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Absorbs changes from release 2.5.2 #7

Merged
merged 210 commits into from
Dec 23, 2019
Merged

Absorbs changes from release 2.5.2 #7

merged 210 commits into from
Dec 23, 2019

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cgpu
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@cgpu cgpu commented Dec 23, 2019 •
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Quoting changelog for Sarek 2.5.2 - Jåkkåtjkaskajekna

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[2.5.2] - Jåkkåtjkaskajekna

Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.

Added

  • #45 - Include Workflow figure in README.md
  • #46 - Add location to abstracts
  • #52 - Add support for mouse data GRCm38
  • #60 - Add no_intervals params
  • #60 - Add automatic generation of intervals file with BuildIntervals process
  • #60 - Add minimal support for minimal genome (only fasta, or fasta + knownIndels)
  • #60 - Add new processes (IndexBamFile, IndexBamRecal) to deal with optional usage of interval files and minimal genome
  • #60 - Add tests for minimal genome usage
  • #60 - Add new minimal genomes (TAIR10, EB2, >UMD3.1, bosTau8, WBcel235, ce10, CanFam3.1, canFam3, GRCz10, danRer10, >BDGP6, dm6, EquCab2, equCab2, EB1, Galgal4, galGal4, Gm01, hg38, hg19, >Mmul_1, mm10, IRGSP-1.0, CHIMP2.1.4, panTro4, Rnor_6.0, rn6, R64-1-1, sacCer3, EF2, Sbi1, Sscrofa10.2, susScr3, AGPv3) to igenomes.config
  • #61 - Add params split_fastq
  • #61 - Add test SPLITFASTQ

Changed

  • #54 - Bump version to 2.5.2dev
  • #60 - Some process (BaseRecalibrator, ApplyBQSR, Mpileup) have now optional usage of interval files
  • #60 - Update documentation
  • #71 - Update README
  • #71 - Update CHANGELOG
  • #74 - Update docs
  • #74 - Improve CI tests (both Jenkins and GitHub actions tests)
  • #74 - Move all CI from ci-extra.yml to ci.yml

Removed

  • #46 - Remove mention of old build.nf script which was included in main.nf
  • #74 - Remove download_image.sh and run_tests.sh scripts

Fixed

  • #40 - Fix issue with publishDirMode within test profile
  • #42 - Fix typos, and minor updates in README.md
  • #43 - Fix automated VEP builds with circleCI
  • #54 - Apply fixes from release 2.5.1
  • #58 - Fix issue with .interval_list file from the GATK bundle #56 that was not recognized in the CreateIntervalsBed process
  • #71 - Fix typos in CHANGELOG
  • #73 - Fix issue with label memory_max for BaseRecalibrator process #72

apeltzer and others added 30 commits May 9, 2019 14:44
@apeltzer
Get base requirements set up
ffabee7
@apeltzer
Merge remote-tracking branch 'upstream/dev' into dev
406f18c
@maxulysse
nf-core bump-version . 2.5.1dev
e223831
@maxulysse
Remove PublishDirMode from test profile (#40)
5a1c386 
* remove PublishDirMode from test profile
@maxulysse
update all tools
436af40
@maxulysse
minor updates + typo fix (#42)
0dd9461 
* minor updates + typo fix
@maxulysse
Merge pull request #41 from MaxUlysse/environmentUpdate
af40f23
@maxulysse
fix VEP automated builds
9c977de
@maxulysse
Merge pull request #43 from MaxUlysse/VEP
db7bac3 
Fix automated VEP builds
@maxulysse
add location for abstracts
f0e8225
@maxulysse
remove reference to old buil.nf script
2eef743
@maxulysse
update CHANGELOG
5df80a5
@maxulysse
Update docs/reference.md
318a7ab 
Co-Authored-By: Szilveszter Juhos <szilveszter.juhos@scilifelab.se>
@maxulysse
Update docs/reference.md
c8f748f
@maxulysse
Update docs/reference.md
4445847
@maxulysse
Worfklow (#45)
f1483ac 
* Add workflow figure
* Include workflow figure in readme
* Update CHANGELOG
@maxulysse
Merge branch 'dev' into docs
907a75f
@maxulysse
Merge pull request #46 from MaxUlysse/docs
f92710c 
Update docs
@maxulysse
add minimal genome and update some processes
2b2f7e8
@apeltzer
Merge remote-tracking branch 'upstream/dev' into dev
89116c7
@apeltzer
Start adding mouse data
065ae50
@apeltzer
Update iGenomes.config
77ec187
@apeltzer
Add tbi
db69d29
@apeltzer
Drop ASCAT files
8995981
@maxulysse
apply changes from 2.5.1 to dev
d1a2e13
@maxulysse
bump version to 2.5.2dev
a0179d4
@maxulysse
update CHANGELOG
7a6650e
@apeltzer
Merge pull request #54 from MaxUlysse/fix
416e7c8 
Apply fixes from 2.5.1 and bump to 2.5.2dev
@maxulysse
update tiddit to 2.8.1
a7cb0f1
@maxulysse
Merge pull request #55 from MaxUlysse/bioconda
f0dfba4 
update tiddit to 2.8.1
@maxulysse
Merge pull request #74 from MaxUlysse/CLEANUP
0612068 
Remove unused scripts and improve CI
@maxulysse
Merge remote-tracking branch 'upstream/dev' into sentieon
4ce48d5
@maxulysse
better comments
dc043d0
@maxulysse
fix error on channel name
68571f4
@maxulysse
fix output for MergeBamRecal
4286ef3
@maxulysse
fix MergeBamRecal output
77de228
@maxulysse
fix TSV file
72fb602
@maxulysse
update comments and docs
d896596
@maxulysse
add warning for sentieon only processes
c75a95b
@maxulysse
Merge pull request #66 from MaxUlysse/sentieon
af57a10 
Add Sentieon possibilities to Sarek
@maxulysse
nf-core bump-version . 2.5.2
09deda6
@maxulysse
manual bump-version . 2.5.2
ce8c4df
@maxulysse
update workflow image
9b2df57
@maxulysse
downgrade tools for release
bd44d7b
@maxulysse
update CHANGELOG
feb8656
@maxulysse
clean up and update workflow image
8cd87a4
@maxulysse
allow a
dee21f5
@maxulysse
fix workflow image
f561227
@maxulysse
Merge pull request #77 from MaxUlysse/2.5.2
6998e17 
Prepare for 2.5.2
@maxulysse
Apply suggestions from code review
e0f843d
@maxulysse
Apply suggestions from code review
c73d94d
@maxulysse
Update docs/output.md
eeb5fec
@maxulysse
Apply suggestions from code review
148ae3c
@maxulysse
Apply suggestions from code review
6fa8693
@maxulysse
Apply suggestions from code review
4faec93
@maxulysse
Merge branch 'master' into dev
eb22a0c
@maxulysse
Merge branch 'dev'
5c30fd8
@cgpu cgpu self-assigned this Dec 23, 2019
@cgpu cgpu merged commit 5c30fd8 into cgpu:master Dec 23, 2019
cgpu
cgpu commented Dec 23, 2019
View reviewed changes
nextflow.config
@@ -24,25 +25,24 @@ params {
genesplicer = null // genesplicer disabled
markdup_java_options = '"-Xms4000m -Xmx7g"' //Established values for markDuplicate memory consumption, see https://github.com/SciLifeLab/Sarek/pull/689 for details
nucleotidesPerSecond = 1000.0 // Default interval size
split_fastq = null // Fastq files will not be split by default
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This one looks nice!

nextflow.config
cadd_InDels_tbi = false // No CADD InDels index
cadd_WG_SNVs = false // No CADD SNVs file
cadd_WG_SNVs_tbi = false // No CADD SNVs index
pon = false // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope
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👀

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@cgpu @apeltzer @maxulysse