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ewels wants to merge 217 commits intoinitial_commitnf-core/pgdb:initial_commitfrom devnf-core/pgdb:devCopy head branch name to clipboard

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Commits on Jan 19, 2021

• change README

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• Merge pull request #1 from bigbio/master

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• configuration files added.

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• Updated the README.md

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• Merge branch 'dev' of https://github.com/bigbio/pgdb into dev

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• Updated the README.md

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• Updated the README.md

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• increase the version of the pipeline.

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Commits on Jan 20, 2021

• increase the version of the pipeline.

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• config paths solved

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• updated the .githubignore

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• change the biotypes to params -> bug fixed

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• decoy = false

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• change .gitignore

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• change .gitignore

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Commits on Jan 21, 2021

• fix error with nextflow get_software_versions

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• Merge pull request #2 from nf-core/dev

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• new ci example

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• new ci example cosmic variants

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• new ci example cosmic variants

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• small change in ci

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• small change in ci

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• small change in ci

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Commits on Feb 5, 2021

• update package version. -> 0.0.10

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• Merge pull request #3 from nf-core/dev

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• fix bug in cosmic

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• disable cosmic tests, to big in files

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Commits on Feb 7, 2021

• Process cosmic cell line data properly

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• update in py-pgatk version -> 0.0.11

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Commits on Feb 8, 2021

• update usage

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• update usage

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• Merge branch 'dev' of https://github.com/bigbio/pgdb into dev

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• add decoy to tests

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• decoy added

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• improved help message and formatting

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• Merge branch 'dev' of https://github.com/nf-core/pgdb into dev

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Commits on Feb 9, 2021

• clean database step added including stop codons processing.

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

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• clean database step added including stop codons processing.

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• removed --split_by_filter_column, issue #6

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• fixed type

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• changed default filter_column for cosmic mutations to Histology subtype 1 to allow filtering by cancer type instead of tissue name

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• clean database step added including stop codons processing.

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

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Commits on Feb 10, 2021

• changed cosmic_tissue_type to cosmic_tissue_type param

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• merge download and gunzip in same process

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

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Commits on Feb 11, 2021

• increase of version, protein_final_name used

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Commits on Feb 13, 2021

• support to download a particulr study from cbio"

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Commits on Feb 15, 2021

• fixed issue in dowloading study from a particular cbiportal study

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• added param to select columnn in cbioportal

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• increased version.

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

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• increased version.

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Commits on Feb 19, 2021

• increased version.

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Commits on Mar 5, 2021

• added task to generate proteinDB for custom vcf files

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• download dna fasta

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Commits on Mar 8, 2021

• increased py-pgatk ->0.0.16.

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• decoy options extended

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• decoy options extended

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• decoy options extended

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• decoy options extended

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• decoy options extended

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• decoy options extended

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• versions added

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Commits on Mar 11, 2021

• fix vcf params

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• fixed vcf error

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Commits on Mar 12, 2021

• changed test and decoy conf

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• change results output

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• update version

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Commits on Mar 13, 2021

• check if the gz files are ok.

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• check if the gz files are ok.

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• check if the gz files are ok.

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Commits on Mar 14, 2021

• change in vfc convert

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Commits on Mar 18, 2021

• Template update for nf-core/tools version 1.13

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Commits on Mar 19, 2021

• Template update for nf-core/tools version 1.13.1

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Commits on Mar 23, 2021

• Template update for nf-core/tools version 1.13.2

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Commits on Mar 25, 2021

• Template update for nf-core/tools version 1.13.3

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Commits on Mar 30, 2021

• fixed chromosme names and af_field in vcf

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• fixed chrM naming

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• fixed escape char in awk

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Commits on Mar 31, 2021

• Skipped gunzip of ensembl downloads because it is done by py-pgatk now

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• fixed ensembl-vcf download and code enhancement

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• updated pypgatk version in yml

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• updated yml

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Commits on Apr 7, 2021

• update the the enviroment

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• preparing for release 1.0.0

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• preparing for release 1.0.0

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• preparing for release 1.0.0

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• preparing for release 1.0.0

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• preparing for release 1.0.0

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• preparing for release 1.0.0

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• preparing for release 1.0.0

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Commits on Apr 8, 2021

• preparing for release 1.0.0

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• update json schema

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• fixing bugs

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• Merge pull request #18 from ypriverol/dev

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• changes for review release

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• Merge branch 'dev' of https://github.com/nf-core/pgdb into dev

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Commits on Apr 9, 2021

• changes for review release

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• Better examples added.

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• update for the PR review

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• update for the PR review

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• identation solved

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• Merge pull request #20 from ypriverol/dev

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• schema changed

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• Merge branch 'dev' of https://github.com/nf-core/pgdb into dev

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• ignore biotypes in the schema

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• Merge branch 'dev' of https://github.com/nf-core/pgdb into dev

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• Merge pull request #28 from ewels/main-nf-whitespace

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• small changes

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• input skip test

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• remove the intermedia files

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• Merge pull request #29 from ypriverol/dev

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• Merged changes from nf-core template

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• Merge pull request #31 from ErikDanielsson/merging-template-updates

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• feat: remove social preview image to use GitHub OpenGraph

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• Fix up markdown in output.md for cleaner rendering & ToC.

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• Refactor to use publishDir to save final output files instead of manual copyTo

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• Remove params.push_s3, minor typos

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• Merge pull request #36 from ewels/master

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