chipathlon issueshttps://git.unl.edu/hcc/chipathlon/-/issues2018-09-13T18:09:40-05:00https://git.unl.edu/hcc/chipathlon/-/issues/16Config parsing & validation2018-09-13T18:09:40-05:00aknecht2Config parsing & validationCurrently there is no validation being done on config files despite their being an expected format.Currently there is no validation being done on config files despite their being an expected format.Input Parsingaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/issues/14Create generator script2018-09-13T18:09:40-05:00Natasha PavlovikjCreate generator scriptInstead of using generator.py and have the parameters encoded, create a generator script where we can pass the parameters as options.Instead of using generator.py and have the parameters encoded, create a generator script where we can pass the parameters as options.Input Parsingaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/issues/13Job Param File Adjustments2018-09-13T18:09:40-05:00aknecht2Job Param File Adjustments* Don't require all jobs to be specified in param file
* Remove gene_annot argument from peakranger
* Include default read distribution / ccat config files* Don't require all jobs to be specified in param file
* Remove gene_annot argument from peakranger
* Include default read distribution / ccat config filesInput Parsingaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/issues/12Enhance Input Run Format / Parsing2017-02-03T02:10:15-06:00aknecht2Enhance Input Run Format / ParsingSeveral things here:
* Genome should have species in addition to assembly
* control / signal files should be specified as lists
* idr specification should be granular i.e. which signal / control files to run for idr
* peak calling type =...Several things here:
* Genome should have species in addition to assembly
* control / signal files should be specified as lists
* idr specification should be granular i.e. which signal / control files to run for idr
* peak calling type == broad / narrow, validate against peak method as wellInput Parsingaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/issues/11Run File Helper Script2017-04-05T10:51:41-05:00aknecht2Run File Helper ScriptCreate a tool for user to make it easier to create input run file.Create a tool for user to make it easier to create input run file.Input Parsingaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/issues/5Add download support for bam files2017-02-03T13:50:12-06:00aknecht2Add download support for bam filesWorkflow should be able to start by downloading fastq files OR bam files.Workflow should be able to start by downloading fastq files OR bam files.Input Parsingaknecht2aknecht2https://git.unl.edu/hcc/chipathlon/-/issues/4Enhance type strictness and parsing2017-02-13T15:16:20-06:00aknecht2Enhance type strictness and parsingCurrently workflow module / workflow jobs don't have strict file type definitions / the file types are interpreted by the argument names.
Specfically arguments have type=file instead of something like type=fastq.Currently workflow module / workflow jobs don't have strict file type definitions / the file types are interpreted by the argument names.
Specfically arguments have type=file instead of something like type=fastq.Input Parsingaknecht2aknecht2