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# Release checklist | ||
This checklist is for our own reference | ||
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1. Check that everything is up to date and ready to go | ||
- Travis tests are passing | ||
- Manual tests on Bianca are passing | ||
2. Increase version numbers | ||
3. Update version numbers in code: `configuration/base.config` | ||
4. Build, and get the containers. | ||
- `./scripts/do_all.sh --push --tag <VERSION>` | ||
- `./scripts/do_all.sh --pull --tag <VERSION>` | ||
5. Test against sample data. | ||
- Check for any command line errors | ||
- Check version numbers are printed correctly | ||
- `./scripts/test.sh -p docker --tag <VERSION>` | ||
- `./scripts/test.sh -p singularity --tag <VERSION>` | ||
- `./scripts/test.sh -p singularityPath --tag <VERSION>` | ||
6. Commit and push version updates | ||
7. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub | ||
8. Choose an appropriate codename for the release | ||
9. Update [bio.tools](https://bio.tools/Sarek) with the new release | ||
10. Tweet that new version is released | ||
11. Commit and push. Continue making more awesome :metal: | ||
12. Have fika :cake: | ||
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> This checklist is for our own reference, to help us prepare a new release | ||
1. Check that everything is ready to go | ||
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- [PRs](https://github.com/SciLifeLab/Sarek/pulls) are merged | ||
- [Travis tests](https://travis-ci.org/SciLifeLab/Sarek/branches) are passing on `dev` | ||
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2. Increase version number following [semantic versioning](http://semver.org/spec/v2.0.0.html) | ||
3. Choose an appropriate codename for the release | ||
- i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography) | ||
4. Build docker containers. | ||
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- `./scripts/do_all.sh --tag <VERSION>` | ||
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5. Test against sample data. | ||
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- `./scripts/test.sh -p docker --tag <VERSION>` | ||
- Check for any command line errors | ||
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6. Use script to update version in files: | ||
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- `./scripts/do_release.sh -r "<VERSION>" -c "<CODENAME>"` | ||
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7. Push latest updates | ||
8. Make a PR against `dev` | ||
9. Merge said PR | ||
10. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub | ||
11. Update [bio.tools](https://bio.tools/Sarek) with the new release details | ||
12. Tweet that a new version is released | ||
13. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version | ||
14. Commit and push. Continue making more awesome :metal: | ||
15. Have fika :cake: |
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# Parameters | ||
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A list of all possible parameter that can be used for the different scripts included in Sarek. | ||
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## Common for all scripts | ||
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### --help | ||
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Display help | ||
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### --noReports | ||
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Disable all QC tools and MultiQC. | ||
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### --outDir | ||
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Choose an output directory | ||
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### --project `ProjectID` | ||
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Specify a project number ID on a UPPMAX cluster. | ||
(optional if not on such a cluster) | ||
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### --sample `file.tsv` | ||
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Use the given TSV file as sample (cf [TSV documentation](TSV.md)). | ||
Is not used for `annotate.nf` and `runMultiQC.nf`. | ||
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### --tools `tool1[,tool2,tool3...]` | ||
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Choose which tools will be used in the workflow. | ||
Different tools to be separated by commas. | ||
Possible values are: | ||
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- haplotypecaller (use `HaplotypeCaller` for VC) (germlineVC.nf) | ||
- manta (use `Manta` for SV) (germlineVC.nf,somaticVC.nf) | ||
- strelka (use `Strelka` for VC) (germlineVC.nf,somaticVC.nf) | ||
- ascat (use `ASCAT` for CNV) (somaticVC.nf) | ||
- mutect2 (use `MuTect2` for VC) (somaticVC.nf) | ||
- snpeff (use `snpEff` for Annotation) (annotate.nf) | ||
- vep (use `VEP` for Annotation) (annotate.nf) | ||
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`--tools` option is case insensitive to avoid easy introduction of errors when choosing tools. | ||
So you can write `--tools mutect2,ascat` or `--tools MuTect2,ASCAT` without worrying about case sensitivity. | ||
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### --verbose | ||
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Display more information about files being processed. | ||
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## Preprocessing script (`main.nf`) | ||
### --step `step` | ||
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Choose from wich step the workflow will start. | ||
Choose only one step. | ||
Possible values are: | ||
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- mapping (default, will start workflow with FASTQ files) | ||
- recalibrate (will start workflow with BAM files and Recalibration Tables | ||
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`--step` option is case insensitive to avoid easy introduction of errors when choosing a step. | ||
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### --test | ||
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Test run Sarek on a smaller dataset, that way you don't have to specify `--sample Sarek-data/testdata/tsv/tiny.tsv` | ||
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### --onlyQC | ||
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Run only QC tools and MultiQC to generate a HTML report. | ||
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## Annotate script (`annotate.nf`) | ||
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### --annotateTools `tool1[,tool2,tool3...]` | ||
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Choose which tools to annotate. | ||
Different tools to be separated by commas. | ||
Possible values are: | ||
- haplotypecaller (Annotate `HaplotypeCaller` output) | ||
- manta (Annotate `Manta` output) | ||
- mutect2 (Annotate `MuTect2` output) | ||
- strelka (Annotate `Strelka` output) | ||
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### --annotateVCF `file1[,file2,file3...]` | ||
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Choose vcf to annotate. | ||
Different vcfs to be separated by commas. | ||
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## MultiQC script (`runMultiQC.nf`) | ||
### --callName `Name` | ||
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Specify a name for MultiQC report (optional) | ||
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### --contactMail `email` | ||
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Specify an email for MultiQC report (optional) | ||
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## References | ||
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For most use cases, the reference information is already in the configuration file [`conf/genomes.config`](https://github.com/SciLifeLab/Sarek/blob/master/conf/genomes.config). | ||
However, if needed, you can specify any reference file at the command line. | ||
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### --acLoci `acLoci file` | ||
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### --bwaIndex `bwaIndex file` | ||
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### --cosmic `cosmic file` | ||
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### --cosmicIndex `cosmicIndex file` | ||
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### --dbsnp `dbsnp file` | ||
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### --dbsnpIndex `dbsnpIndex file` | ||
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### --genomeDict `genomeDict file` | ||
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### --genomeFile `genomeFile file` | ||
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### --genomeIndex `genomeIndex file` | ||
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### --intervals `intervals file` | ||
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### --knownIndels `knownIndels file` | ||
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### --knownIndelsIndex `knownIndelsIndex file` | ||
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### --snpeffDb `snpeffDb file` | ||
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## Hardware Parameters | ||
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For most use cases, the reference information is already in the appropriate [configuration files](https://github.com/SciLifeLab/Sarek/blob/master/conf/). | ||
However, it is still possible to specify these parameters at the command line as well. | ||
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### --runTime `time` | ||
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### --singleCPUMem `memory` | ||
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### --totalMemory `memory` |
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# RELEASE | ||
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> This document is for helping Sarek core developers and anyone joining the team to prepare a new release | ||
## [CHECKLIST](https://github.com/SciLifeLab/Sarek/blob/master/.github/RELEASE_CHECKLIST.md) | ||
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This checklist is for our own reference, to help us prepare a new release. | ||
Just follow it and be sure to check every item on the list. | ||
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## [Helper script](https://github.com/SciLifeLab/Sarek/blob/master/scripts/do_release.sh) | ||
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This script will update the version number in the following files: | ||
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- [CHANGELOG.md](https://github.com/SciLifeLab/Sarek/blob/master/CHANGELOG.md) | ||
- Will change Unreleased to correct version number and add codename and date | ||
- [Dockerfile](https://github.com/SciLifeLab/Sarek/blob/master/Dockerfile) | ||
- Will update to correct version number | ||
- [Singularity](https://github.com/SciLifeLab/Sarek/blob/master/Singularity) | ||
- Will update to correct version number | ||
- [conf/base.config](https://github.com/SciLifeLab/Sarek/blob/master/conf/base.config) | ||
- Will update to correct version number | ||
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### Usage | ||
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### Usage | ||
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```bash | ||
./scripts/do_release.sh -r "<RELEASE>" -c "<CODENAME>" | ||
``` | ||
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- `-r|--release` specify the new version number | ||
- `-c|--codename` specify the codename | ||
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### Example | ||
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```bash | ||
./scripts/do_release.sh -r "2.2.0" -c "Skårki" | ||
``` |
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