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Update hic mapping #17

Merged
merged 13 commits into from
Oct 3, 2023
Merged

Update hic mapping #17

merged 13 commits into from
Oct 3, 2023

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ksenia-krasheninnikova
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HiC mapping from

https://github.com/sanger-tol/treeval/blob/80554a803903183613d49690d5770eeadb3c42c9/subworkflows/local/hic_mapping.nf

was transferred to the main pipeline.

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 sanger-tol/genomeassembly 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).

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github-actions bot commented Jun 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 839c2a5

+| ✅ 131 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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
  • pipeline_todos - TODO string in genomeassembly.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • system_exit - System.exit in WorkflowSanger-tol-genomeassembly.groovy: System.exit(1) [line 51]
  • schema_description - No description provided in schema for parameter: timestamp
  • schema_description - No description provided in schema for parameter: hifiasm
  • schema_description - No description provided in schema for parameter: hifiasmhic

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-10-03 14:38:59

priyanka-surana
priyanka-surana reviewed Jul 18, 2023
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I want to test this after we have a clean template merge. Then happy to approve.

subworkflows/local/hic_mapping.nf Outdated
Comment on lines 60 to 66
file(cram_info[0]),
cram_info[1],
cram_info[2],
cram_info[3],
cram_info[4],
cram_info[5],
cram_info[6],
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Can you add comments to describe what each of these fields actually contains?

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Done.

priyanka-surana
priyanka-surana approved these changes Oct 3, 2023
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LGTM 👍🏼 The following test worked for me:

nextflow run . -ansi-log false -profile test,singularity,longranger_lsf_sanger --outdir results

@priyanka-surana priyanka-surana merged commit e9d81e2 into dev Oct 3, 2023
4 of 6 checks passed
@priyanka-surana priyanka-surana deleted the update_hic_mapping branch October 3, 2023 15:37
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@priyanka-surana priyanka-surana priyanka-surana approved these changes

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2 participants
@ksenia-krasheninnikova @priyanka-surana