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remove unused subworkflow #105

Merged
merged 1 commit into from
Jul 16, 2024
Merged

remove unused subworkflow #105

merged 1 commit into from
Jul 16, 2024

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atrigila
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Closes #104

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 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).

@atrigila atrigila requested a review from LouisLeNezet July 15, 2024 23:23
@atrigila atrigila self-assigned this Jul 15, 2024
@LouisLeNezet LouisLeNezet merged commit 4dde6eb into nf-core:dev Jul 16, 2024
7 of 8 checks passed
LouisLeNezet pushed a commit to LouisLeNezet/phaseimpute that referenced this pull request Jul 16, 2024
@atrigila
remove unused subworkflow (nf-core#105)
9cb558a
LouisLeNezet added a commit that referenced this pull request Jul 16, 2024
@LouisLeNezet @atrigila
Fix chr name errors (#102)
a05575c 
* 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]>
LouisLeNezet pushed a commit to LouisLeNezet/phaseimpute that referenced this pull request Jul 16, 2024
@atrigila
remove unused subworkflow (nf-core#105)
74c841a
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 added the enhancement New feature or request label Jul 18, 2024
@LouisLeNezet LouisLeNezet added this to the v0.99.0 milestone Jul 18, 2024
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Reviewers

@LouisLeNezet LouisLeNezet LouisLeNezet approved these changes

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@atrigila atrigila

Labels
enhancement New feature or request
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Milestone
v0.99.0
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Successfully merging this pull request may close these issues.

Remove POSFILE_PREPARE_GAWK
2 participants
@atrigila @LouisLeNezet