input paired-end FASTQ files from a RNASeq experiment
regex: ".*(fastq|fq)*"
min: 1
@@ -101,7 +101,7 @@ workflow_parameters:
- [ '2', 'Reverse Stranded']
description: |
In the case that the sequence libraries where generated using a stranded specific protocol.
-
+
- id: pairs
type: select
required: true
@@ -119,7 +119,7 @@ workflow_parameters:
- [ 'star', 'STAR']
description: |
Alignment tool
-
+
- id: fusion
type: select
required: true
@@ -174,7 +174,7 @@ workflow_parameters:
- ['c5.all.v5.1.entrez.gmt','Gene Ontology Gene Sets']
- ['c6.all.v5.1.symbols.gmt','Oncogenic Signatures']
- ['c7.all.v5.1.entrez.gmt','Immunological Signatures']
-
+
required: true
description: |
Gene Set Definitions used for QuSAGE Analysis -- see http://software.broadinstitute.org/gsea/msigdb/ for geneset descriptions
@@ -218,4 +218,4 @@ vizapp_bioc_packages:
- edgeR
- DESeq2
vizapp_github_packages:
- - js229/Vennerable
\ No newline at end of file
+ - js229/Vennerable
--
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