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Add assembled check to samplesheet, fix report use read_rearrangement #266

Merged
merged 17 commits into from
Jul 20, 2023
Merged

Add assembled check to samplesheet, fix report use read_rearrangement #266

merged 17 commits into from
Jul 20, 2023

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ggabernet
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@ggabernet ggabernet commented Jun 20, 2023 •
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  • fix report use read_rearrangement for speed and validation reasons
  • add samplesheet check to assembled subworkflow
  • improve readme and usage docs for single cell and assembled data
  • Add sampleID to filename to keep it unique
  • Convert required columns to strings when needed
  • Add clonal report tables to final report folder

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/airrflow branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@ggabernet ggabernet changed the title Add assembled check to samplesheet, fix report use read_rearrangemnet Add assembled check to samplesheet, fix report use read_rearrangement Jun 20, 2023
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github-actions bot commented Jun 20, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 3c79415

+| ✅ 149 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
-| ❌   9 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - assets/nf-core-airrflow_logo_light.png does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • schema_params - Param genomes from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-19 20:41:57

@ggabernet
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@nf-core-bot fix linting

@ggabernet ggabernet merged commit 5d8cdb4 into nf-core:dev Jul 20, 2023
23 of 24 checks passed
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@ssnn-airr ssnn-airr ssnn-airr approved these changes

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@ggabernet @ssnn-airr @nf-core-bot