Joint Germline subworkflow haplotypecaller -> Vqsr#595

Merged

FriederikeHanssen merged 90 commits intonf-core:devfrom

nickhsmith:vqsr

Jul 21, 2022

Commits on May 13, 2022

add vqsr from Atholl, very early WIP
Gavin.Mackenzie
committed

Commits on Jun 1, 2022

added meta.yml for vqsr subworkflow
GCJMackenzie
authored

Commits on Jun 9, 2022

Merge pull request #9 from GCJMackenzie/add_vqsr_subworkflow
nickhsmith
authored

Commits on Jun 17, 2022

joint variant calling updates to gatk best practices
Smith Nicholas
committed
group by interval and exclude sample info
Smith Nicholas
committed

Commits on Jun 20, 2022

interval and no_interval grouping
Smith Nicholas
committed

Commits on Jun 22, 2022

add params and vqsr process
Smith Nicholas
committed

Commits on Jun 23, 2022

print statements
Smith Nicholas
committed

Commits on Jun 27, 2022

joint variantcalling
Smith Nicholas
committed

Commits on Jun 28, 2022

update
Smith Nicholas
committed

Commits on Jun 29, 2022

add interval_names to meta
Smith Nicholas
committed
Merge remote-tracking branch 'NF-core/dev' into vqsr
Smith Nicholas
committed

Commits on Jul 4, 2022

prepare vqsr
Smith Nicholas
committed
remove inclusion of local config
Smith Nicholas
committed
lint
Smith Nicholas
committed

Commits on Jul 6, 2022

force bcftools sort
Smith Nicholas
committed

Commits on Jul 7, 2022

fix typo and clearer naming
Smith Nicholas
committed
include variant_recalibration param
Smith Nicholas
committed

Commits on Jul 8, 2022

apply vqsr and merge
Smith Nicholas
committed
snp and indels must be present for recalibration
Smith Nicholas
committed

Commits on Jul 11, 2022

fix typo
Smith Nicholas
committed
typo
Smith Nicholas
committed

Commits on Jul 12, 2022

improve resource channels
Smith Nicholas
committed
pre-merge
Smith Nicholas
committed
merge with nf-core dev
Smith Nicholas
committed
improve haplotypecaller merging
Smith Nicholas
committed
fix naming
Smith Nicholas
committed

Commits on Jul 13, 2022

update known_sites
Smith Nicholas
committed
Merge remote-tracking branch 'NF-core/dev' into vqsr
Smith Nicholas
committed

Commits on Jul 14, 2022

update
Smith Nicholas
committed

Commits on Jul 15, 2022

fix typo
Smith Nicholas
committed
publishDir
Smith Nicholas
committed

Commits on Jul 18, 2022

flatten known_sites
Smith Nicholas
committed
merge with dev
Smith Nicholas
committed
add joint_germline
Smith Nicholas
committed
update modules
Smith Nicholas
committed
fix no_intervals and tests
Smith Nicholas
committed
lint
Smith Nicholas
committed
update to dev
Smith Nicholas
committed
lint
Smith Nicholas
committed
fix empty module
Smith Nicholas
committed
correct prepare_genome input
Smith Nicholas
committed

Commits on Jul 19, 2022

merge with dev
Smith Nicholas
committed
change name to match tests
nickhsmith
committed
update test
nickhsmith
committed
Update workflows/sarek.nf

nickhsmith
and
FriederikeHanssen
authored
Update workflows/sarek.nf

nickhsmith
and
FriederikeHanssen
authored
Apply suggestions from code review

nickhsmith
and
FriederikeHanssen
authored
Update conf/modules.config

nickhsmith
and
FriederikeHanssen
authored
Update subworkflows/nf-core/variantcalling/haplotypecaller/main.nf

nickhsmith
and
FriederikeHanssen
authored
Update conf/modules.config

nickhsmith
and
FriederikeHanssen
authored
Update nextflow_schema.json
nickhsmith
authored
remove unneeded when statements
Smith Nicholas
committed
update paths
nickhsmith
committed
Merge branch 'vqsr' of github.com:nickhsmith/sarek into vqsr
nickhsmith
committed
fix warnings
nickhsmith
committed
fix warnings
nickhsmith
committed
update path
nickhsmith
committed
remove lane from csv
nickhsmith
committed
add step_variant calling
nickhsmith
committed
Update conf/modules.config

nickhsmith
and
FriederikeHanssen
authored
Update conf/modules.config

nickhsmith
and
FriederikeHanssen
authored
Update modules.config
nickhsmith
authored
Merge remote-tracking branch 'NF-core/dev' into vqsr
Smith Nicholas
committed

Commits on Jul 20, 2022

Apply suggestions from code review

authored
Apply suggestions from code review
nickhsmith
authored
hg19 sample names
Smith Nicholas
committed
change tool inputs
Smith Nicholas
committed
Merge branch 'vqsr' of github.com:nickhsmith/sarek into vqsr
Smith Nicholas
committed
Update subworkflows/nf-core/variantcalling/haplotypecaller/main.nf

nickhsmith
and
FriederikeHanssen
authored
Update after code review
Smith Nicholas
committed
groupTuple
Smith Nicholas
committed
merge with dev
Smith Nicholas
committed
improve meta and tupleGrouping
Smith Nicholas
committed
Update conf/igenomes.config

nickhsmith
and
maxulysse
authored
Update conf/modules.config

nickhsmith
and
FriederikeHanssen
authored
Update nextflow_schema.json

nickhsmith
and
maxulysse
authored
Update subworkflows/local/germline_variant_calling.nf

nickhsmith
and
FriederikeHanssen
authored
Update subworkflows/local/germline_variant_calling.nf

nickhsmith
and
FriederikeHanssen
authored
Update germline_variant_calling.nf
nickhsmith
authored
Update subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf

nickhsmith
and
maxulysse
authored
meta format
Smith Nicholas
committed
undo publishDir change
Smith Nicholas
committed
hardcode joint_variant_calling publish path
Smith Nicholas
committed
fix typo
Smith Nicholas
committed
Merge remote-tracking branch 'NF-core/dev' into vqsr
Smith Nicholas
committed
Merge branch 'dev' into vqsr
nickhsmith
authored
fix haplotypecaller cram input
nickhsmith
committed

Commits on Jul 21, 2022

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