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Release 2.0.0 #26

Merged
merged 22 commits into from
Feb 12, 2025
Merged

Release 2.0.0 #26

merged 22 commits into from
Feb 12, 2025

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famosab
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@famosab famosab commented Feb 11, 2025

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
  • Make sure your code lints (nf-core pipelines 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).

famosab and others added 20 commits January 8, 2025 15:49
@famosab
bump-version
297e6b4
@famosab
Template update for nf-core/tools version 3.1.1
e4ff713
@famosab @mapo9
template update to v3.1.1 (#15)
9dc69a0 
* add author to enable pipeline sync

* Template update for nf-core/tools version 3.1.1

* correct Changelog

* correct Changelog

* GATK in igenomes

* revert changes that do not belong to template update

* revert changes that do not belong to template update

* fix yml

* prettier

* update tests

* fix: indentation

* Apply suggestions from code review

Co-authored-by: Mark Polster <[email protected]>

---------

Co-authored-by: Mark Polster <[email protected]>
@famosab @mapo9
Fix bcftools/reheader bug (#16)
2a3e4eb 
* add author to enable pipeline sync

* fix issues with samples file

* finalize

* update changelog

* template update to v3.1.1 (#15)

* add author to enable pipeline sync

* Template update for nf-core/tools version 3.1.1

* correct Changelog

* correct Changelog

* GATK in igenomes

* revert changes that do not belong to template update

* revert changes that do not belong to template update

* fix yml

* prettier

* update tests

* fix: indentation

* Apply suggestions from code review

Co-authored-by: Mark Polster <[email protected]>

---------

Co-authored-by: Mark Polster <[email protected]>

* remove unused conf

* swap back to map in process

* put txt in work dir

* back to start dir

* add view() statement

* add retry

* change error strategy

---------

Co-authored-by: Mark Polster <[email protected]>
@famosab
Template update for nf-core/tools version 3.2.0
768cfa1
@famosab
Template update for nf-core/tools version 3.2.0
25ab79b
@famosab
Merge branch 'TEMPLATE' into dev
ced48da
@famosab
revert obsolete changes
9d299f6
@famosab
update changelog
39b93d4
@famosab
fix input schema
90d0065
@famosab
prettier
3ffdc22
@famosab
revert a few changes
05e37e6
@famosab
revert a few changes
b0edc51
@famosab
prettier
9dfa624
@famosab
update the workflow
3a493e4
@famosab
Merge pull request #21 from famosab/dev
a6a1456 
template update to v3.2.0
@famosab
Remove ID column entries from VCFs (#22)
15db32f 
* use bcftools annotate to remove entries in ID column

* update changelog

* fix modules config

* try with local module

* remove index from annotate

* remove .view()

* swap back to nf-core module

* make ID removal optional

* remove trailing whitespace

* update docs

* update readme
@famosab
Add filtering of VEP annotated VCF files using bcftools/view (#23)
5708e09 
* first steps toward including VEP filtering

* swap to bcftools view for filtering

* update schema

* add test based on file hosted locally

* add test data for filtering step

* fix: prettier

* update docs and changelog

* prettier

* move the filtering

* add gitpod yml

* swap order in docs

* fix linting

* add filter test to ci

* update resource limits to enable CI testing

* specify docs

* update title
@famosab
Change branching logic to enable caching again + rename vcf2mat to vc…
0a0c3a1 
…f2counts (#24)

* move samplefilecreation to own module to enable caching

* update changelog

* pre-commit fix

* rename vcf2mat to vcf2counts

* update gatk naming

* try changing samplesheet read in

* comment out mapping steps

* Arthurs suggestions

* move tabix

* remove commented out code

* fix pre-commit

* add @awgymer to Changelog

* add checks for meta similarity

* remove name from meta map

* fix branching
@famosab
Rename pipeline to VCFTOCOUNTS + Prepare Release 2.0.0 (#25)
bff4e4d 
* rename pipeline and prepare release

* prettier

* update subwaymap

* set release date

* Update CHANGELOG.md
@famosab
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famosab commented Feb 12, 2025 

nextflow run . -profile test,conda --outdir testing
Nextflow 24.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.10.1

Launching `./main.nf` [shrivelled_shirley] DSL2 - revision: 138ed788ef

Input/output options
  input                     : /home/paifb01/vcftomat/tests/input.csv
  outdir                    : testing

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function. Skips processes GATK_GENOTYPEGVCFS and BCFTOOLS_MERGE.

Generic options
  trace_report_suffix       : 2025-02-12_09-19-33

Core Nextflow options
  runName                   : shrivelled_shirley
  launchDir                 : /home/paifb01/vcftomat
  workDir                   : /home/paifb01/vcftomat/work
  projectDir                : /home/paifb01/vcftomat
  userName                  : paifb01
  profile                   : test,conda
  configFiles               : /home-link/paifb01/.nextflow/config, /home/paifb01/vcftomat/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/famke-baeuerle/watch/2q6SyZzbOy0890
executor >  local (7)
[72/1f4b55] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:TABIX_TABIX (chr22)        [100%] 1 of 1 ✔
[-        ] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:GATK4_GENOTYPEGVCFS        -
[-        ] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_CONCAT            -
[92/1218d7] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:CREATE_SAMPLE_FILE (chr22) [100%] 1 of 1 ✔
[f6/6401fa] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_REHEADER (chr22)  [100%] 1 of 1 ✔
[-        ] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_MERGE             -
[78/f1626d] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_ANNOTATE (chr22)  [100%] 1 of 1 ✔
[d7/43cf87] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:VCF2COUNTS (chr22)         [100%] 2 of 2 ✔
[4a/44a379] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:MULTIQC                    [100%] 1 of 1 ✔
-[qbic-pipelines/vcftocounts] Pipeline completed successfully-

@famosab
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famosab commented Feb 12, 2025 

nextflow run . -profile test_filter,docker --outdir testing
Nextflow 24.10.4 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.10.1

Launching `./main.nf` [high_shockley] DSL2 - revision: 138ed788ef

Input/output options
  input                     : /home/paifb01/vcftomat/tests/input-filter.csv
  filter                    : INFO/CSQ ~ "HIGH"
  outdir                    : testing

Reference genome options
  fasta                     : https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta
  fai                       : https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.fasta.fai
  dict                      : https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/genome.dict

Institutional config options
  config_profile_name       : Filter test profile
  config_profile_description: Filter test dataset to check pipeline function

Generic options
  trace_report_suffix       : 2025-02-12_09-20-19

Core Nextflow options
  runName                   : high_shockley
  containerEngine           : docker
  launchDir                 : /home/paifb01/vcftomat
  workDir                   : /home/paifb01/vcftomat/work
  projectDir                : /home/paifb01/vcftomat
  userName                  : paifb01
  profile                   : test_filter,docker
  configFiles               : /home-link/paifb01/.nextflow/config, /home/paifb01/vcftomat/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/famke-baeuerle/watch/Fwi39lcP3yiN6
executor >  local (8)
[da/c437e8] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:TABIX_TABIX (chr21_ann)        [100%] 1 of 1 ✔
[-        ] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:GATK4_GENOTYPEGVCFS            -
[3a/6dc2d1] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_VIEW (chr21_ann)      [100%] 1 of 1 ✔
[-        ] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_CONCAT                -
[3a/ac5751] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:CREATE_SAMPLE_FILE (chr21_ann) [100%] 1 of 1 ✔
[81/3794ac] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_REHEADER (chr21_ann)  [100%] 1 of 1 ✔
[-        ] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_MERGE                 -
[e8/309e6c] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:BCFTOOLS_ANNOTATE (chr21_ann)  [100%] 1 of 1 ✔
[15/aee490] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:VCF2COUNTS (chr21_ann)         [100%] 2 of 2 ✔
[9b/27869f] process > QBICPIPELINES_VCFTOCOUNTS:VCFTOCOUNTS:MULTIQC                        [100%] 1 of 1 ✔
-[qbic-pipelines/vcftocounts] Pipeline completed successfully-
Completed at: 12-Feb-2025 09:22:10
Duration    : 1m 49s
CPU hours   : (a few seconds)
Succeeded   : 8

@famosab
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famosab commented Feb 12, 2025

This failing test nf-core CI / Run pipeline with test data (24.04.2 | test_filter | conda) (pull_request) is a known issue: nextflow-io/nextflow#5485 and can maybe be ignored?

@famosab
add note on filtering step (#27)
25c739b 
* add note on filtering step

* change date on changelog
mapo9
mapo9 requested changes Feb 12, 2025
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generally very good. some minor things came to mind. maybe i overlooked sth though

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@famosab @mapo9
Move test data to test-datasets, create filter nf-test (#28)
a308ff8 
* add filter test and fix small remarks

* finalize name changes

* Update CHANGELOG.md

Co-authored-by: Mark Polster <[email protected]>

---------

Co-authored-by: Mark Polster <[email protected]>
mapo9
mapo9 reviewed Feb 12, 2025
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lgtm, great job! 🚀

mapo9
mapo9 approved these changes Feb 12, 2025
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simon says no

@famosab famosab merged commit e0b7ed9 into master Feb 12, 2025
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@famosab @mapo9