Code

Concatenating germline vcfs#792

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maxulysse merged 36 commits intonf-core:devnf-core/sarek:devfrom asp8200:concatenating_vcfsasp8200/sarek:concatenating_vcfsCopy head branch name to clipboardDec 7, 2022

+326-21

Commits

Commits on Oct 11, 2022

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

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• Merge branch 'dev' into concatenating_vcfs

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Commits on Oct 12, 2022

• Adding the germline vcf-file from manta to the list of germline vcf-files being concatenated

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• Making sure the channel manta_vcf_tbi is defined even if manta isnt run

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Commits on Nov 10, 2022

• merge from dev

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Commits on Nov 13, 2022

• Adding support for concatenation of germline vcf-files. Now also for vcf-files from deepvariant.

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• Adding CLI-open concatenate_vcf to the schema-json

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Commits on Nov 14, 2022

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

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• WIP: Adding support for concatenation of germline vcf-files. Now also for vcf-files from tiddit.

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• Merge branch 'dev' into concatenating_vcfs

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Commits on Nov 25, 2022

• Merge branch 'dev' into concatenating_vcfs

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Commits on Nov 28, 2022

• Adding support for concatenation of vcf from mpileup

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• Changing CLI-option concatenate_vcf to concatenate_vcfs.

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• Merge branch 'dev' into concatenating_vcfs

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• Initializing CLI-option concatenate_vcfs to false.

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• Sorting concatenated germline-vcf-file and adding tbi.

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• Updating schema. Grouping the CLI-option concatenate_vcfs together with the other variant-calling-parameters.

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• prettier

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Commits on Dec 1, 2022

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

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• renaming postprocessing_vcfs.config to post_variant_calling.config

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• Adding INFO-field SOURCE=<input-vcf> to germline-vcf-files before concatenating them.

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• cleaner

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• Fixed typo in INFO-field SOURCE in concatenated germline-vcf

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Commits on Dec 5, 2022

• Temporary and fixed copy of mapped_joint_bam.csv in which sample-id and patient-id correspond to id in bam-files. See nf-core#872

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• WIP: Adding test of the concatenation of germline-vcfs

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• Trying to add new tests

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• Trying to get new test running

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• Avoiding publishing files from GERMLINE_VCFS_CONCAT

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Commits on Dec 6, 2022

• Skip CI-test concatenate_vcfs in conda test-env

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• prettier

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• Adding synonym for module BCFTOOLS_CONCAT in order to disable publishing from that module

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• Updating changelog

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• Moving config from modules.config to post_variant_calling.config

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• fixing comment

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• Remove code to pass back tbi-files to sarek.nf

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• Comments added

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