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Feat/clin 2947 add exomiser #25
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assets/schema_input.json
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"errorMessage": "Filename of the pedigree file, mandatory for exomiser", | ||
"meta": ["familypheno"], | ||
"format": "file-path", | ||
"pattern": "^\\S*.y(a)?ml$", |
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on acceptait les json aussi?
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Ah oui c'est vrai bon point. Will do.
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Done
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Also included a pattern for the analysis files in the parameters schema.
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@@ -140,11 +95,10 @@ The documentation of the various tools used in this workflow are available here: | |||
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Remove last parenthesis + update link
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Done
docs/reference_data.md
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- 1000G reference file : 1000G_phase1.snps.high_confidence.hg38.vcf.gz | ||
- SNP database : Homo_sapiens_assembly38.dbsnp138.vcf.gz | ||
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## Reference Genome |
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I think we can put this part in first before VQSR no?
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Sure, good point
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Done
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This commit introduces the exomiser tool in the pipeline. Additionally, it introduces a new parameter called `tools`, which allows users to specify whether VEP, Exomiser, or both should be executed. Other changes: - Group vep output files (i.e. vcf + .tbi files) in subfolder `vep`. - Improve documentation (README, OUTPUT, USAGE, REFERENCE_DATA). - Refactor postprocessing workflow to use `def` for local variables and standardize variable names. - Update GitHub CI nf-test command: remove local tag constraint and activate CI mode. - Replace workflow diagram in README.
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This PR introduce the exomiser tool in the pipeline. Additionally, it introduces a new parameter called
tools
, which allows users to specify whether VEP, Exomiser, or both should be executed.Additionally, there is some refactoring in the main workflow (
postprocessing.nf
) to use thedef
keyword and more standard variable names. I could not do it only for exomiser variables as, strangely, the code was not compiling when a channel with local scope was derived from a channel with non-local scope.Here is the associated JIRA for exomiser:
https://ferlab-crsj.atlassian.net/browse/CLIN-2947
Limitations
For the schema, if-else blocks are used to conditionally require exomiser/vep parameters based on the value of the
tools
parameter.If an exomiser or vep parameter is removed/added/modified, the logic in the if-else block will need to be manually updated. For example, if the removed parameter was required, it must be manually removed from the list of required parameters.
Tests
Running the pipeline:
Note: the V3 dataset covers REMM and CADD data sources and produces non empty exomiser files.
Linter:
Test the schema:
Check that the nf-core schema build commands still works and does not break the added if-else blocks.
nf-core schema lint
nf-core schema docs
nf-core schema validate . data-test/paramsJuno.json
nf-core schema build
Test exomiser/vep parameter validation (stub mode)
Extra tests with CADD/REMM
Validate json format is supported for analysis files and familyPheno files:
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).