Support for topic channels
#258
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edmundmiller
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Sep 10, 2024
edmundmiller
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Nov 7, 2024
* build: Add wave * build: Set strategy to dockerfile, conda then container * refactor: Remove container * build: Add a repo to push to * ci(wave): Add wave build https://github.com/nodejs/docker-node/blob/3c4fa6daf06a4786d202f2f610351837806a0380/.github/workflows/build-test.yml#L29 * ci(wave): Switch to all_changed_files * ci(wave): Only look for envronment.ymls * dummy: Change env * ci(wave): Remove raw format * ci(wave): Try a bunch of different things at once * ci(wave): Remove redundant fromJson and wrap in an array * ci(wave): I have no idea what I'm doing * ci(wave): Wrap it * ci(wave): Found an example https://github.com/tj-actions/changed-files/blob/main/.github/workflows/matrix-test.yml * ci(wave): Maybe quotes? * ci(wave): That'll do it * ci(wave): Fix wave install * ci(wave): Hard code an image * ci(wave): Add secrets * feat: Try a different files structure * ci(wave): First stab at building singularity images * fixup! feat: Try a different files structure * ci(wave): Add profile to matrix * ci(wave): Give up on fancy substitution * ci(wave): Add await Co-authored-by: ewels <ewels@users.noreply.github.com> * ci(wave): Switch to quay * test(wave): Add freeze and update build repo * refactor(wave): What happens if I add a container? * refactor(wave): Have both bowtie modules use the same env For the sake of demonstration * test: Cut out using wave on tests * refactor: What happens if we use the singularity one? * refactor: Keep container directives for offline download seqeralabs/wave#323 * feat: Try new singularity OCI setting nextflow-io/nextflow@f5362a7 * build: Update container name Guess #4327 broke that * chore: Bump wave-cli version * ci: Install runc * ci: Switch to singularityhub action nextflow-io/nextflow#4543 * ci: Install new singularity manually Why that action trys to build from source, idk. * ci: Install dependancies for singularity * ci: runc => crun * ci: Fix cgroup error https://blog.misharov.pro/2021-05-16/systemd-github-actions * ci: That'll do it * ci: Remove Dockerfile We'll have a seperate action for this I think * ci: Update name * ci: Push to the correct repos * ci: Remove OCI stuff * ci: Need a full URL * ci: Fix // in container name * ci: Remove push Build once, renovate should bump the images automagically * build: Add containers back * ci: Add cache repos Idk what this does exactly * ci: Change registry name to use _ Because "build" is a api end point on quay.io. So `bowtie/build` doesn't work. Other plus is this matches the conda env name. * build: / => _ in container name * Try ociAutoPull * chore: Add renovate comments to samtools Just to trigger wave build * test: Add ociAutoPull to nf-test * ci: Bump wave version * chore: Bump containers with new wave version Not sure why that's happening... * build: Update to use commity.wave.seqera.io * ci: Bump wave-cli to 1.4.1 * ci: Try apptainer * ci: Remove build-repo to see what happens * build: Bump Nextflow version requirement * fix: Get rid of the environment name? Maybe this will get the auto generated tag? * ci: Bump action versions * ci: Try name-strategy tagPrefix seqeralabs/wave-cli@269df0e * ci: Remove singularity build for now * ci: Try imageSuffix * ci: Try none * ci: What is the bowtie container name * ci: Remove --name-strategy * style: Add back in container elvis operator * ci: Remove cache repo * Revert "build: Bump Nextflow version requirement" This reverts commit 69e1ea5. * Revert "test: Add ociAutoPull to nf-test" This reverts commit 5a3d546. * test(#6505): Snapshot the versions contents, not the hash * ci(#6505): Update version snapshot after building containers * test(#6505): Attempt a topic channel with tests askimed/nf-test#258 * chore: Bump to 1.5.0 * fix: Remove shard and filter on test bumping * build: Bump images to match environment * ci: Fix nf-test setup * ci: Remove snapshot bumping * build: Fix containers in bowtie --------- Co-authored-by: ewels <ewels@users.noreply.github.com>
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Wondering if we could get support for topic channels.
https://www.nextflow.io/docs/latest/channel.html#topic
Mainly for nf-core/modules
Docs: https://www.nextflow.io/docs/latest/channel.html#topic
Example in pipelines: https://github.com/nf-core/nascent/pull/150/files
nf-core/modules issues: nf-core/modules#5834 nf-core/modules#4517
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