Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Joint Germline subworkflow haplotypecaller -> Vqsr #595

Merged
merged 90 commits into from
Jul 21, 2022
Merged

Joint Germline subworkflow haplotypecaller -> Vqsr #595

merged 90 commits into from
Jul 21, 2022

Commits on May 13, 2022

  1. add vqsr from Atholl, very early WIP

    Gavin.Mackenzie committed May 13, 2022
    Configuration menu
    Copy the full SHA
    19e5e0e View commit details
    Browse the repository at this point in the history

Commits on Jun 1, 2022

  1. added meta.yml for vqsr subworkflow

    @GCJMackenzie
    GCJMackenzie authored Jun 1, 2022
    Configuration menu
    Copy the full SHA
    cd8d767 View commit details
    Browse the repository at this point in the history

Commits on Jun 9, 2022

  1. Merge pull request #9 from GCJMackenzie/add_vqsr_subworkflow 

    Add vqsr subworkflow
    @nickhsmith
    nickhsmith authored Jun 9, 2022
    Configuration menu
    Copy the full SHA
    03909c9 View commit details
    Browse the repository at this point in the history

Commits on Jun 17, 2022

  1. joint variant calling updates to gatk best practices

    Smith Nicholas committed Jun 17, 2022
    Configuration menu
    Copy the full SHA
    c22a64f View commit details
    Browse the repository at this point in the history

  2. group by interval and exclude sample info

    Smith Nicholas committed Jun 17, 2022
    Configuration menu
    Copy the full SHA
    028ad1a View commit details
    Browse the repository at this point in the history

Commits on Jun 20, 2022

  1. interval and no_interval grouping

    Smith Nicholas committed Jun 20, 2022
    Configuration menu
    Copy the full SHA
    57c2dff View commit details
    Browse the repository at this point in the history

Commits on Jun 22, 2022

  1. add params and vqsr process

    Smith Nicholas committed Jun 22, 2022
    Configuration menu
    Copy the full SHA
    ea8dd93 View commit details
    Browse the repository at this point in the history

Commits on Jun 23, 2022

  1. print statements

    Smith Nicholas committed Jun 23, 2022
    Configuration menu
    Copy the full SHA
    d6cc403 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2022

  1. joint variantcalling

    Smith Nicholas committed Jun 27, 2022
    Configuration menu
    Copy the full SHA
    b78ad1c View commit details
    Browse the repository at this point in the history

Commits on Jun 28, 2022

  1. update

    Smith Nicholas committed Jun 28, 2022
    Configuration menu
    Copy the full SHA
    37aa902 View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2022

  1. add interval_names to meta

    Smith Nicholas committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    d49a5ac View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'NF-core/dev' into vqsr

    Smith Nicholas committed Jun 29, 2022
    Configuration menu
    Copy the full SHA
    d574b0c View commit details
    Browse the repository at this point in the history

Commits on Jul 4, 2022

  1. prepare vqsr

    Smith Nicholas committed Jul 4, 2022
    Configuration menu
    Copy the full SHA
    dd7445f View commit details
    Browse the repository at this point in the history

  2. remove inclusion of local config

    Smith Nicholas committed Jul 4, 2022
    Configuration menu
    Copy the full SHA
    06c66ad View commit details
    Browse the repository at this point in the history

  3. lint

    Smith Nicholas committed Jul 4, 2022
    Configuration menu
    Copy the full SHA
    8686dfb View commit details
    Browse the repository at this point in the history

Commits on Jul 6, 2022

  1. force bcftools sort

    Smith Nicholas committed Jul 6, 2022
    Configuration menu
    Copy the full SHA
    f9fcb65 View commit details
    Browse the repository at this point in the history

Commits on Jul 7, 2022

  1. fix typo and clearer naming

    Smith Nicholas committed Jul 7, 2022
    Configuration menu
    Copy the full SHA
    6e5e8dd View commit details
    Browse the repository at this point in the history

  2. include variant_recalibration param

    Smith Nicholas committed Jul 7, 2022
    Configuration menu
    Copy the full SHA
    9a29759 View commit details
    Browse the repository at this point in the history

Commits on Jul 8, 2022

  1. apply vqsr and merge

    Smith Nicholas committed Jul 8, 2022
    Configuration menu
    Copy the full SHA
    aa110ab View commit details
    Browse the repository at this point in the history

  2. snp and indels must be present for recalibration

    Smith Nicholas committed Jul 8, 2022
    Configuration menu
    Copy the full SHA
    fa41fa0 View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2022

  1. fix typo

    Smith Nicholas committed Jul 11, 2022
    Configuration menu
    Copy the full SHA
    17924d0 View commit details
    Browse the repository at this point in the history

  2. typo

    Smith Nicholas committed Jul 11, 2022
    Configuration menu
    Copy the full SHA
    50de0de View commit details
    Browse the repository at this point in the history

Commits on Jul 12, 2022

  1. improve resource channels

    Smith Nicholas committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    7947ce0 View commit details
    Browse the repository at this point in the history

  2. pre-merge

    Smith Nicholas committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    3463c56 View commit details
    Browse the repository at this point in the history

  3. merge with nf-core dev

    Smith Nicholas committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    1c48729 View commit details
    Browse the repository at this point in the history

  4. improve haplotypecaller merging

    Smith Nicholas committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    b835c37 View commit details
    Browse the repository at this point in the history

  5. fix naming

    Smith Nicholas committed Jul 12, 2022
    Configuration menu
    Copy the full SHA
    d45423f View commit details
    Browse the repository at this point in the history

Commits on Jul 13, 2022

  1. update known_sites

    Smith Nicholas committed Jul 13, 2022
    Configuration menu
    Copy the full SHA
    ed5ccea View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'NF-core/dev' into vqsr

    Smith Nicholas committed Jul 13, 2022
    Configuration menu
    Copy the full SHA
    3de8f7f View commit details
    Browse the repository at this point in the history

Commits on Jul 14, 2022

  1. update

    Smith Nicholas committed Jul 14, 2022
    Configuration menu
    Copy the full SHA
    b2fd565 View commit details
    Browse the repository at this point in the history

Commits on Jul 15, 2022

  1. fix typo

    Smith Nicholas committed Jul 15, 2022
    Configuration menu
    Copy the full SHA
    bfaf48d View commit details
    Browse the repository at this point in the history

  2. publishDir

    Smith Nicholas committed Jul 15, 2022
    Configuration menu
    Copy the full SHA
    cb25481 View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2022

  1. flatten known_sites

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    8fd7ff9 View commit details
    Browse the repository at this point in the history

  2. merge with dev

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    4eac972 View commit details
    Browse the repository at this point in the history

  3. add joint_germline

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    ced2398 View commit details
    Browse the repository at this point in the history

  4. update modules

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    66a7f00 View commit details
    Browse the repository at this point in the history

  5. fix no_intervals and tests

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    0ea9747 View commit details
    Browse the repository at this point in the history

  6. lint

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    0717286 View commit details
    Browse the repository at this point in the history

  7. update to dev

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    37e5e77 View commit details
    Browse the repository at this point in the history

  8. lint

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    1db8bc8 View commit details
    Browse the repository at this point in the history

  9. fix empty module

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    ff6b530 View commit details
    Browse the repository at this point in the history

  10. correct prepare_genome input

    Smith Nicholas committed Jul 18, 2022
    Configuration menu
    Copy the full SHA
    aa7127a View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2022

  1. merge with dev

    Smith Nicholas committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    5be916a View commit details
    Browse the repository at this point in the history

  2. change name to match tests

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    21182a3 View commit details
    Browse the repository at this point in the history

  3. update test

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    9eebd71 View commit details
    Browse the repository at this point in the history

  4. Update workflows/sarek.nf 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    69feebd View commit details
    Browse the repository at this point in the history

  5. Update workflows/sarek.nf 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    20a7e2e View commit details
    Browse the repository at this point in the history

  6. Apply suggestions from code review 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    3cbe260 View commit details
    Browse the repository at this point in the history

  7. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    e9fb076 View commit details
    Browse the repository at this point in the history

  8. Update subworkflows/nf-core/variantcalling/haplotypecaller/main.nf 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    6ea35cc View commit details
    Browse the repository at this point in the history

  9. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    8d7235d View commit details
    Browse the repository at this point in the history

  10. Update nextflow_schema.json

    @nickhsmith
    nickhsmith authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    13f9bd7 View commit details
    Browse the repository at this point in the history

  11. remove unneeded when statements

    Smith Nicholas committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    e75a7f3 View commit details
    Browse the repository at this point in the history

  12. update paths

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    fb7c594 View commit details
    Browse the repository at this point in the history

  13. Merge branch 'vqsr' of github.com:nickhsmith/sarek into vqsr

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    04b3191 View commit details
    Browse the repository at this point in the history

  14. fix warnings

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    9e31397 View commit details
    Browse the repository at this point in the history

  15. fix warnings

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    fc0c251 View commit details
    Browse the repository at this point in the history

  16. update path

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    2e9a724 View commit details
    Browse the repository at this point in the history

  17. remove lane from csv

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    748947d View commit details
    Browse the repository at this point in the history

  18. add step_variant calling

    @nickhsmith
    nickhsmith committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    7e3a11e View commit details
    Browse the repository at this point in the history

  19. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    77eb3d6 View commit details
    Browse the repository at this point in the history

  20. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    3fe7927 View commit details
    Browse the repository at this point in the history

  21. Update modules.config

    @nickhsmith
    nickhsmith authored Jul 19, 2022
    Configuration menu
    Copy the full SHA
    acb9fce View commit details
    Browse the repository at this point in the history

  22. Merge remote-tracking branch 'NF-core/dev' into vqsr

    Smith Nicholas committed Jul 19, 2022
    Configuration menu
    Copy the full SHA
    c793d5f View commit details
    Browse the repository at this point in the history

Commits on Jul 20, 2022

  1. Apply suggestions from code review 

    Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @maxulysse @FriederikeHanssen
    3 people authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    87f3405 View commit details
    Browse the repository at this point in the history

  2. Apply suggestions from code review

    @nickhsmith
    nickhsmith authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    ef8f526 View commit details
    Browse the repository at this point in the history

  3. hg19 sample names

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    72b4bc8 View commit details
    Browse the repository at this point in the history

  4. change tool inputs

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    e5b1703 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'vqsr' of github.com:nickhsmith/sarek into vqsr

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    d6c006e View commit details
    Browse the repository at this point in the history

  6. Update subworkflows/nf-core/variantcalling/haplotypecaller/main.nf 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    c94e00b View commit details
    Browse the repository at this point in the history

  7. Update after code review

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    0dd0976 View commit details
    Browse the repository at this point in the history

  8. groupTuple

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    717e271 View commit details
    Browse the repository at this point in the history

  9. merge with dev

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    da17db9 View commit details
    Browse the repository at this point in the history

  10. improve meta and tupleGrouping

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    4b9bd9f View commit details
    Browse the repository at this point in the history

  11. Update conf/igenomes.config 

    Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
    @nickhsmith @maxulysse
    nickhsmith and maxulysse authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    9bae10f View commit details
    Browse the repository at this point in the history

  12. Update conf/modules.config 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    b77a116 View commit details
    Browse the repository at this point in the history

  13. Update nextflow_schema.json 

    Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
    @nickhsmith @maxulysse
    nickhsmith and maxulysse authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    468dedb View commit details
    Browse the repository at this point in the history

  14. Update subworkflows/local/germline_variant_calling.nf 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    e919d09 View commit details
    Browse the repository at this point in the history

  15. Update subworkflows/local/germline_variant_calling.nf 

    Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
    @nickhsmith @FriederikeHanssen
    nickhsmith and FriederikeHanssen authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    46bc423 View commit details
    Browse the repository at this point in the history

  16. Update germline_variant_calling.nf

    @nickhsmith
    nickhsmith authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    f057709 View commit details
    Browse the repository at this point in the history

  17. Update subworkflows/nf-core/gatk4/joint_germline_variant_calling/main.nf 

    Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
    @nickhsmith @maxulysse
    nickhsmith and maxulysse authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    4d50caf View commit details
    Browse the repository at this point in the history

  18. meta format

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    c707f7c View commit details
    Browse the repository at this point in the history

  19. undo publishDir change

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    ac0a1f5 View commit details
    Browse the repository at this point in the history

  20. hardcode joint_variant_calling publish path

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    a6d6e9a View commit details
    Browse the repository at this point in the history

  21. fix typo

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    7f5a916 View commit details
    Browse the repository at this point in the history

  22. Merge remote-tracking branch 'NF-core/dev' into vqsr

    Smith Nicholas committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    1fc9e2a View commit details
    Browse the repository at this point in the history

  23. Merge branch 'dev' into vqsr

    @nickhsmith
    nickhsmith authored Jul 20, 2022
    Configuration menu
    Copy the full SHA
    d842fe0 View commit details
    Browse the repository at this point in the history

  24. fix haplotypecaller cram input

    @nickhsmith
    nickhsmith committed Jul 20, 2022
    Configuration menu
    Copy the full SHA
    73e84db View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2022

  1. fix indents, commas etc

    @FriederikeHanssen
    FriederikeHanssen committed Jul 21, 2022
    Configuration menu
    Copy the full SHA
    9fa1a5c View commit details
    Browse the repository at this point in the history

  2. remove test file

    @nickhsmith
    nickhsmith committed Jul 21, 2022
    Configuration menu
    Copy the full SHA
    b0c32c7 View commit details
    Browse the repository at this point in the history