Release 0.4.0 #514

fellen31 · 2024-11-22T13:13:11Z

Release 0.4.0 which brings:

Severus as the new default SV caller
LongPhase as the new default phaser
Family (case) level annotations for all variants
FOUND_IN= tags in VCFs
CNV and SV merging with SVDB
GitHub pages documentation
DeepVariant vcfstatsreport
Annotation of SVs and CNVs
Ranking of SVs and CNVs
Filtering of variants (clinical set)
Renamed output files, directories and parameters
More and improved nf-tests
Dynamic methods description
A metro map
and more...

PR checklist

Bump version to 0.4.0dev

Add metro map

Rename and add nf-test to structural variant calling

Update paraphase to compress and index VCFs within the module

…o output docs

Remove filter_vep, add missing SNV section and PED file information t…

Change SV multisample merging to allow for other callers

* Remove fastq QC concatenation * Fix configs * Fix outputs and tests * fix config formatting * fix schema * Fix CHANGELOG.md

Merge patch into dev

* Add Zenodo badge * Add Zenodo text

* Add CI test profiles to nf-test, and only use nf-test * Fix configs * Fix configs

…#366)

* Sort output SNVs * Link to issue

* Fixed, added and updated minimap2 presets * Update CHANGELOG.md Co-authored-by: Anders Jemt <[email protected]> * prettier --------- Co-authored-by: Anders Jemt <[email protected]>

* Fix release test profile paths * Update changelog and schema

rannick

Amazing work! A few comments on things that I think we should make sure work as intended

.nf-core.yml

CHANGELOG.md

README.md

rannick · 2025-01-08T10:07:31Z

conf/base.config

    withLabel:error_ignore {
        errorStrategy = 'ignore'
    }
    withLabel:error_retry {
        errorStrategy = 'retry'
        maxRetries    = 2
    }
-
-    withName: '.*:SAMTOOLS_MERGE' {
+    withName: 'SAMTOOLS_MERGE|SAMTOOLS_INDEX' {


In the base.config? I would have put it in a more specific config, but if it complicates things too much, nevermind

Was suggested to put it here previously, do you think it would be better in the subworkflow config?

rannick · 2025-01-08T12:46:15Z

modules/local/add_most_severe_pli.nf


    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
-        add_most_severe_pli: v1.0
+        add_most_severe_pli: 1.0


Would it make sense to version the script in addition?

I think so, I added a version (as 1.0) for the MultiQC-report, but the script is from raredisease: https://github.com/nf-core/raredisease/blob/dev/bin/add_most_severe_pli.py

Do you have a good idea on how to do it, for both pipelines?

How about a module? One such as DOUBLETDETECTION, with the script in a templates folder? I am not sure it solves the versioning issue completely but at least you would have an easy way to share the script

Cool, I was not aware that it could be done that way. I will look into it (but not before for the release), and see if we can have it as a module in nf-core.

Continuing here: nf-core/raredisease#663

modules/local/create_pedigree_file/main.nf

nextflow_schema.json

subworkflows/local/utils_nfcore_nallo_pipeline/main.nf

Co-authored-by: Annick Renevey <[email protected]>

* without collect only one family per run is filtered * CHANGELOG * CHANGELOG

Schmytzi

Great Job! 🚀

fellen31 and others added 30 commits August 30, 2024 11:34

Bump version to 0.4.0dev

d9091c5

Merge pull request #344 from fellen31/bump-version

a7d1879

Bump version to 0.4.0dev

Add metro map

16c4139

Merge pull request #345 from fellen31/add-metro-map

ad3dbde

Add metro map

Merge pull request #345 from fellen31/add-metro-map

87c67ef

Add metro map

Merge pull request #346 from fellen31/test-sv-calling

72a5bb8

Rename and add nf-test to structural variant calling

Change SV multisample merging to allow for other callers

dfafae9

Delete modules/nf-core/bcftools/reheader/bcftools-reheader.diff

d6b8f35

Update paraphase to compress and index VCFs within the module

690dadc

Change SV multisample merging to allow for other callers

34c4bbd

Merge pull request #355 from fellen31/fix-paraphase

bc1b3ac

Update paraphase to compress and index VCFs within the module

Remove filter_vep, add missing SNV section and PED file information t…

ae40b9d

…o output docs

Merge branch 'dev' into replace-sniffles-multisample

610bfcd

Fix VEP sha in modules.json

d423172

Merge pull request #356 from fellen31/remove-filter-vep-from-docs

fa2772f

Remove filter_vep, add missing SNV section and PED file information t…

Merge pull request #351 from fellen31/replace-sniffles-multisample

ec852a8

Change SV multisample merging to allow for other callers

Remove fastq QC concatenation (#352)

79aaae5

* Remove fastq QC concatenation * Fix configs * Fix outputs and tests * fix config formatting * fix schema * Fix CHANGELOG.md

Merge branch 'master' into patch-merge

af56bc8

Merge pull request #360 from genomic-medicine-sweden/patch-merge

26d2ca8

Merge patch into dev

Add Zenodo link (#363)

57ec840

* Add Zenodo badge * Add Zenodo text

Add CI test profiles to nf-test, and only use nf-test for CI (#365)

47d48a5

* Add CI test profiles to nf-test, and only use nf-test * Fix configs * Fix configs

Sort inputs when creating PED-files, so the output it always the same (…

a8874db

…#366)

Add Severus as the default SV caller (#367)

c1e64e5

Add found_in tag (#371)

2902436

Sort output SNVs (#370)

7b3f100

* Sort output SNVs * Link to issue

Remove VEP plugins from test-data (#379)

c9d3e6b

Fix untar VEP cache (#381)

832847e

Update schema and docs (#382)

1450dd4

Fixed, added and updated minimap2 presets (#393)

e5ab7fe

* Fixed, added and updated minimap2 presets * Update CHANGELOG.md Co-authored-by: Anders Jemt <[email protected]> * prettier --------- Co-authored-by: Anders Jemt <[email protected]>

Patch to dev, pin dev version test-data (#397)

f0b6e73

* Fix release test profile paths * Update changelog and schema

rannick self-requested a review January 8, 2025 09:21

rannick previously approved these changes Jan 8, 2025

View reviewed changes

Update conf/modules/annotate_svs.config

e383a4a

Co-authored-by: Annick Renevey <[email protected]>

fellen31 dismissed rannick’s stale review via e383a4a January 8, 2025 15:12

fellen31 and others added 20 commits January 8, 2025 16:19

Update conf/modules/genome_assembly.config

034de30

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/genome_assembly.config

7329b7b

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/rank_variants.config

809d058

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/rank_variants.config

5061b09

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/rank_variants.config

5af8631

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/snv_annotation.config

a8b1ed4

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/snv_annotation.config

5405de5

Co-authored-by: Annick Renevey <[email protected]>

Update conf/modules/snv_annotation.config

d3c0dde

Co-authored-by: Annick Renevey <[email protected]>

Update modules/local/add_found_in_tag/main.nf

d7692f1

Co-authored-by: Annick Renevey <[email protected]>

Update modules/local/add_found_in_tag/main.nf

6f5f108

Co-authored-by: Annick Renevey <[email protected]>

Update modules/local/add_found_in_tag/main.nf

2c9b215

Co-authored-by: Annick Renevey <[email protected]>

Update modules/local/add_found_in_tag/main.nf

6cd933c

Co-authored-by: Annick Renevey <[email protected]>

Update modules/local/add_found_in_tag/main.nf

67cb026

Co-authored-by: Annick Renevey <[email protected]>

Update modules/local/add_found_in_tag/main.nf

e75da99

Co-authored-by: Annick Renevey <[email protected]>

Update subworkflows/local/utils_nfcore_nallo_pipeline/main.nf

424d392

Co-authored-by: Annick Renevey <[email protected]>

Update CHANGELOG

03ca02d

Update README with clearer descriptions

dfebad4

Clarify comments and docs

079080f

rename metas to sample_metas for more descriptive naming

6c73e21

Add .collect() to allow filtering more than one family per run. (#523)

ec77943

* without collect only one family per run is filtered * CHANGELOG * CHANGELOG

fellen31 requested a review from Schmytzi January 13, 2025 13:24

Schmytzi approved these changes Jan 14, 2025

View reviewed changes

fellen31 added 3 commits January 15, 2025 09:09

Trigger CI

7982d35

Update release date

90ebda8

Correct year

f99a3c7

fellen31 merged commit 9d9d550 into master Jan 15, 2025
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Release 0.4.0 #514

Release 0.4.0 #514

fellen31 commented Nov 22, 2024 •

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Release 0.4.0 #514

Release 0.4.0 #514

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