Candidate release 3.2.0 #1057

maxulysse · 2023-06-01T14:38:54Z

To get the process started as I'm hoping to release ASAP.
Would need to include:

CHORES: bump to 3.2.0 #1056
FIX: VCFTOOLS public ecr registry #1058
FIX: join duplication for manta/strelka annotation #1063
Would love to include:
FIX: pattern for fasta file #1055
remove exit strategy for MANTA/STRELKA #882, but waiting for FIX: Add error_retry label modules#3473
don't publish genomicsdb files #1061

Fix missing annotation keys for vep/snpeff

Add failsafe options for Nextflow join operator

update paths

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

ADD: Annotation cache usage docs

Don't mutate channel elements in-place

…cing

Co-authored-by: Maxime U Garcia <[email protected]>

docs/usage.md

Co-authored-by: Friederike Hanssen <[email protected]>

modules/nf-core/bcftools/sort/main.nf

Co-authored-by: Friederike Hanssen <[email protected]>

lib/WorkflowMain.groovy

Co-authored-by: Friederike Hanssen <[email protected]>

modules/nf-core/cnvkit/batch/main.nf

docs/usage.md

don't publish genomicsdb files

modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff

modules/nf-core/gatk4/markduplicatesspark/main.nf

subworkflows/local/bam_variant_calling_deepvariant/main.nf

subworkflows/local/bam_variant_calling_germline_all/main.nf

CHANGELOG.md

subworkflows/local/bam_markduplicates/main.nf

subworkflows/local/prepare_intervals/main.nf

subworkflows/local/vcf_annotate_all/main.nf

tests/test_mutect2.yml

Co-authored-by: Friederike Hanssen <[email protected]>

CHANGELOG.md

CHORES: remove version from pictures

docs update

maxulysse and others added 30 commits March 2, 2023 10:09

Merge pull request #954 from maxulysse/annotation_hg19

4e60e8c

Fix missing annotation keys for vep/snpeff

add failsafe with join()

59de143

update CHANGELOG

bc16cbc

expand to all join operators

c2e3e44

update nf-core subworkflows

1a4af5d

code polish

49c7d55

update CHANGELOG

6ea33d2

no failOnMismatch for this join

15c2328

update md5sum

a11fbff

no failOnDuplicate for this one

c09f240

no failOnMismatch for this one

8524d37

fix map

59b3d0d

Merge pull request #957 from maxulysse/mutect2

b2a8891

Add failsafe options for Nextflow join operator

update paths

7d56fa4

Merge pull request #965 from FriederikeHanssen/new_paths

4e46048

update paths

add outdir_cache + update annotation docs for cache

50f0652

Apply suggestions from code review

2448bc0

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

fix annotation cache test with conda

e1fe104

Apply suggestions from code review

4221d5d

Merge pull request #967 from maxulysse/annotation_cache_docs

3b5f2a4

ADD: Annotation cache usage docs

Merge branch 'dev' into ubam

9f6f8c9

update all modules

3538373

Don't mutate channel elements in-place

86c684e

Changelog update

6d60fd9

Merge pull request #971 from nf-core/sort-fix

d9675e6

Don't mutate channel elements in-place

Validate that sample/patient does not contain space and add test

8227588

Added how to generate ASCAT reference files for exome/targeted sequen…

b4f54a3

…cing

Fixed link formatting

7cf1d3b

Add validation_checks tag to spaces test

4174f0d

Co-authored-by: Maxime U Garcia <[email protected]>

Add new test to github actions workflow

d48cc24