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Implement Neo subworkflow #8

Merged
merged 23 commits into from
May 30, 2024
Merged

Implement Neo subworkflow #8

merged 23 commits into from
May 30, 2024

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scwatts
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@scwatts scwatts commented Mar 12, 2024

I've now rebased this subworkflow on the alignment-subworkflow branch since that will be merged soon and includes important changes across the pipeline. (The base branch is also set as alignment-subworkflow to give us a clearer commit history below.)

@scwatts scwatts added this to the Release 1.0.0 milestone Mar 12, 2024
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github-actions bot commented Mar 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f1a365f

+| ✅ 182 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  14 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-30 00:07:15

@scwatts
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scwatts commented Mar 16, 2024

Force pushing after rebase on top of alignment-subworkflow

Base automatically changed from alignment-subworkflow to dev April 24, 2024 01:28
@scwatts
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scwatts commented May 17, 2024

Descoping from the 1.0.0 release.

/cc @charlesshale

@scwatts scwatts removed this from the Release 1.0.0 milestone May 17, 2024
@scwatts scwatts changed the base branch from dev to features-block-one-preview May 29, 2024 04:35
@scwatts scwatts force-pushed the features-block-one-preview branch from 50d77a2 to 02fb0de Compare May 29, 2024 04:46
scwatts and others added 21 commits May 30, 2024 09:01
@scwatts
Frame out Neo subworkflow
9898841
@charlesshale @scwatts
First cut of Neoepitope subworkflow
70ccdad
@scwatts
Get stub runs working
e9a04b3
@scwatts
Clean up
98ffac0
@scwatts
Get local run working on sample data
8b6df01
@scwatts
Set Neo to run only when specified
45226f3
@scwatts
Fix Neo stubs
37d18d5
@scwatts
Provide Neo cancer type from samplesheet
ea1fc26
@scwatts
Fix Neo scorer RNA sample ID and VCF input
cb94b8b
@scwatts
Minor fixes
0f4cdda
@scwatts
Update to latest Neo 1.2_beta build artefact
480dffb
@scwatts
Update Neo reference data paths
efa42fb
@scwatts
Move neo_prediction.nf subworkflow for consistency
ff6330b
@scwatts
Adjust Neo to fit with alignment subworkflow
2b01ded 
* add source selection for RNA BAM (samplesheet, alignment subworkflow)
* use appropriate function call to determine present of RNA
* relocate isofox_read_length assignment (wgts and targeted workflows)
@scwatts
Adjust indenting
92d95ad
@scwatts
Indent Neo subworkflow to match nf-core style
c861d50
@scwatts
Use Bioconda for Neo annotate fusion process
0fde563
@scwatts
Add environment file for annotate fusion process
c367898
@scwatts
Rename some Neo subworkflow variables for clarity
f3be064
@scwatts
Add meta.yml for annotate fusion process
d997b37
@scwatts
Add meta.yml for Neo finder process
f46eacf
@scwatts scwatts force-pushed the features-block-one-preview branch from 02fb0de to f86b1d9 Compare May 29, 2024 23:50
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scwatts commented May 29, 2024

Rolling this feature in with feature block one - I've rebased changes on top of features-block-one-preview and integrated as needed, now force pushing.

@scwatts scwatts force-pushed the neo-subworkflow branch from b978910 to 3cd29a9 Compare May 29, 2024 23:54
@scwatts scwatts requested a review from charlesshale May 29, 2024 23:54
@scwatts scwatts marked this pull request as ready for review May 29, 2024 23:54
@scwatts scwatts merged commit a34b7b4 into features-block-one-preview May 30, 2024
4 checks passed
@scwatts scwatts deleted the neo-subworkflow branch May 30, 2024 00:11
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@charlesshale charlesshale charlesshale approved these changes

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@scwatts @charlesshale