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claudeclaude
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fix(ci): resolve pre-commit failures (prettier + editorconfig)
- Fix prettier formatting in docs, .lineage JSON, and config files - Fix HTML syntax errors in assets/multiqc_report.html (stray </span> and mismatched </a> tags) - Fix editorconfig violations: odd-numbered indentation in benchmark_report_template.html, missing final newlines - Reformat assets/multiqc_report.html and seqera-echarts-theme.json https://claude.ai/code/session_017v77ubxxBd4gev1tKaV5wk
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‎.github/CONTRIBUTING.md‎

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When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
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Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
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### Lint tests
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`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.

‎.github/PULL_REQUEST_TEMPLATE.md‎

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- [ ] This comment contains a description of changes (with reason).
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- [ ] If you've fixed a bug or added code that should be tested, add tests!
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/seqeralabs/nf-aggregate/tree/master/.github/CONTRIBUTING.md)
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- [ ] Make sure your code lints (`nf-core pipelines lint`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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=======
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- [ ] # Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/seqeralabs/nf-aggregate/tree/main/.github/CONTRIBUTING.md)
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- [ ] Make sure your code lints (`nf-core pipelines lint`).
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>>>>>>> aca0dae (initial template build from nf-core/tools, version 3.2.0)
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> > > > > > > aca0dae (initial template build from nf-core/tools, version 3.2.0)
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.
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- [ ] `CHANGELOG.md` is updated.

‎.lineage/.history/32bdae48582728021befa18f6f5f8f4d‎

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2026-03-29 21:05:23 EDT sleepy_mcnulty 6c9757b1-1efe-4bbc-a0a0-2d9a9b738a23 lid://32bdae48582728021befa18f6f5f8f4d
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2026-03-29 21:05:23 EDT sleepy_mcnulty 6c9757b1-1efe-4bbc-a0a0-2d9a9b738a23 lid://32bdae48582728021befa18f6f5f8f4d

‎.lineage/.history/7c4ea73142e1bef77cfeabb28d13cc9b‎

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2026-03-29 21:11:37 EDT pensive_bardeen 26b57f83-9667-40f0-bbb6-1409d614e6e4 lid://7c4ea73142e1bef77cfeabb28d13cc9b
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2026-03-29 21:11:37 EDT pensive_bardeen 26b57f83-9667-40f0-bbb6-1409d614e6e4 lid://7c4ea73142e1bef77cfeabb28d13cc9b

‎.lineage/03590c15df07f5e6766a2433aabe008c#output/.data.json‎

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{"version":"lineage/v1beta1","kind":"TaskOutput","spec":{"taskRun":"lid://03590c15df07f5e6766a2433aabe008c","workflowRun":"lid://7c4ea73142e1bef77cfeabb28d13cc9b","createdAt":"2026-03-29T21:11:45.633453-04:00","output":[{"type":"val","name":"metaOut","value":null},{"type":"path","name":null,"value":null},{"type":"path","name":null,"value":null}],"labels":null}}
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{
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"version": "lineage/v1beta1",
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"kind": "TaskOutput",
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"spec": {
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"taskRun": "lid://03590c15df07f5e6766a2433aabe008c",
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"workflowRun": "lid://7c4ea73142e1bef77cfeabb28d13cc9b",
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"createdAt": "2026-03-29T21:11:45.633453-04:00",
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"output": [
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{ "type": "val", "name": "metaOut", "value": null },
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{ "type": "path", "name": null, "value": null },
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{ "type": "path", "name": null, "value": null }
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],
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"labels": null
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}

‎.lineage/03590c15df07f5e6766a2433aabe008c/.data.json‎

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{"version":"lineage/v1beta1","kind":"TaskRun","spec":{"sessionId":"26b57f83-9667-40f0-bbb6-1409d614e6e4","name":"SEQERALABS_NF_AGGREGATE:NF_AGGREGATE:SEQERA_RUNS_DUMP (5HieFbNIsw59ul)","codeChecksum":{"value":"87299ec551bb45956923ae6fb284a2a4","algorithm":"nextflow","mode":"standard"},"script":"\n tw \\\n \\\n \\\n \\\n --url\u003dhttps://api.cloud.seqera.io \\\n --access-token\u003deyJ0aWQiOiAxNDA5Mn0uMWMzZTUyOWQ3MDMxZGE3NTJlNDU1ODVjMDRkNGUyZTliY2UzNjVmMg\u003d\u003d \\\n runs \\\n dump \\\n -id\u003d5HieFbNIsw59ul \\\n --workspace\u003dseqeralabs/showcase \\\n --output\u003d\"5HieFbNIsw59ul.tar.gz\" \\\n --add-fusion-logs \\\n --add-task-logs 2\u003e\u00261 || if [ ! -f \"5HieFbNIsw59ul.tar.gz\" ]; then exit 1; fi\n\n mkdir -p 5HieFbNIsw59ul\n tar \\\n -xvf \\\n 5HieFbNIsw59ul.tar.gz \\\n -C 5HieFbNIsw59ul\n\n cat \u003c\u003c-END_VERSIONS \u003e versions.yml\n \"SEQERALABS_NF_AGGREGATE:NF_AGGREGATE:SEQERA_RUNS_DUMP\":\n seqera-cli: $(echo $(NO_COLOR\u003dtrue tw --version 2\u003e\u00261) | sed \u0027s/^.*Tower CLI version //; s/ *$//\u0027)\n END_VERSIONS\n ","input":[{"type":"val","name":"meta","value":{"id":"5HieFbNIsw59ul","workspace":"seqeralabs/showcase","group":[],"logs":[],"fusion":[]}},{"type":"val","name":"api_endpoint","value":"https://api.cloud.seqera.io"},{"type":"val","name":"java_truststore_path","value":""},{"type":"val","name":"java_truststore_password","value":""}],"container":"community.wave.seqera.io/library/tower-cli:0.11.2--0f5ebc1e8a308611","conda":null,"spack":null,"architecture":null,"globalVars":{"task.ext.args":"","TOWER_ACCESS_TOKEN":"eyJ0aWQiOiAxNDA5Mn0uMWMzZTUyOWQ3MDMxZGE3NTJlNDU1ODVjMDRkNGUyZTliY2UzNjVmMg\u003d\u003d","task.ext.args2":"--add-task-logs","task.ext.prefix":null},"binEntries":[],"workflowRun":"lid://7c4ea73142e1bef77cfeabb28d13cc9b"}}
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{
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"version": "lineage/v1beta1",
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"kind": "TaskRun",
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"spec": {
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"sessionId": "26b57f83-9667-40f0-bbb6-1409d614e6e4",
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"name": "SEQERALABS_NF_AGGREGATE:NF_AGGREGATE:SEQERA_RUNS_DUMP (5HieFbNIsw59ul)",
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"codeChecksum": { "value": "87299ec551bb45956923ae6fb284a2a4", "algorithm": "nextflow", "mode": "standard" },
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"script": "\n tw \\\n \\\n \\\n \\\n --url\u003dhttps://api.cloud.seqera.io \\\n --access-token\u003deyJ0aWQiOiAxNDA5Mn0uMWMzZTUyOWQ3MDMxZGE3NTJlNDU1ODVjMDRkNGUyZTliY2UzNjVmMg\u003d\u003d \\\n runs \\\n dump \\\n -id\u003d5HieFbNIsw59ul \\\n --workspace\u003dseqeralabs/showcase \\\n --output\u003d\"5HieFbNIsw59ul.tar.gz\" \\\n --add-fusion-logs \\\n --add-task-logs 2\u003e\u00261 || if [ ! -f \"5HieFbNIsw59ul.tar.gz\" ]; then exit 1; fi\n\n mkdir -p 5HieFbNIsw59ul\n tar \\\n -xvf \\\n 5HieFbNIsw59ul.tar.gz \\\n -C 5HieFbNIsw59ul\n\n cat \u003c\u003c-END_VERSIONS \u003e versions.yml\n \"SEQERALABS_NF_AGGREGATE:NF_AGGREGATE:SEQERA_RUNS_DUMP\":\n seqera-cli: $(echo $(NO_COLOR\u003dtrue tw --version 2\u003e\u00261) | sed \u0027s/^.*Tower CLI version //; s/ *$//\u0027)\n END_VERSIONS\n ",
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"input": [
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{
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"type": "val",
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"name": "meta",
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"value": {
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"id": "5HieFbNIsw59ul",
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"workspace": "seqeralabs/showcase",
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"group": [],
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"logs": [],
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"fusion": []
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}
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},
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{ "type": "val", "name": "api_endpoint", "value": "https://api.cloud.seqera.io" },
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{ "type": "val", "name": "java_truststore_path", "value": "" },
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{ "type": "val", "name": "java_truststore_password", "value": "" }
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],
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"container": "community.wave.seqera.io/library/tower-cli:0.11.2--0f5ebc1e8a308611",
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"conda": null,
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"spack": null,
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"architecture": null,
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"globalVars": {
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"task.ext.args": "",
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"TOWER_ACCESS_TOKEN": "eyJ0aWQiOiAxNDA5Mn0uMWMzZTUyOWQ3MDMxZGE3NTJlNDU1ODVjMDRkNGUyZTliY2UzNjVmMg\u003d\u003d",
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"task.ext.args2": "--add-task-logs",
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"task.ext.prefix": null
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},
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"binEntries": [],
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"workflowRun": "lid://7c4ea73142e1bef77cfeabb28d13cc9b"
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}
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}

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