Closed
Milestone
v0.0.1
Milestone ID: 67
Make tag with name release candidate (RC) first then test.
Unstarted Issues (open and unassigned)
0
Ongoing Issues (open and assigned)
0
Completed Issues (closed)
42
- Bash script to run entire study
- Add pytest for parseMeta unit test
- Add read length as metadata tracking
- Retighten template for fastq renaming in getData
- Add optional to change getBag source
- CI: pytest dataQC test for data in line 2+
- Move inference to start of pipeline
- Error if fastq's don't match naming convention
- inferMetadata stranded logic error
- change getRef output
- Clean singularity cache at in before_script CI
- getRef Failing
- Update design docs
- Alignment output chromosome number replaced with contig ID
- process_RSeQC
- Combine align and dedup
- Set getData unit test to fetch small file
- Harmonize log out err files
- Apply for AWS public data status for our references
- Decide on reference versioning convension
- process_getRef
- Remove nproc limiter on trim CI unit
- Add "Consistency Tests"
- New test data for paired-end and single-end
- Change ref GTF to GENCODE
- Code Review
- Make scripts input files for processes
- Add integration CI test
- Set up nextflow configs
- Add CI for Trim
- Add automated download of bagit through deriva
- Add Unit Tests for splitData and getData processes
- Output fastq's from getData process into object where if PE pairs are linked
- process_qc
- process_fastqc
- process_makeBigWig
- process_count
- process_dedup
- process_align
- process_trim
- process_createManifest
- process_getData
