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Nf core master #8

Merged
merged 211 commits into from
Dec 23, 2019
Merged

Nf core master #8

merged 211 commits into from
Dec 23, 2019

Commits on May 9, 2019

  1. Get base requirements set up

    @apeltzer
    apeltzer committed May 9, 2019
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Commits on Sep 6, 2019

  1. Merge remote-tracking branch 'upstream/dev' into dev

    @apeltzer
    apeltzer committed Sep 6, 2019
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Commits on Oct 8, 2019

  1. nf-core bump-version . 2.5.1dev

    @maxulysse
    maxulysse committed Oct 8, 2019
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Commits on Oct 9, 2019

  1. Remove PublishDirMode from test profile (nf-core#40) 

    * remove PublishDirMode from test profile
    @maxulysse
    maxulysse authored Oct 9, 2019
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  2. update all tools

    @maxulysse
    maxulysse committed Oct 9, 2019
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  3. minor updates + typo fix (nf-core#42) 

    * minor updates + typo fix
    @maxulysse
    maxulysse authored Oct 9, 2019
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  4. Merge pull request nf-core#41 from MaxUlysse/environmentUpdate

    @maxulysse
    maxulysse authored Oct 9, 2019
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Commits on Oct 10, 2019

  1. fix VEP automated builds

    @maxulysse
    maxulysse committed Oct 10, 2019
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  2. Merge pull request nf-core#43 from MaxUlysse/VEP 

    Fix automated VEP builds
    @maxulysse
    maxulysse authored Oct 10, 2019
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Commits on Oct 11, 2019

  1. add location for abstracts

    @maxulysse
    maxulysse committed Oct 11, 2019
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  2. remove reference to old buil.nf script

    @maxulysse
    maxulysse committed Oct 11, 2019
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Oct 11, 2019
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  4. Update docs/reference.md 

    Co-Authored-By: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
    @maxulysse
    maxulysse and Szilveszter Juhos authored Oct 11, 2019
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  5. Update docs/reference.md

    @maxulysse
    maxulysse authored Oct 11, 2019
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  6. Update docs/reference.md

    @maxulysse
    maxulysse authored Oct 11, 2019
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  7. Worfklow (nf-core#45) 

    * Add workflow figure
* Include workflow figure in readme
* Update CHANGELOG
    @maxulysse
    maxulysse authored Oct 11, 2019
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  8. Merge branch 'dev' into docs

    @maxulysse
    maxulysse authored Oct 11, 2019
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Commits on Oct 21, 2019

  1. Merge pull request nf-core#46 from MaxUlysse/docs 

    Update docs
    @maxulysse
    maxulysse authored Oct 21, 2019
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  2. add minimal genome and update some processes

    @maxulysse
    maxulysse committed Oct 21, 2019
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  3. Merge remote-tracking branch 'upstream/dev' into dev

    @apeltzer
    apeltzer committed Oct 21, 2019
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  4. Start adding mouse data

    @apeltzer
    apeltzer committed Oct 21, 2019
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  5. Update iGenomes.config

    @apeltzer
    apeltzer committed Oct 21, 2019
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  6. Add tbi

    @apeltzer
    apeltzer committed Oct 21, 2019
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  7. Drop ASCAT files

    @apeltzer
    apeltzer committed Oct 21, 2019
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Commits on Oct 22, 2019

  1. apply changes from 2.5.1 to dev

    @maxulysse
    maxulysse committed Oct 22, 2019
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  2. bump version to 2.5.2dev

    @maxulysse
    maxulysse committed Oct 22, 2019
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Oct 22, 2019
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Commits on Oct 23, 2019

  1. Merge pull request nf-core#54 from MaxUlysse/fix 

    Apply fixes from 2.5.1 and bump to 2.5.2dev
    @apeltzer
    apeltzer authored Oct 23, 2019
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Commits on Oct 28, 2019

  1. update tiddit to 2.8.1

    @maxulysse
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  2. Merge pull request nf-core#55 from MaxUlysse/bioconda 

    update tiddit to 2.8.1
    @maxulysse
    maxulysse authored Oct 28, 2019
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  3. Use Version 98 of Mouse

    @apeltzer
    apeltzer committed Oct 28, 2019
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  4. Add for grcm38

    @apeltzer
    apeltzer committed Oct 28, 2019
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  5. Adjust mus musculus DB

    @apeltzer
    apeltzer committed Oct 28, 2019
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  6. Annotation

    @apeltzer
    apeltzer committed Oct 28, 2019
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  7. add smallerGRCh37 and minimalGRCh37

    @maxulysse
    maxulysse committed Oct 28, 2019
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  8. use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals cu… 

    …rrently in the process of being added everywhere
    @maxulysse
    maxulysse committed Oct 28, 2019
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Commits on Oct 29, 2019

  1. don't use bwa aln

    @maxulysse
    maxulysse committed Oct 29, 2019
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  2. add automatic generation of intervals file based on fastaFai file

    @maxulysse
    maxulysse committed Oct 29, 2019
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Commits on Oct 30, 2019

  1. Adjusted genomes.config

    @apeltzer
    apeltzer committed Oct 30, 2019
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  2. Should be list

    @apeltzer
    apeltzer committed Oct 30, 2019
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  3. Set genomes_base to something

    @apeltzer
    apeltzer committed Oct 30, 2019
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  4. Revert back

    @apeltzer
    apeltzer committed Oct 30, 2019
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  5. enable CreateIntervalsBed for intervals_list from GATK Bundle

    @maxulysse
    maxulysse committed Oct 30, 2019
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  6. Add proper calling list

    @apeltzer
    apeltzer committed Oct 30, 2019
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  7. Use the bed file

    @apeltzer
    apeltzer committed Oct 30, 2019
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  8. remove temp file

    @maxulysse
    maxulysse committed Oct 30, 2019
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  9. update CHANGELOG

    @maxulysse
    maxulysse committed Oct 30, 2019
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  10. Fix genome fa.fai

    @apeltzer
    apeltzer committed Oct 30, 2019
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  11. Add in mgpv5

    @apeltzer
    apeltzer committed Oct 30, 2019
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Commits on Oct 31, 2019

  1. Try short track

    @apeltzer
    apeltzer committed Oct 31, 2019
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  2. Add in species handling

    @apeltzer
    apeltzer committed Oct 31, 2019
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  3. Document new parameter species

    @apeltzer
    apeltzer committed Oct 31, 2019
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  4. Add changelog

    @apeltzer
    apeltzer committed Oct 31, 2019
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  5. Fix iGenomes stuff

    @apeltzer
    apeltzer committed Oct 31, 2019
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  6. Add in note about GRCm38

    @apeltzer
    apeltzer committed Oct 31, 2019
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  7. Merge branch 'dev' into dev

    @maxulysse
    maxulysse authored Oct 31, 2019
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  8. Fix small fai index issue

    @apeltzer
    apeltzer committed Oct 31, 2019
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  9. Merge branch 'dev' of https://github.com/apeltzer/sarek into dev

    @apeltzer
    apeltzer committed Oct 31, 2019
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  10. Adjusted quotes in genomes.config

    @apeltzer
    apeltzer committed Oct 31, 2019
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  11. And the same for igenomes

    @apeltzer
    apeltzer committed Oct 31, 2019
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  12. Better folder structure for Mouse Genome Project data

    @apeltzer
    apeltzer committed Oct 31, 2019
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  13. Minor adjustment to propoer paths

    @apeltzer
    apeltzer committed Oct 31, 2019
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  14. Apply suggestions from code review 

    Add changes by Maxime

Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
    @apeltzer @maxulysse
    apeltzer and maxulysse authored Oct 31, 2019
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  15. Remove space

    @apeltzer
    apeltzer committed Oct 31, 2019
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  16. Move it up

    @apeltzer
    apeltzer committed Oct 31, 2019
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  17. Update CHANGELOG.md 

    Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
    @apeltzer @maxulysse
    apeltzer and maxulysse authored Oct 31, 2019
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Commits on Nov 4, 2019

  1. Merge remote-tracking branch 'upstream/dev' into minimal

    @maxulysse
    maxulysse committed Nov 4, 2019
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  2. Merge pull request nf-core#52 from apeltzer/dev 

    Mouse Genome Support
    @maxulysse
    maxulysse authored Nov 4, 2019
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  3. Merge remote-tracking branch 'upstream/dev' into minimal

    @maxulysse
    maxulysse committed Nov 4, 2019
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  4. Merge pull request nf-core#58 from MaxUlysse/Intervals 

    Fix issue with `wholegenome.interval_list` file
    @maxulysse
    maxulysse authored Nov 4, 2019
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  5. add minimal tests

    @maxulysse
    maxulysse committed Nov 4, 2019
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  6. fix processes with no intervals

    @maxulysse
    maxulysse committed Nov 4, 2019
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  7. add comments

    @maxulysse
    maxulysse committed Nov 4, 2019
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  8. Merge remote-tracking branch 'upstream/dev' into minimal

    @maxulysse
    maxulysse committed Nov 4, 2019
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  9. params noIntervals -> no_intervals

    @maxulysse
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  10. sort genomes + add news

    @maxulysse
    maxulysse committed Nov 4, 2019
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  11. code polishing

    @maxulysse
    maxulysse committed Nov 4, 2019
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  12. update CHANGELOG

    @maxulysse
    maxulysse committed Nov 4, 2019
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Commits on Nov 5, 2019

  1. add split_fastq params to split the fastq files with the splitFastq()… 

    … nf method
    @maxulysse
    maxulysse committed Nov 5, 2019
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  2. add tests

    @maxulysse
    maxulysse committed Nov 5, 2019
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  3. temporarely remove TIDDIT tests

    @maxulysse
    maxulysse committed Nov 5, 2019
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  4. add sention for bwa mem

    @maxulysse
    maxulysse committed Nov 5, 2019
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  5. disable docker and singularity

    @maxulysse
    maxulysse committed Nov 5, 2019
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  6. disable container

    @maxulysse
    maxulysse committed Nov 5, 2019
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  7. add fastaFai for bwamem

    @maxulysse
    maxulysse committed Nov 5, 2019
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  8. remove module samtools from label sentieon

    @maxulysse
    maxulysse committed Nov 5, 2019
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  9. fix output from bwa mem

    @maxulysse
    maxulysse committed Nov 5, 2019
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  10. fix output channel BamMapped from MapReads

    @maxulysse
    maxulysse committed Nov 5, 2019
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  11. set params.sentieon to null by default

    @maxulysse
    maxulysse committed Nov 5, 2019
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  12. add SentieonDedup process

    @maxulysse
    maxulysse committed Nov 5, 2019
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  13. fix typo

    @maxulysse
    maxulysse committed Nov 5, 2019
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  14. add fastaFai to SentieonDedup process

    @maxulysse
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  15. fix bam indexing

    @maxulysse
    maxulysse committed Nov 5, 2019
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  16. fix bam indexing

    @maxulysse
    maxulysse committed Nov 5, 2019
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  17. fix bam indexing

    @maxulysse
    maxulysse committed Nov 5, 2019
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  18. add SentieonBQSR

    @maxulysse
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  19. add label sentieon to SentieonBQSR

    @maxulysse
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  20. fix metrics output for SentieonBQSR

    @maxulysse
    maxulysse committed Nov 5, 2019
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Commits on Nov 8, 2019

  1. increase cpus for Sentieon BQSR

    @maxulysse
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  2. remove indexing

    @maxulysse
    maxulysse committed Nov 8, 2019
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Commits on Nov 11, 2019

  1. add index for dedup

    @maxulysse
    maxulysse committed Nov 11, 2019
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Commits on Nov 12, 2019

  1. bwa mem sentieon specific process

    @maxulysse
    maxulysse committed Nov 12, 2019
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  2. TSV file for sentieon Dedup

    @maxulysse
    maxulysse committed Nov 12, 2019
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  3. TSV for every step for Sentieon

    @maxulysse
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  4. recal -> deduped

    @maxulysse
    maxulysse committed Nov 12, 2019
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  5. fix input for TSV recalibrate

    @maxulysse
    maxulysse committed Nov 12, 2019
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  6. enable restart from recalibrate with TSV with Sentieon

    @maxulysse
    maxulysse committed Nov 12, 2019
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  7. fix sention variant calling from mapping and recalibrate

    @maxulysse
    maxulysse committed Nov 12, 2019
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  8. code polishing

    @maxulysse
    maxulysse committed Nov 12, 2019
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  9. add dump tag for imput sample

    @maxulysse
    maxulysse committed Nov 12, 2019
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  10. add dump tag for bamDedupedSentieon

    @maxulysse
    maxulysse committed Nov 12, 2019
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  11. code polishing

    @maxulysse
    maxulysse committed Nov 12, 2019
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  12. code polishing

    @maxulysse
    maxulysse committed Nov 12, 2019
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  13. code polishing

    @maxulysse
    maxulysse committed Nov 12, 2019
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  14. code polishing

    @maxulysse
    maxulysse committed Nov 12, 2019
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  15. remove when statement

    @maxulysse
    maxulysse committed Nov 12, 2019
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  16. fix typo

    @maxulysse
    maxulysse committed Nov 12, 2019
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  17. remove tsv for recalibrate with sentieon

    @maxulysse
    maxulysse committed Nov 12, 2019
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  18. add dnascope dnaseq

    @maxulysse
    maxulysse committed Nov 12, 2019
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  19. fix dnascope

    @maxulysse
    maxulysse committed Nov 12, 2019
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Commits on Nov 13, 2019

  1. add TNscope process

    @maxulysse
    maxulysse committed Nov 13, 2019
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  2. fix TNscope output

    @maxulysse
    maxulysse committed Nov 13, 2019
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  3. add pon for TNscope

    @maxulysse
    maxulysse committed Nov 13, 2019
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  4. add params.pon_index

    @maxulysse
    maxulysse committed Nov 13, 2019
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  5. add annotation for sention DNAseq, DNAscope, TNscope

    @maxulysse
    maxulysse committed Nov 13, 2019
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  6. add default pon_index

    @maxulysse
    maxulysse committed Nov 13, 2019
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  7. typo

    @maxulysse
    maxulysse committed Nov 13, 2019
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  8. fix typo

    @maxulysse
    maxulysse committed Nov 13, 2019
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  9. improve automatic annotation

    @maxulysse
    maxulysse committed Nov 13, 2019
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  10. typo

    @maxulysse
    maxulysse committed Nov 13, 2019
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  11. typo

    @maxulysse
    maxulysse committed Nov 13, 2019
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  12. add condition on when statement on TNscope

    @maxulysse
    maxulysse committed Nov 13, 2019
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Commits on Nov 14, 2019

  1. clean up

    @maxulysse
    maxulysse committed Nov 14, 2019
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  2. code polish

    @maxulysse
    maxulysse committed Nov 14, 2019
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Commits on Nov 15, 2019

  1. add CODEOWNERS file

    @maxulysse
    maxulysse committed Nov 15, 2019
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Commits on Nov 18, 2019

  1. add when statement on all sentieon processes with params.sentieon

    @maxulysse
    maxulysse committed Nov 18, 2019
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Commits on Nov 19, 2019

  1. Merge pull request nf-core#69 from MaxUlysse/CODEOWNERS 

    add CODEOWNERS file
    @maxulysse
    maxulysse authored Nov 19, 2019
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Commits on Nov 20, 2019

  1. remove munin sentieon specific configs from config

    @maxulysse
    maxulysse committed Nov 20, 2019
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  2. load sarek specific config

    @maxulysse
    maxulysse committed Nov 20, 2019
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  3. update path to specific config

    @maxulysse
    maxulysse committed Nov 20, 2019
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Commits on Nov 28, 2019

  1. update docs

    @maxulysse
    maxulysse committed Nov 28, 2019
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  2. remove Freebayes

    @maxulysse
    maxulysse committed Nov 28, 2019
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  3. update workflow image

    @maxulysse
    maxulysse committed Nov 28, 2019
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  4. remove old logo

    @maxulysse
    maxulysse committed Nov 28, 2019
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  5. Merge remote-tracking branch 'upstream/dev' into splitFastq

    @maxulysse
    maxulysse committed Nov 28, 2019
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Commits on Nov 29, 2019

  1. fix tests

    @maxulysse
    maxulysse committed Nov 29, 2019
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  2. add docs about params split_fastq

    @maxulysse
    maxulysse committed Nov 29, 2019
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Nov 29, 2019
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Commits on Dec 2, 2019

  1. improve docs

    @maxulysse
    maxulysse committed Dec 2, 2019
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  2. more tests but less NF versions

    @maxulysse
    maxulysse committed Dec 2, 2019
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  3. actually run the tests

    @maxulysse
    maxulysse committed Dec 2, 2019
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  4. typo

    @maxulysse
    maxulysse committed Dec 2, 2019
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  5. Merge pull request nf-core#61 from MaxUlysse/splitFastq 

    add split_fastq
    @maxulysse
    maxulysse authored Dec 2, 2019
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  6. Merge branch 'dev' into minimal

    @maxulysse
    maxulysse authored Dec 2, 2019
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  7. simplify configs

    @maxulysse
    maxulysse committed Dec 2, 2019
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  8. add test for mpileup

    @maxulysse
    maxulysse committed Dec 2, 2019
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  9. Merge remote-tracking branch 'upstream/dev' into DOCS

    @maxulysse
    maxulysse committed Dec 2, 2019
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Commits on Dec 3, 2019

  1. go crazy with tests

    @maxulysse
    maxulysse committed Dec 3, 2019
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  2. fix tests

    @maxulysse
    maxulysse committed Dec 3, 2019
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  3. includ test.config

    @maxulysse
    maxulysse committed Dec 3, 2019
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  4. restore FreeBayes

    @maxulysse
    maxulysse committed Dec 3, 2019
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  5. remove label memory_max from BaseRecalibrator process to fix nf-core#72

    @maxulysse
    maxulysse committed Dec 3, 2019
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Commits on Dec 4, 2019

  1. Merge pull request nf-core#73 from MaxUlysse/MemoryBaseRecalibrator 

    Remove label memory_max from BaseRecalibrator process
    @maxulysse
    maxulysse authored Dec 4, 2019
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  2. Merge branch 'dev' into DOCS

    @maxulysse
    maxulysse authored Dec 4, 2019
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  3. Merge pull request nf-core#71 from MaxUlysse/DOCS 

    Improve tests and docs
    @maxulysse
    maxulysse authored Dec 4, 2019
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Commits on Dec 6, 2019

  1. Merge remote-tracking branch 'upstream/dev' into minimal

    @maxulysse
    maxulysse committed Dec 6, 2019
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  2. add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome … 

    …tests
    @maxulysse
    maxulysse committed Dec 6, 2019
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  3. update Nextflow version

    @maxulysse
    maxulysse committed Dec 6, 2019
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  4. update Nextflow version

    @maxulysse
    maxulysse committed Dec 6, 2019
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  5. update Nextflow

    @maxulysse
    maxulysse committed Dec 6, 2019
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  6. add --step annotation to profile

    @maxulysse
    maxulysse committed Dec 6, 2019
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  7. don't need to specify step here

    @maxulysse
    maxulysse committed Dec 6, 2019
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  8. move params initalization

    @maxulysse
    maxulysse committed Dec 6, 2019
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  9. add docs

    @maxulysse
    maxulysse committed Dec 6, 2019
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  10. fix markdownlint

    @maxulysse
    maxulysse committed Dec 6, 2019
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  11. more complete docs + sort genomes

    @maxulysse
    maxulysse committed Dec 6, 2019
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  12. Merge pull request nf-core#60 from MaxUlysse/minimal 

    Add minimal genomes possibilities
    @maxulysse
    maxulysse authored Dec 6, 2019
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Commits on Dec 9, 2019

  1. improve tests

    @maxulysse
    maxulysse committed Dec 9, 2019
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  2. update docs

    @maxulysse
    maxulysse committed Dec 9, 2019
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  3. update CHANGELOG

    @maxulysse
    maxulysse committed Dec 9, 2019
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  4. improve script

    @maxulysse
    maxulysse committed Dec 9, 2019
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  5. fix tests

    @maxulysse
    maxulysse committed Dec 9, 2019
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  6. better comments

    @maxulysse
    maxulysse committed Dec 9, 2019
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  7. Merge pull request nf-core#74 from MaxUlysse/CLEANUP 

    Remove unused scripts and improve CI
    @maxulysse
    maxulysse authored Dec 9, 2019
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  8. Merge remote-tracking branch 'upstream/dev' into sentieon

    @maxulysse
    maxulysse committed Dec 9, 2019
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  9. better comments

    @maxulysse
    maxulysse committed Dec 9, 2019
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  10. fix error on channel name

    @maxulysse
    maxulysse committed Dec 9, 2019
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  11. fix output for MergeBamRecal

    @maxulysse
    maxulysse committed Dec 9, 2019
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Commits on Dec 10, 2019

  1. fix MergeBamRecal output

    @maxulysse
    maxulysse committed Dec 10, 2019
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  2. fix TSV file

    @maxulysse
    maxulysse committed Dec 10, 2019
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  3. update comments and docs

    @maxulysse
    maxulysse committed Dec 10, 2019
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  4. add warning for sentieon only processes

    @maxulysse
    maxulysse committed Dec 10, 2019
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  5. Merge pull request nf-core#66 from MaxUlysse/sentieon 

    Add Sentieon possibilities to Sarek
    @maxulysse
    maxulysse authored Dec 10, 2019
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Commits on Dec 11, 2019

  1. nf-core bump-version . 2.5.2

    @maxulysse
    maxulysse committed Dec 11, 2019
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  2. manual bump-version . 2.5.2

    @maxulysse
    maxulysse committed Dec 11, 2019
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  3. update workflow image

    @maxulysse
    maxulysse committed Dec 11, 2019
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  4. downgrade tools for release

    @maxulysse
    maxulysse committed Dec 11, 2019
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  5. update CHANGELOG

    @maxulysse
    maxulysse committed Dec 11, 2019
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Commits on Dec 12, 2019

  1. clean up and update workflow image

    @maxulysse
    maxulysse committed Dec 12, 2019
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  2. allow a

    @maxulysse
    maxulysse committed Dec 12, 2019
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  3. fix workflow image

    @maxulysse
    maxulysse committed Dec 12, 2019
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  4. Merge pull request nf-core#77 from MaxUlysse/2.5.2 

    Prepare for 2.5.2
    @maxulysse
    maxulysse authored Dec 12, 2019
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  5. Apply suggestions from code review

    @maxulysse
    maxulysse authored Dec 12, 2019
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  6. Apply suggestions from code review

    @maxulysse
    maxulysse authored Dec 12, 2019
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  7. Update docs/output.md

    @maxulysse
    maxulysse authored Dec 12, 2019
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Commits on Dec 13, 2019

  1. Apply suggestions from code review

    @maxulysse
    maxulysse authored Dec 13, 2019
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  2. Apply suggestions from code review

    @maxulysse
    maxulysse authored Dec 13, 2019
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  3. Apply suggestions from code review

    @maxulysse
    maxulysse authored Dec 13, 2019
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Commits on Dec 16, 2019

  1. Merge branch 'master' into dev

    @maxulysse
    maxulysse committed Dec 16, 2019
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  2. Merge branch 'dev'

    @maxulysse
    maxulysse committed Dec 16, 2019
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Commits on Dec 23, 2019

  1. Restores mapping to nf-core; Keeps gatk *Spark

    @cgpu
    cgpu committed Dec 23, 2019
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