diff --git a/astrocyte_package.yml b/astrocyte_package.yml index 6bc210a2bbdf06636b039605241f74f38d8a6c9e..2a9f17cca026652c788791e4069ef525a62677f7 100644 --- a/astrocyte_package.yml +++ b/astrocyte_package.yml @@ -17,7 +17,7 @@ title: 'BICF ChIP-seq Analysis Workflow' # A summary of the workflow package in plain text description: | This is a workflow package for the BioHPC/BICF ChIP-seq workflow system. - It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker MAnorm and HOMER, visualization application. + It implements a simple ChIP-seq analysis workflow using deepTools, Diffbind, ChipSeeker and MEME-ChIP, visualization application. # ----------------------------------------------------------------------------- # DOCUMENTATION @@ -76,22 +76,13 @@ workflow_modules: workflow_parameters: - - id: bams - type: files - required: true - description: | - One or more BAM alignments from a ChIP-Seq experiment and a design file with the link between the same name and the sample group. All files will be imported from GreenCenter ChIP-seq peak calling pipeline - regex: ".*(bam)*" - min: 1 - - - id: design type: file required: true regex: ".*csv" description: | A design file listing pairs of sample name and sample group. - Columns must include: SampleID,SampleName,SampleGroup,FullPathToFqR1,FullPathToFqR2 + Columns must include: SampleID,Tissue, Factor, Condition, Replicate, Peaks, bamReads, bamControl, ControlID, PeakCaller - id: genome type: select @@ -101,9 +92,13 @@ workflow_parameters: - [ '/project/shared/bicf_workflow_ref/GRCm38', 'Mouse GRCh38'] required: true description: | - Reference genome for alignment - + Reference genome for annotation + - id: toppeak + type: integer + required: true + description: | + The number of top peaks to use for motif discovery. # ----------------------------------------------------------------------------- # SHINY APP CONFIGURATION # -----------------------------------------------------------------------------