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Dp24 pretextgraph #164

Merged
merged 39 commits into from
Nov 7, 2023
Merged

Dp24 pretextgraph #164

merged 39 commits into from
Nov 7, 2023

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DLBPointon
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Pretext Ingestion!

The accessory files are now ingested into the pretext file, rather than needing the end user to ingest them independently.
coverage, log2 coverage and repeat density are ingested by default and telomere + gap are ingested if they contain > 0 bytes.

This highlighted a small bug with the new log_coverage track, which has been corrected with a round(value, 2) ensuring that there will always be a whole number for ingestion and no data is skipped.

@DLBPointon DLBPointon added bug Something isn't working enhancement New feature or request Release 1.1 Issues to be resolved for minor release 1.1 labels Oct 26, 2023
@DLBPointon DLBPointon self-assigned this Oct 26, 2023
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github-actions bot commented Oct 26, 2023 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bf90f0e

+| ✅ 126 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • 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-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_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
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-11-06 10:59:24

@DLBPointon
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Pipeline fails as it needs Pretext_hires to be emitted from hic_mapping but can't as pretext_hires needs 16GB minimum

DLBPointon and others added 12 commits October 27, 2023 13:34
@DLBPointon
Adding support for the nf-co2footprint plugin, to enable use -c co2fo…
f227e99 
…otprint.config in your nextflow command
@DLBPointon
Updating to allow for optional outputs
7886ff0
@DLBPointon
Updated workflow logic
1e2a223
@DLBPointon
Commented out PRETEXT_INGEST_HIRES due to emit limitations and resour…
5dcdca2 
…ce limits
@DLBPointon
Commenting out hires subworkflow to enable pipeline to run
45f29e5
@DLBPointon
Effects #162, removed an embaressing amount of spelling and grammar m…
dd71558 
…istakes
@DLBPointon
Closes #166, removed unnecessary version call
c6b7aab
@DLBPointon
Rename .sorted.genome to .genome
80409fa
@DLBPointon
fixing channel naming that wasnt caught in the rapid tests
05b1733
@DLBPointon
Merge branch 'dp24_pretextgraph' into dp24_better_docs
cee865a
@DLBPointon
Fixed the structure of pretext graph to allow for better github testing
9381aef
@DLBPointon
Merge pull request #167 from sanger-tol/dp24_better_docs
2b49fc0 
Dp24 better docs
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DLBPointon commented Oct 30, 2023 •
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PR is practically done.
Made up of two PR's - pretext_ingestion and better_docs.

Includes re-write of pretext-graph subworkflow from the main treeval level workflow into hic_mapping. This makes it much easier to control when and where the hires versions run.

I just need to update the pictures in the docs and done.

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This PR has grown a bit, so to summarise:

  • Multiple fixes to longreadlogcoverage
  • Adding logcoverage to pretextgraph
  • Adding pretextgraph
  • Updating and fixing docs (will become clear once added to dev)
  • Stopped exporting pre.bed
  • Start exporting another repeat coverage file for use in JBrowse2

weaglesBio
weaglesBio requested changes Nov 6, 2023
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docs/images/v1-1-0/treeval_1_1_0_generate_genome.png Show resolved Hide resolved
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@DLBPointon DLBPointon requested a review from weaglesBio November 6, 2023 10:57
weaglesBio
weaglesBio approved these changes Nov 7, 2023
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Same Fasta issue on gap_finder, insilico_digest (with Genome also) and the full diagram. This is not a blocker though.

@DLBPointon DLBPointon merged commit 82f21d8 into dev Nov 7, 2023
6 checks passed
@DLBPointon DLBPointon deleted the dp24_pretextgraph branch January 11, 2024 16:02
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@weaglesBio weaglesBio weaglesBio approved these changes

@yumisims yumisims Awaiting requested review from yumisims

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