Comments (4)
The workflow.png diagram is also now outdated, as workflow structure has changed along with changes to inferring strandness, handling annotation, etc.
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@lcolladotor I was unsure how to handle the "Version Description" section at the bottom of the README. Specifically, we have not been updating GitHub version/release for SPEAQeasy since the work from Winter Genomics: is this something we should start doing and include in the README, or should this section be removed? Also, is the list of tested operating systems still appropriate for the README, or should it be moved to the docs (or removed)?
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I guess that the actual commit (the SHA id) is the "version number" for SPEAQeasy right now. So you can remove the version number that the WG team was using.
GitHub allows having "releases", so we could do that too at some point. Actually, I see that that's exactly what the WG team had been using at https://github.com/LieberInstitute/SPEAQeasy/releases. So hm... maybe we can bump it to 1.0.0
whenever we are ready for the pre-print release.
Anyway, is there a way to include the GitHub SHA on the log files created by Nextflow? That would be useful for debugging whenever a user asks a question. Maybe using https://stackoverflow.com/questions/1161869/how-to-get-sha-of-the-latest-commit-from-remote-git-repository.
As for the OS section, you can remove that now.
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For now, I've added the commit SHA in the main output from nextflow as you suggested (this commit)
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Related Issues (20)
- [JHPCE] repeated fastqc failure on trimmed paired data HOT 15
- Guide for all setups that are atypical in some way
- Develop a 1 day (max 2) workshop
- Videos documenting how to install and run SPEAQeasy + describing outputs
- Translate course and intro documentation to Spanish
- Add support for MultiQC and maybe other tools
- Add QC metrics generated by Monorail / recount3
- Adapt code to DSL2
- Create a contribution guidelines documentation
- improve storage usage, minimize duplication of FASTQ data HOT 2
- transcript quantification (Salmon/Kallisto) should use trimmed reads HOT 1
- Add support for running SPEAQeasy with one sample
- allow starting the workflow with existing read alignments (sorted BAM/CRAM files) HOT 3
- InferStrandness failure, --force_strand not supported HOT 3
- Construct `rse_tx` for rat HOT 5
- `BuildAnnotationObjects` halts with current version of R
- Add support for more executors
- Improve or clarify what's supported for custom annotation
- PullTranscriptFasta failing HOT 1
- BuildAnnotationObjects fails HOT 19
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