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Fix chr name errors #102

Merged
merged 15 commits into from
Jul 16, 2024
Merged

Fix chr name errors #102

merged 15 commits into from
Jul 16, 2024

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LouisLeNezet
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Compute chr list from whole vcf and not from their head (as #<contig=> might be absent)

  • 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/phaseimpute 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@LouisLeNezet LouisLeNezet self-assigned this Jul 12, 2024
@LouisLeNezet LouisLeNezet added bug Something isn't working enhancement New feature or request labels Jul 12, 2024
@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Jul 12, 2024
@LouisLeNezet LouisLeNezet linked an issue Jul 12, 2024 that may be closed by this pull request
chr check does not work on dog datasets #98
Closed
@LouisLeNezet
Update all nf-core modules (nf-core#100)
b1cb2d3 
* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>
@LouisLeNezet LouisLeNezet mentioned this pull request Jul 12, 2024
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@LouisLeNezet LouisLeNezet requested a review from atrigila July 12, 2024 20:17
@atrigila
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Could you also add the dog dataset to the CI? Thanks!

@LouisLeNezet
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I've tested the dog dataset but the fasta seems a bit strange.
I'll reupload it to make it work.

atrigila
atrigila approved these changes Jul 14, 2024
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Great job, overall looks good to me, just some minor comments and after the addition of the dog CI test is good to go.

@atrigila atrigila mentioned this pull request Jul 14, 2024
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atrigila
atrigila approved these changes Jul 16, 2024
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I appreciate the effort you put into fixing the error related to the megatest and organizing the test data. This PR fixes how chromosomes comparisons are done. The dog data still does not move forward the whole pipeline, but this can be addressed in a future PR.

@LouisLeNezet LouisLeNezet merged commit a05575c into nf-core:dev Jul 16, 2024
8 checks passed
LouisLeNezet added a commit to LouisLeNezet/phaseimpute that referenced this pull request Jul 16, 2024
@LouisLeNezet @atrigila
Fix chr name errors (nf-core#102)
b452dbe 
* Compute chr list from vcf not from whole file

* Update all nf-core modules (nf-core#100)

* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Update getFileExtension

* Fix checkFileIndex

* Set ch_regions as intersect of contigs, add test and documentation

* Add more comment

* Add test for checkFileIndex

* remove unused subworkflow (nf-core#105)

* Update data tests sets

* Update Quilt sbwf, fix checkFileIndex, update snapshot

* Update snapshot and function test

* Add dog test

* Update subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/function.nf.test

Co-authored-by: Anabella Trigila <[email protected]>

* Add more test to vcf_chr_rename

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>
LouisLeNezet added a commit that referenced this pull request Jul 16, 2024
@LouisLeNezet @atrigila
Update glimpse2_phase gunzip & multiqc (#103)
fa4f103 
* Update glimpse2 phase to nf-core

* Update gunzip

* Update multiqc

* Update changelog

* remove unused subworkflow (#105)

* Fix chr name errors (#102)

* Compute chr list from vcf not from whole file

* Update all nf-core modules (#100)

* Update Bcftools annotate

* Update Bcftools concat

* Update Bcftools convert

* Update Bcftools index

* Update Bcftools norm

* Update bcftools pluginsplit

* Remove unused bcftools query

* Update bcftools view

* Update dumpsoftwareversions

* Update Gawk

* Update glimpse2 chunk

* Update glimpse2 concordance

* Update glimpse2 ligate splitreference

* Update glimpse2 phase

* Update Gunzip

* Update multiqc

* Update samtools faidx

* Update samtools merge

* Update samtools index

* Update samtools reheader

* Update samtools view

* Update modules.json

* Patch samtools view

* Update bcftools

* Patch bcftools concat

* Fix getfilesextension for null file, add debug and fix variable

* Update gawk

* Fix samtools index

* Update changelog

* Remove uncessary process

* Fix chunking

* Update snapshot

* Update snapshot

* Update snapshot

* Update checkFileIndex function to collect the file before checking

---------

Co-authored-by: LouisLeNezet <[email protected]>

* Update getFileExtension

* Fix checkFileIndex

* Set ch_regions as intersect of contigs, add test and documentation

* Add more comment

* Add test for checkFileIndex

* remove unused subworkflow (#105)

* Update data tests sets

* Update Quilt sbwf, fix checkFileIndex, update snapshot

* Update snapshot and function test

* Add dog test

* Update subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/function.nf.test

Co-authored-by: Anabella Trigila <[email protected]>

* Add more test to vcf_chr_rename

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>

---------

Co-authored-by: LouisLeNezet <[email protected]>
Co-authored-by: Anabella Trigila <[email protected]>
@LouisLeNezet LouisLeNezet deleted the checkchr branch October 1, 2024 13:12
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@atrigila atrigila atrigila approved these changes

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@LouisLeNezet LouisLeNezet

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chr check does not work on dog datasets
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@LouisLeNezet @atrigila