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Nf core master#8

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cgpu merged 211 commits intomastercgpu/sarek:masterfrom nf-core-mastercgpu/sarek:nf-core-masterCopy head branch name to clipboardDec 23, 2019

+5,949-1,775

Commits

Commits on May 9, 2019

• Get base requirements set up

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Commits on Sep 6, 2019

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

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Commits on Oct 8, 2019

• nf-core bump-version . 2.5.1dev

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Commits on Oct 9, 2019

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

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• update all tools

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• minor updates + typo fix (nf-core#42)

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• Merge pull request nf-core#41 from MaxUlysse/environmentUpdate

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Commits on Oct 10, 2019

• fix VEP automated builds

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• Merge pull request nf-core#43 from MaxUlysse/VEP

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Commits on Oct 11, 2019

• add location for abstracts

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• remove reference to old buil.nf script

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• update CHANGELOG

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• Update docs/reference.md

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• Update docs/reference.md

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• Update docs/reference.md

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• Worfklow (nf-core#45)

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• Merge branch 'dev' into docs

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Commits on Oct 21, 2019

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

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• add minimal genome and update some processes

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

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• Start adding mouse data

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• Update iGenomes.config

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• Add tbi

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• Drop ASCAT files

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Commits on Oct 22, 2019

• apply changes from 2.5.1 to dev

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• bump version to 2.5.2dev

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• update CHANGELOG

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Commits on Oct 23, 2019

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

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Commits on Oct 28, 2019

• update tiddit to 2.8.1

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• Merge pull request nf-core#55 from MaxUlysse/bioconda

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• Use Version 98 of Mouse

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• Add for grcm38

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• Adjust mus musculus DB

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• Annotation

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• add smallerGRCh37 and minimalGRCh37

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• use bwa aln when no knowIndels, otherwise use bwa mem, noIntervals currently in the process of being added everywhere

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Commits on Oct 29, 2019

• don't use bwa aln

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• add automatic generation of intervals file based on fastaFai file

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Commits on Oct 30, 2019

• Adjusted genomes.config

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• Should be list

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• Set genomes_base to something

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• Revert back

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• enable CreateIntervalsBed for intervals_list from GATK Bundle

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• Add proper calling list

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• Use the bed file

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• remove temp file

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• update CHANGELOG

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• Fix genome fa.fai

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• Add in mgpv5

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Commits on Oct 31, 2019

• Try short track

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• Add in species handling

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• Document new parameter species

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• Add changelog

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• Fix iGenomes stuff

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• Add in note about GRCm38

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• Merge branch 'dev' into dev

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• Fix small fai index issue

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• Merge branch 'dev' of https://github.com/apeltzer/sarek into dev

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• Adjusted quotes in genomes.config

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• And the same for igenomes

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• Better folder structure for Mouse Genome Project data

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• Minor adjustment to propoer paths

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• Apply suggestions from code review

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• Remove space

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• Move it up

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• Update CHANGELOG.md

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Commits on Nov 4, 2019

• Merge remote-tracking branch 'upstream/dev' into minimal

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• Merge pull request nf-core#52 from apeltzer/dev

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• Merge remote-tracking branch 'upstream/dev' into minimal

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• Merge pull request nf-core#58 from MaxUlysse/Intervals

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• add minimal tests

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• fix processes with no intervals

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• add comments

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• Merge remote-tracking branch 'upstream/dev' into minimal

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• params noIntervals -> no_intervals

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• sort genomes + add news

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• code polishing

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• update CHANGELOG

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Commits on Nov 5, 2019

• add split_fastq params to split the fastq files with the splitFastq() nf method

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• add tests

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• temporarely remove TIDDIT tests

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• add sention for bwa mem

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• disable docker and singularity

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• disable container

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• add fastaFai for bwamem

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• remove module samtools from label sentieon

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• fix output from bwa mem

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• fix output channel BamMapped from MapReads

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• set params.sentieon to null by default

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• add SentieonDedup process

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• fix typo

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• add fastaFai to SentieonDedup process

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• fix bam indexing

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• fix bam indexing

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• fix bam indexing

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• add SentieonBQSR

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• add label sentieon to SentieonBQSR

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• fix metrics output for SentieonBQSR

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Commits on Nov 8, 2019

• increase cpus for Sentieon BQSR

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• remove indexing

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Commits on Nov 11, 2019

• add index for dedup

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Commits on Nov 12, 2019

• bwa mem sentieon specific process

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• TSV file for sentieon Dedup

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• TSV for every step for Sentieon

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• recal -> deduped

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• fix input for TSV recalibrate

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• enable restart from recalibrate with TSV with Sentieon

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• fix sention variant calling from mapping and recalibrate

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• code polishing

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• add dump tag for imput sample

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• add dump tag for bamDedupedSentieon

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• code polishing

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• code polishing

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• code polishing

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• code polishing

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• remove when statement

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• fix typo

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• remove tsv for recalibrate with sentieon

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• add dnascope dnaseq

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• fix dnascope

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Commits on Nov 13, 2019

• add TNscope process

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• fix TNscope output

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• add pon for TNscope

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• add params.pon_index

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• add annotation for sention DNAseq, DNAscope, TNscope

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• add default pon_index

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• typo

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• fix typo

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• improve automatic annotation

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• typo

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• typo

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• add condition on when statement on TNscope

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Commits on Nov 14, 2019

• clean up

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• code polish

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Commits on Nov 15, 2019

• add CODEOWNERS file

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Commits on Nov 18, 2019

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

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Commits on Nov 19, 2019

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

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Commits on Nov 20, 2019

• remove munin sentieon specific configs from config

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• load sarek specific config

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• update path to specific config

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Commits on Nov 28, 2019

• update docs

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• remove Freebayes

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• update workflow image

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• remove old logo

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• Merge remote-tracking branch 'upstream/dev' into splitFastq

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Commits on Nov 29, 2019

• fix tests

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• add docs about params split_fastq

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• update CHANGELOG

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Commits on Dec 2, 2019

• improve docs

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• more tests but less NF versions

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• actually run the tests

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• typo

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• Merge pull request nf-core#61 from MaxUlysse/splitFastq

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• Merge branch 'dev' into minimal

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• simplify configs

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• add test for mpileup

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• Merge remote-tracking branch 'upstream/dev' into DOCS

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Commits on Dec 3, 2019

• go crazy with tests

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• fix tests

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• includ test.config

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• restore FreeBayes

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• remove label memory_max from BaseRecalibrator process to fix nf-core#72

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Commits on Dec 4, 2019

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

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• Merge branch 'dev' into DOCS

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• Merge pull request nf-core#71 from MaxUlysse/DOCS

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Commits on Dec 6, 2019

• Merge remote-tracking branch 'upstream/dev' into minimal

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• add --skipQC all and --tools Manta,mpileup,Strelka to minimal genome tests

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• update Nextflow version

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• update Nextflow version

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• update Nextflow

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• add --step annotation to profile

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• don't need to specify step here

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• move params initalization

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• add docs

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• fix markdownlint

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• more complete docs + sort genomes

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• Merge pull request nf-core#60 from MaxUlysse/minimal

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Commits on Dec 9, 2019

• improve tests

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• update docs

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• update CHANGELOG

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• improve script

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• fix tests

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• better comments

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• Merge pull request nf-core#74 from MaxUlysse/CLEANUP

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• Merge remote-tracking branch 'upstream/dev' into sentieon

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• better comments

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• fix error on channel name

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• fix output for MergeBamRecal

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Commits on Dec 10, 2019

• fix MergeBamRecal output

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• fix TSV file

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• update comments and docs

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• add warning for sentieon only processes

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• Merge pull request nf-core#66 from MaxUlysse/sentieon

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Commits on Dec 11, 2019

• nf-core bump-version . 2.5.2

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• manual bump-version . 2.5.2

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• update workflow image

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• update CHANGELOG

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Commits on Dec 12, 2019

• clean up and update workflow image

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• allow a

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• Merge pull request nf-core#77 from MaxUlysse/2.5.2

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• Update docs/output.md

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Commits on Dec 16, 2019

• Merge branch 'master' into dev

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Commits on Dec 23, 2019

• Restores mapping to nf-core; Keeps gatk *Spark

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