Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Restores mapping to nf-core; Keeps gatk *Spark #84

Closed
wants to merge 70 commits into from
Closed

Restores mapping to nf-core; Keeps gatk *Spark #84

wants to merge 70 commits into from

Conversation

cgpu
Copy link

@cgpu cgpu commented Dec 23, 2019

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

cgpu and others added 30 commits October 21, 2019 07:59
@cgpu
Adds GenomeChronicler; Changes "withLabel:VEP" -> "withName:VEP"
d4201e4
@cgpu
Creates minimal bam channel with only file
48c51c9
@cgpu
C-out for testing
b0107f6
@cgpu
Added url; baseDir doee not work when on aws instance
e264e9f
@cgpu
Adds back nf-core functions; WIP testing
a3f5b3a
Adds genomechronicler; Comments out all following processes; WIP
ad06d26
Changes outpit dir; WIP
39d99e8
@cgpu
Fixes reports for GenomeChronicler; WIP (vep html not implemented)
a50fded
@cgpu
WIP; report update
982cf87
@cgpu
Absorbs path-release 2.5.1-Årjep-Ålkatjjekna 🎉
de24ddc
@cgpu
Merge branch 'nf-core-master'
299057d
@cgpu
Restores channel name from nfcore
4969b57
@cgpu
Changes MultiQC loc; enables display
034057b
@cgpu
Updated docker build used
58215f3
@cgpu
Added --resultsDir to reflect .pl changes
4b3686b
Adds --resultsDir flag requirement
804053e
@cgpu
Update to reflect PGP-UK/GenomeChronicler@65df2a9
7f59320
@cgpu
Removed resources limitation from samtools sort
ad6386f
@cgpu
Decreased --MAX_RECORDS_IN_RAM
dc6c16a
@cgpu
Restoring to default 500000
eb8615d
@cgpu
Removes java options, MAX_RECORDS_IN_RAM and TMP_DIR
eeb3078
@cgpu
Revert "Removes java options, MAX_RECORDS_IN_RAM and TMP_DIR"
ecccfd6 
This reverts commit eeb3078.
@cgpu
Added labels memory and cpus max to MarkDuplicates
0c877b8
@cgpu
Updated MAX_RECORDS_IN_RAM to extremely low value (500)
b64788d
@cgpu
Merge pull request #2 from nf-core/master
b5d9f7e 
Update README.md
@cgpu
Updates container version
6e19b5f
@cgpu
Reverts to previous container tag
ed6b72f
@cgpu
Adds spark version of MarkDuplicates and BaseRecalibrator
a378a12
@cgpu
Merge branch 'master' of https://github.com/cgpu/sarek
79ced20
@cgpu
Adds cpus and container declaration for Spark versions of gatk tools
b2b6023
cgpu and others added 25 commits November 26, 2019 12:15
@cgpu
Removes residue bwaIndex from GRCh38
c560cc1
@cgpu
Removes GenomeChronicler .dict, .fa.fai
752b953
@cgpu
Testing 2FA
e574989
@cgpu
Update nextflow.config
d2cfa80
@cgpu
Adds explicit memory definition for processes
25c74b7
@cgpu
Merge branch 'master' of cgpu/sarek
7fcdaeb
@cgpu
Adds more resources to BaseRecalibratorSpark processes
2fe8908
@cgpu
Adds less resources to BaseRecalibratorSpark processes
379a35d
@cgpu
Adds ultra many resources; To revert back after test
96fd293
@cgpu
Restricts resources; Needed for using instances with Mem.GB/vCPU rati…
46a7a5b 
…o equal to 4
@cgpu
Update resources for PGP-UK
5d54bd8
@cgpu
Addresses #3 ; Known issue with bwa | smatools pipe
3ad4a0c
@cgpu
Updates resource alloc to *Spark versions; Adds retry for MultiQC
c67c282
@cgpu
Adds new image built with PGP-UK/GenomeChronicler@5513c6f
9725de1
@cgpu
Adds verbosity INFO for debugging
97c7d5e
@cgpu
Freezes broadinstitute/gatk to 4.1.4.0
0a56cdb
@cgpu
Change GATK Spark tools verbosity to debug
e2f6d08
@cgpu
Restricts resource alloc of MarkDuplicatesSpark
88e08a2
@cgpu
Removes explicit resource alloc from bamqc (qualimap)
40bd743
@cgpu
Removes metrics file; Refer to this: https://gatkforums.broadinstitut…
d577d68 
…e.org/gatk/discussion/23441/markduplicatespark-is-slower-than-normal-markduplicates
@cgpu
Downgrades gatk from 4.1.4.0 to 4.1.3.0
ca60c30
@cgpu
Returns mapping to nfcore version 2.5.1
d353841
@cgpu
Reformats bwa mem | samtools sort command; WIP suboptimal resource …
c3a9567 
…usage
@cgpu
Addresses PGP-UK#5 ;WIP
126603a
@cgpu
Restores mapping to nf-core; Keeps gatk *Spark
70ad1e3
@cgpu cgpu requested a review from maxulysse as a code owner December 23, 2019 16:11
@cgpu cgpu closed this Dec 23, 2019
@cgpu
Copy link
Author

cgpu commented Dec 23, 2019

Intended for my fork and then PGP-UK fork. Forgot to update branches before PRing 🤦🏻‍♀️, ignore freely.

@maxulysse
Copy link
Member

No problem at all, glad that you're using sarek ;-)

@cgpu cgpu deleted the nf-core-master branch March 5, 2020 09:47
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@cgpu @maxulysse