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feat(wave): adding profile seqera_containers #1291

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feat(wave): adding profile seqera_containers #1291

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b78b8e3
feat(wave): adding profile wave
maxulysse Apr 30, 2024
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sort
maxulysse Apr 30, 2024
4293c6d
Update nextflow.config
maxulysse Apr 30, 2024
acf329a
update CHANGELOG
maxulysse Apr 30, 2024
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Merge branch 'dev' into profile_wave
maxulysse May 6, 2024
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Apply suggestions from code review
drpatelh May 13, 2024
d7b0037
Update CHANGELOG.md
drpatelh May 13, 2024
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drpatelh May 13, 2024
7275ce3
Merge branch 'dev' into profile_wave
drpatelh May 13, 2024
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Update usage.md
drpatelh May 13, 2024
c27b63f
Update nextflow.config
drpatelh May 13, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -67,6 +67,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1278](https://github.com/nf-core/rnaseq/pull/1278) - Delocalise pseudo quant workflow
- [PR #1280](https://github.com/nf-core/rnaseq/pull/1280) - Reorganise pipeline level tests into flat directory structure
- [PR #1283](https://github.com/nf-core/rnaseq/pull/1283) - Add output files to nf-test snapshot
- [PR #1291](https://github.com/nf-core/rnaseq/pull/1291) - Add `seqera_containers` profile
- [PR #1293](https://github.com/nf-core/rnaseq/pull/1293) - Update subworkflow utils_nfcore_pipeline
- [PR #1297](https://github.com/nf-core/rnaseq/pull/1297) - Important! Template update for nf-core/tools v2.14.1

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4 changes: 2 additions & 2 deletions docs/usage.md
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Expand Up @@ -314,8 +314,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
- `apptainer`
- A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
- `wave`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
- `seqera_containers`
- A generic configuration profile to enable [Wave](https://seqera.io/wave/) to build and pull from the Seqera public containers repository. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
- `conda`
- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.

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7 changes: 7 additions & 0 deletions nextflow.config
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Expand Up @@ -256,6 +256,13 @@ profiles {
wave.freeze = true
wave.strategy = 'conda,container'
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}
seqera_containers {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
Comment on lines +260 to +261
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This should be removed otherwise it will cause the use of a docker container to be converted to singularity one ..

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also worth adding wave.build.conda.mambaImage = 'mambaorg/micromamba:1.5.8-lunar' to prevent containers changes quietly when the base image will change on wave side

wave.enabled = true
wave.freeze = true
wave.strategy = 'conda'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
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