Clean up and fix astrocyte configurations.

LICENSE

-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.

LICENSE.md

@@ -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.
-

astrocyte_pkg.yml

@@ -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

docs/references.md

@@ -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.

workflow/conf/multiqc_config.yaml

@@ -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.

workflow/main.nf

 #!/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"
@@ -23,10 +24,57 @@ 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
+}
+
+
+
+
+genomes {
+  'GRCh38' {
+
+    blacklistfile = '/project/shared/bicf_workflow_ref/GRCh38/ENCFF356LFX.bed'
+    geneNames = '/project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt'
+  }
+  'GRCm38' {
+    bwa = '/project/shared/bicf_workflow_ref/GRCm38'
+    genomesize = 'mm'
+    chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
+    gtffile = '/project/shared/bicf_workflow_ref/GRCm38/gencode.vM20.annotation.gtf'
+    blacklistfile = '/project/shared/bicf_workflow_ref/GRCm38/ENCFF999QPV.bed'
+    geneNames = '/project/shared/bicf_workflow_ref/mouse/GRCm38/genenames.txt'
+  }
+}
+
 // Check inputs
-if(params.bwaIndex) {
-  bwaIndex = Channel
-    .fromPath(params.bwaIndex)
+if(params.bwa) {
+  bwa= Channel
+    .fromPath(params.bwa\)
     .ifEmpty { exit 1, "BWA index not found: ${params.bwaIndex}" }
 } else {
   exit 1, "No reference genome specified."

workflow/nextflow.config

@@ -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'
 }