From eb8e3e7351a18d3286f88548d89f055d94632b5a Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 18 Apr 2019 15:50:29 -0500
Subject: [PATCH] Update to be astrocyte compatible.
---
astrocyte_pkg.yml | 25 ++++++++++++-------------
workflow/main.nf | 20 +++++++++++---------
2 files changed, 23 insertions(+), 22 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index e1a1846..9c8cc94 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -51,6 +51,7 @@ workflow_modules:
- 'UCSC_userApps/v317'
- 'R/3.3.2-gccmkl'
- 'meme/4.11.1-gcc-openmpi'
+ - 'pandoc/2.7'
# A list of parameters used by the workflow, defining how to present them,
@@ -93,7 +94,7 @@ workflow_parameters:
description: |
One or more input FASTQ files from a ChIP-seq expereiment and a design
file with the link bewetwen the same file name and sample id
- regex: ".*(fastq|fq)*"
+ regex: ".*(fastq|fq)*gz"
min: 2
- id: pairedEnd
@@ -115,7 +116,7 @@ workflow_parameters:
description: |
A design file listing sample id, fastq files, corresponding control id
and additional information about the sample.
- regex: ".*tsv"
+ regex: ".*txt"
- id: genome
type: select
@@ -128,12 +129,14 @@ workflow_parameters:
Reference species and genome used for alignment and subsequent analysis.
- id: astrocyte
- type: string
- required: true
- default: 'true'
- regex: "true"
- description: |
- Ensure configuraton for astrocyte
+ type: select
+ choices:
+ - [ 'true', 'true' ]
+ required: true
+ default: 'true'
+ description: |
+ Ensure configuraton for astrocyte.
+
# -----------------------------------------------------------------------------
@@ -154,8 +157,4 @@ vizapp_cran_packages:
# List of any Bioconductor packages, not provided by the modules,
# that must be made available to the vizapp
-vizapp_bioc_packages:
- - none
-
-vizapp_github_packages:
- - js229/Vennerable
+vizapp_bioc_packages: []
diff --git a/workflow/main.nf b/workflow/main.nf
index 80d0d34..068006e 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -7,6 +7,7 @@
params.reads = "$baseDir/../test_data/*.fastq.gz"
params.pairedEnd = 'false'
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
+params.genome = 'GRCm38'
params.cutoffRatio = 1.2
params.outDir= "$baseDir/output"
params.extendReadsLen = 100
@@ -17,25 +18,26 @@ params.skipMotif = false
params.references = "$baseDir/../docs/references.md"
// Assign variables if astrocyte
-params.genome = 'GRCm38'
-if (params.astrocyte == 'false') {
- params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
- params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
- params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
- params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
-} else if (params.astrocyte == 'true') {
+if (params.astrocyte) {
+ print("Running under astrocyte")
referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$genome"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
- params.chromSizes = 'hs'
+ params.genomeSize = 'hs'
} else if (params.chromSizes == 'GRCm38') {
- params.chromSizes = 'mm'
+ params.genomeSize = 'mm'
}
+} else {
+ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
+ params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
+ params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
+ params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
}
+
// Check inputs
if( params.bwaIndex ){
bwaIndex = Channel
--
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