Code

CI: add gpu tag test job#478

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sateeshperi merged 82 commits intofasta-align-dedup-bwamethnf-core/methylseq:fasta-align-dedup-bwamethfrom ci-gpu-testsnf-core/methylseq:ci-gpu-testsCopy head branch name to clipboardDec 12, 2024

+1,328-343

Commits

Commits on Dec 2, 2024

• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• CI: add gpu tag test job

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• add bwameth_gpu test

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• add gpu profile to config

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• add bwameth gpu test + snap

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• update bwameth default test formatting

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• update bwameth use_gpu test with index name

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• minor formatting fix

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• add fq2bammeth config + test + snap, ci: nf-test job filter by tag cpu

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• ci: nf-test job filter by tag cpu

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• add cpu/gpu tags to tests

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• touch cpu and gpu test for debug

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• add bwameth run_qualimap test

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• add setup python step

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Commits on Dec 3, 2024

• restrict num shards for cpu/gpu to 2

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• add nf-test-shard and nf-test actions

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• add ci triggers

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• lint: ignore ci.yml

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• update nf-test-shard action

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• update nf-test-shard action

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• add tags input for nf-test action

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• Update .github/actions/nf-test-shard/action.yml

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• install pdiff

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• nf-test-shard output checkout

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• nf-test-shard output checkout

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• fix job outputs

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• fix job outputs

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• fix nf-test-shard action

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• fix nf-test-shard action

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• fix nf-test-shard action

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• fix nf-test-shard action

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• get-shards matrix json parse

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• get-shards matrix json parse

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• get-shards matrix json parse

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• fix sharding

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• Now filtering nf-test dry-run by --tag, picking up Executed instead of related and capped shards with max_shards

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• Fixed gpu typo, removed docker_self_hosted and bumped default resources

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• Reduced resources

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Commits on Dec 4, 2024

• add back docker_self_hosted profile + remove disk cleanup step

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• test latest-everything also for cpu tests

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• update bwameth cpu tests snaps

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Commits on Dec 5, 2024

• update bwameth gpu test snap

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• setup-nextflow use v2.0.0

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• Update .github/workflows/linting.yml

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• Update .github/workflows/linting.yml

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• going back to uriginal setup-nextflow version

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• try v2.1.1

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• try 2.1.2

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• try 2.1.3

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• reset to broader v2 now that it is working again

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• try again 2.1.3 explicitly

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• try 2.1.4

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• and now reset back to v2

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• increase max_shards to 15

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Commits on Dec 9, 2024

• Corrected test labels, GPU tests with latest-everything, corrected env vars and excluded cancelled from confirm-pass

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• Disabled latest-everything for now

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• Bumped nxf min version to 24.10.2

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• update qualimap paths in nftignore

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Commits on Dec 10, 2024

• remove test folder contents only

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• use ubuntu-latest as default runner

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• use ubuntu-latest as default runner

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• use ubuntu-latest as default runner

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• use ubuntu-latest as default runner

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• add latest-everything to matrix

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• correct NXF VER for nf-test

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• rm latest-everything from matrix

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Commits on Dec 11, 2024

• use gpu profile in tests config

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• update test gpu configs

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Commits on Dec 12, 2024

• use gpu+docker/singularity profile for nf-test

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• use gpu,docker/singularity profile for nf-test

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• use gpu,docker/singularity profile for nf-test

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• update changelog

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