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Commit eb8e3e73 authored by Venkat Malladi's avatar Venkat Malladi
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Update to be astrocyte compatible.

parent 7b79b436
1 merge request!25Resolve "Test Astrocyte"
Pipeline #3559 failed with stages
in 11 seconds
...@@ -51,6 +51,7 @@ workflow_modules: ...@@ -51,6 +51,7 @@ workflow_modules:
- 'UCSC_userApps/v317' - 'UCSC_userApps/v317'
- 'R/3.3.2-gccmkl' - 'R/3.3.2-gccmkl'
- 'meme/4.11.1-gcc-openmpi' - 'meme/4.11.1-gcc-openmpi'
- 'pandoc/2.7'
# A list of parameters used by the workflow, defining how to present them, # A list of parameters used by the workflow, defining how to present them,
...@@ -93,7 +94,7 @@ workflow_parameters: ...@@ -93,7 +94,7 @@ workflow_parameters:
description: | description: |
One or more input FASTQ files from a ChIP-seq expereiment and a design 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 file with the link bewetwen the same file name and sample id
regex: ".*(fastq|fq)*" regex: ".*(fastq|fq)*gz"
min: 2 min: 2
- id: pairedEnd - id: pairedEnd
...@@ -115,7 +116,7 @@ workflow_parameters: ...@@ -115,7 +116,7 @@ workflow_parameters:
description: | description: |
A design file listing sample id, fastq files, corresponding control id A design file listing sample id, fastq files, corresponding control id
and additional information about the sample. and additional information about the sample.
regex: ".*tsv" regex: ".*txt"
- id: genome - id: genome
type: select type: select
...@@ -128,12 +129,14 @@ workflow_parameters: ...@@ -128,12 +129,14 @@ workflow_parameters:
Reference species and genome used for alignment and subsequent analysis. Reference species and genome used for alignment and subsequent analysis.
- id: astrocyte - id: astrocyte
type: string type: select
required: true choices:
default: 'true' - [ 'true', 'true' ]
regex: "true" required: true
description: | default: 'true'
Ensure configuraton for astrocyte description: |
Ensure configuraton for astrocyte.
# ----------------------------------------------------------------------------- # -----------------------------------------------------------------------------
...@@ -154,8 +157,4 @@ vizapp_cran_packages: ...@@ -154,8 +157,4 @@ vizapp_cran_packages:
# List of any Bioconductor packages, not provided by the modules, # List of any Bioconductor packages, not provided by the modules,
# that must be made available to the vizapp # that must be made available to the vizapp
vizapp_bioc_packages: vizapp_bioc_packages: []
- none
vizapp_github_packages:
- js229/Vennerable
...@@ -7,6 +7,7 @@ ...@@ -7,6 +7,7 @@
params.reads = "$baseDir/../test_data/*.fastq.gz" params.reads = "$baseDir/../test_data/*.fastq.gz"
params.pairedEnd = 'false' params.pairedEnd = 'false'
params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt" params.designFile = "$baseDir/../test_data/design_ENCSR238SGC_SE.txt"
params.genome = 'GRCm38'
params.cutoffRatio = 1.2 params.cutoffRatio = 1.2
params.outDir= "$baseDir/output" params.outDir= "$baseDir/output"
params.extendReadsLen = 100 params.extendReadsLen = 100
...@@ -17,25 +18,26 @@ params.skipMotif = false ...@@ -17,25 +18,26 @@ params.skipMotif = false
params.references = "$baseDir/../docs/references.md" params.references = "$baseDir/../docs/references.md"
// Assign variables if astrocyte // Assign variables if astrocyte
params.genome = 'GRCm38' if (params.astrocyte) {
if (params.astrocyte == 'false') { print("Running under astrocyte")
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') {
referenceLocation = "/project/shared/bicf_workflow_ref" referenceLocation = "/project/shared/bicf_workflow_ref"
params.bwaIndex = "$referenceLocation/$genome" params.bwaIndex = "$referenceLocation/$genome"
params.chromSizes = "$referenceLocation/$genome/genomefile.txt" params.chromSizes = "$referenceLocation/$genome/genomefile.txt"
params.fasta = "$referenceLocation/$genome/genome.fa.txt" params.fasta = "$referenceLocation/$genome/genome.fa.txt"
if (params.genome == 'GRCh37' || params.genome == 'GRCh38') { if (params.genome == 'GRCh37' || params.genome == 'GRCh38') {
params.chromSizes = 'hs' params.genomeSize = 'hs'
} else if (params.chromSizes == 'GRCm38') { } 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 // Check inputs
if( params.bwaIndex ){ if( params.bwaIndex ){
bwaIndex = Channel bwaIndex = Channel
......
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