Code

DSL2: genotyping#1016

Code

Merged

TCLamnidis merged 121 commits intodevnf-core/eager:devfrom dsl2-genotypingnf-core/eager:dsl2-genotypingCopy head branch name to clipboardMar 20, 2024

+2,710-104

Commits

Commits on Jun 23, 2023

• add pileupcaller params to config and schema

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  67220ce

• genotyping parameter requirement checks

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  eb61d10

Commits on Jun 30, 2023

• Add required modules

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  1bf3529

• Install modules

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  05f1b13

Commits on Jul 3, 2023

• wip genotyping

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  1b82eaa

Commits on Jul 14, 2023

• Install GATK UG modules

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• Merge remote-tracking branch 'origin/dev' into dsl2-genotyping

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  d35ff76

• started adding GATK_UG

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  c0cd49c

Commits on Jul 21, 2023

• Update gatk3 modules

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  9e6b407

• Add genotyping SWF

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  ecc4257

• work on gatk ug

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  5ca5043

• Add gatk UG

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  89a7aab

• no intervals in ug call

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• add version

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  29a3e89

• emit UG output

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  2d7b622

• tweak gatk UG outputs

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• rename emissions

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• delete leftover debug print from map.nf

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Commits on Jul 28, 2023

• Add params for gatk and gatkUG

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  8b4b79d

• WIP adding params to GATK UG

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  8575592

• reorder params

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• add dbSNP placeholder to be able to test. parameters passes to gatk now

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Commits on Aug 4, 2023

• convert bcftools_stats to skip

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• finish schema

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• Merge branch 'dev' into dsl2-genotyping

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• Merge branch 'dsl2-genotyping' of github.com:nf-core/eager into dsl2-genotyping

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• merge conflict

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Commits on Aug 11, 2023

• Update bcftools_stats

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  16d567a

• add bcftools stats to UG

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• add todo comment

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• Add config for bcftools stats

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• record manual tests

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  2cf5eac

• remove unnecessary bash block

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Commits on Oct 27, 2023

• Merge branch 'dev' into dsl2-genotyping

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Commits on Nov 3, 2023

• attempt to add dbsnp to reference sheet

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• pass dbsnp to genotyping

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  a056508

Commits on Nov 24, 2023

• Include ploidy into ref_meta

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  f312446

• gatk UG done with dbsnp

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  05675d5

• fix indentation

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  dcc3e47

• update haplotypecaller module

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• port UG channels to HC

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Commits on Dec 8, 2023

• Add gatk HC params. Update some gatk UG param text

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• add gatk HC params

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• add gatk HC. Add patterns to genotyping module publishDir

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  bf9cd87

• add HC. fix indent. move bcftools

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  edb5e58

• HC manual tests. update UG tests

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  49d531d

• update TODOs

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  f86bdad

Commits on Dec 13, 2023

• update freebayes module

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• Add Freebayes

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• manual tests

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  8f1aa9d

Commits on Jan 12, 2024

• add pileupcaller aux files

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  68386e4

• remove old dbsnp input. fix genotyping swf cardinality

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  a963652

• add pileupcaller bed and snp files

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  b070eea

• Add pileupcaller. simplify input channels.

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  69dae31

• add pileupcaller and samtools mpileup

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Commits on Jan 26, 2024

• no mpileup output. add pattern to pileupcaller

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  0f1d71b

• deal with optional files.

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• clearer formatting of Genotyping call

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• add warning todo for inconsistent options

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• manual tests for genotyping. add multiref per block

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  4e0bb0d

• add small todos

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Commits on Feb 2, 2024

• Merge remote-tracking branch 'origin/dev' into dsl2-genotyping

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  a6e8274

• Merge remote-tracking branch 'origin/dev' into dsl2-genotyping

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  cc94772

• remove empty defaults

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  e732f27

• Update all modules

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  be20f06

• fix linting warnings

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  5d4eaf6

• add collect_genotypes

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  2e38e63

• add genotype collection

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  0c9f4ac

• update manual tests

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• linting

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  1279891

• oopsie bugfix

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Commits on Feb 6, 2024

• add test for each genotyper.

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  5f6d466

• Add errors when pileupcaller is used without bed or snp file

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• small tweaks

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• small changes

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• reposition a line

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• fix error condition

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• fix error conditional

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  bd063fa

• remove library ids from genotyping configs (libs merged)

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  73b7d0a

• fix file name collision in GATK RTC

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  0b19335

Commits on Feb 7, 2024

• remove debug statements. add python version to version yml

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  7a3ea2a

• add coverage stats. add mqc files to mqc channel

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  a3b16a2

• update manual tests

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  97bdc0b

Commits on Feb 8, 2024

• Merge remote-tracking branch 'origin/dev' into dsl2-genotyping

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  d273610

Commits on Feb 23, 2024

• Apply suggestions from code review to modules.conf

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  and

  scarlhoff

  authored
  6d4ac28

• remove commented lines, update comments

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  156e132

• Update parameter name for keeping realigned bam

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• rename parameter

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  d74de23

• Apply suggestions from code review to schema wording

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  and

  jfy133

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  5046dfe

• standardise mpileup helptext wording

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  ea27287

• Update genotyping_pileupcaller_method helptext

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  756c170

• Apply suggestions from code review to schema

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  and

  scarlhoff

  authored
  51400cd

• Remove TODO about parameter validation

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  committed
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• Merge branch 'dsl2-genotyping' of github.com:nf-core/eager into dsl2-genotyping

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  784103a

• Apply suggestions from code review to genotype swf

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  3 peopleauthored
  9020037

• remove todo about issue #1054

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  61df8b9

Commits on Mar 1, 2024

• merge both ploidy parameters into one genotyping_reference_ploidy param

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  3f95223

• Install BCFTOOLS_INDEX

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  bc1c924

• update gatk_HC module

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• index VCF files

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Commits on Mar 8, 2024

• add warning about angsd

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  8edd468

• rename meta attribute id -> sample_id for consistency

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  f34045e

• simplify output channels

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  c461478

Commits on Mar 14, 2024

• Update GATK_UG

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  322ffa1

• remove dumps

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  83808ed

• update manual_tests.md

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  9b4a484

Commits on Mar 15, 2024

• add genotyper to meta of genotypes

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  9b448f3

• Merge branch 'dev' into dsl2-genotyping

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  1036da2

• remove todos

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  8df94c4

Commits on Mar 18, 2024

• Add output information on genotypers

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  d20d2ce

• Clarify pileupcaller

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Commits on Mar 19, 2024

• add citations

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• add bcftools citation

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• Merge branch 'dev' into dsl2-genotyping

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  7f9d6b7

• update modules.json (remove dumpSV)

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  309b8b8

• validate parameter combinations

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  b78c3f1

• linting

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  e8b27df

• remove lib dependency

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  0b93d81

• typo

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• minor edits and linting

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  committed
  ccd118c

• Merge branch 'dev' into dsl2-genotyping

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  authored
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