Commit fc1a4e59 authored by Venkat Malladi's avatar Venkat Malladi

Merge branch '40-astrocyte_fixes' into 'master'

Resolve "Astrocyte fixes"

Closes #40

See merge request !28
parents 54529fc9 3178fa73
Pipeline #7371 passed with stages
in 11 seconds
......@@ -2,7 +2,7 @@
All notable changes to this project will be documented in this file.
## [publish_2.0.0 ] - 2020-06-12
## [publish_2.0.1 ] - 2020-06-19
### Fixed
- Removed biosample, factor, treatment from design file
- Updated documentation
......
MIT License
Copyright (c) 2019, University of Texas Southwestern Medical Center.
All rights reserved.
Contributors: Spencer D. Barnes, Holly Ruess, Venkat S. Malladi
Department: Bioinformatic Core Facility, Department of Bioinformatics
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
......@@ -4,7 +4,7 @@ Copyright (c) 2019, University of Texas Southwestern Medical Center.
All rights reserved.
Contributors: Spencer D. Barnes, Holly Ruess, Venkat S. Malladi
Contributors: Holly Ruess, Spencer D. Barnes, Venkat S. Malladi
Department: Bioinformatic Core Facility, Department of Bioinformatics
......@@ -13,4 +13,3 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
......@@ -108,7 +108,7 @@ workflow_parameters:
end to the other, generating the sequence of base pairs. In paired-end
reading it starts at one read, finishes this direction at the specified
read length, and then starts another round of reading from the opposite
end of the fragment.
end of the fragment. If Paired-end: True, if Single-end: False.
- id: blacklist
type: select
......
......@@ -42,7 +42,7 @@
14. **BICF ChIP-seq Analysis Workflow**:
* Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.0). Zenodo. doi:[10.5281/zenodo.3891417](https://doi.org/10.5281/zenodo.3891417)
* Holly Ruess, Spencer D. Barnes and Venkat S. Malladi. 2020. BICF ATAC-seq Analysis Workflow (publish_2.0.1). Zenodo. doi:[10.5281/zenodo.3891417](https://doi.org/10.5281/zenodo.3891417)
15. **Nextflow**:
* Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.
......
......@@ -7,7 +7,7 @@ report_header_info:
- Contact E-mail: 'bicf@utsouthwestern.edu'
- Application Type: 'ATAC-seq'
- Department: 'Bioinformatic Core Facility, Department of Bioinformatics'
- Contributors and Licensing: 'See https://zenodo.org/record/3526149#.XsPhny2ZPBI'
- Contributors and Licensing: 'See https://zenodo.org/record/3526149'
# Title to use for the report.
......
#!/usr/bin/env nextflow
// Path to an input file, or a pattern for multiple inputs
// Note - $baseDir is the location of this workflow file main.nf
/*
BICF ATAC-seq Analysis Workflow
#### Homepage / Documentation
https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/
Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/LICENSE.md)
*/
// Define Input variables
params.reads = "$baseDir/../test_data/*.fastq.gz"
......@@ -10,12 +17,6 @@ params.blacklist = false
params.designFile = "$baseDir/../test_data/design_ENCSR265ZXX_SE.txt"
params.genome = 'GRCh38'
params.genomes = []
params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false : false
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.gtfFile = params.genome ? params.genomes[ params.genome ].gtffile ?: false : false
params.blacklistFile = params.genome ? params.genomes[ params.genome ].blacklistfile ?: false : false
params.geneNames = params.genome ? params.genomes[ params.genome ].geneNames ?: false : false
params.astrocyte = false
params.outDir= "${baseDir}/output"
params.references = "${baseDir}/../docs/references.md"
......@@ -23,6 +24,34 @@ params.multiqc = "${baseDir}/conf/multiqc_config.yaml"
params.ci = false
params.dev = false
// Assign variables if astrocyte
if (params.astrocyte) {
print("Running under astrocyte")
referenceLocation = "/project/shared/bicf_workflow_ref"
if (params.genome == 'GRCh38') {
params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.gtfFile = "$referenceLocation/$params.genome/gencode.v25.chr_patch_hapl_scaff.annotation.gtf"
params.geneNames = "$referenceLocation/$params.genome/genenames.txt"
params.blacklistFile = "$referenceLocation/$params.genome/ENCFF356LFX.bed"
params.genomeSize = 'hs'
} else if (params.genome == 'GRCm38') {
params.bwaIndex = "$referenceLocation/$params.genome"
params.chromSizes = "$referenceLocation/$params.genome/genomefile.txt"
params.gtfFile = "$referenceLocation/$params.genome/gencode.vM20.annotation.gtf"
params.geneNames = "$referenceLocation/$params.genome/genenames.txt"
params.blacklistFile = "$referenceLocation/$params.genome/ENCFF999QPV.bed"
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.gtfFile = params.genome ? params.genomes[ params.genome ].gtffile ?: false : false
params.blacklistFile = params.genome ? params.genomes[ params.genome ].blacklistfile ?: false : false
params.geneNames = params.genome ? params.genomes[ params.genome ].geneNames ?: false : false
}
// Check inputs
if(params.bwaIndex) {
bwaIndex = Channel
......
......@@ -25,7 +25,7 @@ manifest {
name = 'atacseq_analysis'
description = 'BICF ATAC-seq Analysis Workflow.'
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis'
version = '2.0.0'
version = '2.0.1'
mainScript = 'main.nf'
nextflowVersion = '>=0.31.0'
}
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