Closed
Milestone
expired on Mar 20, 2020
v0.1.0 release
Name for workflow found; workflow functional on various Linux machines; MultiQC finish rule and all other Snakemake rules planned to include as of 2020-Feb-16 added; integration test for entire workflow; all known bugs resolved; open discussions around workflow wiring resolved; description of all tools and workflow parameters added; dev branch added and protected (master branch only to be used for pushing releases); version tag added
Unstarted Issues (open and unassigned)
0
Ongoing Issues (open and assigned)
0
Completed Issues (closed)
30
- Bedtools not found while testing master branch
- Correct cutadapt parameters for polyA/T tail trimming
- Issue with trimming adapter log file
- Change project name
- Update cluster configuration
- Replace cufflinks image with gffread image
- Typos
- Minor typo in log file for single-end kallisto
- Separate STDOUT & STDERR streams in Snakemake rules
- Test snakemake rules individually
- Create new default branch
- Create log directories in Snakefile
- Pipeline crashes on OS X
- Make test output more verbose
- Minify Docker images
- Pulling of Singularity containers times out
- Add rule to create transcriptome from genome and gene annotations
- Add project version and release tag
- Document workflow parameters
- Name the pipeline
- Write documentation for pipeline rules
- snakemake conda env cannot be created from environment.yml
- Singularity image pull kallisto:0.46.1 does not work on macOS 10.14.6
- Add rules for generating gene expression & count tables
- Transcripts to consider for analysis
- Add rule to generate normalized coverage tracks
- Add rule for TIN score calculation
- Preprocessing remove polyAs from reads
- Add final rule for multiqc
- Add rule for ALFA
Loading
Loading
Loading