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Concatenating germline vcfs #792

Merged
merged 36 commits into from
Dec 7, 2022
Merged

Concatenating germline vcfs #792

merged 36 commits into from
Dec 7, 2022

Commits on Oct 11, 2022

  1. WIP. Just concatenating germline-vcfs from strelka and hyplotypecaller

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    asp8200 committed Oct 11, 2022
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  2. Merge branch 'dev' into concatenating_vcfs

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    asp8200 committed Oct 11, 2022
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Commits on Oct 12, 2022

  1. Adding the germline vcf-file from manta to the list of germline vcf-f… 

    …iles being concatenated
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    asp8200 committed Oct 12, 2022
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  2. Making sure the channel manta_vcf_tbi is defined even if manta isnt run

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    asp8200 committed Oct 12, 2022
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Commits on Nov 10, 2022

  1. merge from dev

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Commits on Nov 13, 2022

  1. Adding support for concatenation of germline vcf-files. Now also for … 

    …vcf-files from deepvariant.
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  2. Adding CLI-open concatenate_vcf to the schema-json

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    asp8200 committed Nov 13, 2022
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Commits on Nov 14, 2022

  1. WIP: Adding support for concatenation of germline vcf-files. Now also… 

    … for vcf-files from freebayes.
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  2. WIP: Adding support for concatenation of germline vcf-files. Now also… 

    … for vcf-files from tiddit.
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  3. Merge branch 'dev' into concatenating_vcfs

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    asp8200 committed Nov 14, 2022
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Commits on Nov 25, 2022

  1. Merge branch 'dev' into concatenating_vcfs

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    asp8200 committed Nov 25, 2022
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Commits on Nov 28, 2022

  1. Adding support for concatenation of vcf from mpileup

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  2. Changing CLI-option concatenate_vcf to concatenate_vcfs.

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  3. Merge branch 'dev' into concatenating_vcfs

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  4. Initializing CLI-option concatenate_vcfs to false.

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    asp8200 committed Nov 28, 2022
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  5. Sorting concatenated germline-vcf-file and adding tbi.

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  6. Updating schema. Grouping the CLI-option concatenate_vcfs together wi… 

    …th the other variant-calling-parameters.
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  7. prettier

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    asp8200 committed Nov 28, 2022
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Commits on Dec 1, 2022

  1. Moving some config to new config-file for post-processing of vcfs

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    asp8200 committed Dec 1, 2022
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  2. renaming postprocessing_vcfs.config to post_variant_calling.config

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    asp8200 committed Dec 1, 2022
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  3. Adding INFO-field SOURCE=<input-vcf> to germline-vcf-files before con… 

    …catenating them.
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    asp8200 committed Dec 1, 2022
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  4. cleaner

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    asp8200 committed Dec 1, 2022
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  5. Fixed typo in INFO-field SOURCE in concatenated germline-vcf

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    asp8200 committed Dec 1, 2022
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Commits on Dec 5, 2022

  1. Temporary and fixed copy of mapped_joint_bam.csv in which sample-id a… 

    …nd patient-id correspond to id in bam-files. See nf-core#872
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    asp8200 committed Dec 5, 2022
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  2. WIP: Adding test of the concatenation of germline-vcfs

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    asp8200 committed Dec 5, 2022
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  3. Trying to add new tests

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    asp8200 committed Dec 5, 2022
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  4. Trying to get new test running

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    asp8200 committed Dec 5, 2022
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  5. Avoiding publishing files from GERMLINE_VCFS_CONCAT

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    asp8200 committed Dec 5, 2022
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Commits on Dec 6, 2022

  1. Skip CI-test concatenate_vcfs in conda test-env

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    asp8200 committed Dec 6, 2022
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  2. prettier

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    asp8200 committed Dec 6, 2022
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  3. Adding synonym for module BCFTOOLS_CONCAT in order to disable publish… 

    …ing from that module
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    asp8200 committed Dec 6, 2022
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  4. Updating changelog

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    asp8200 committed Dec 6, 2022
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  5. Moving config from modules.config to post_variant_calling.config

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    asp8200 committed Dec 6, 2022
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  6. fixing comment

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    asp8200 committed Dec 6, 2022
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  7. Remove code to pass back tbi-files to sarek.nf

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    asp8200 committed Dec 6, 2022
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  8. Comments added

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    asp8200 committed Dec 6, 2022
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