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Update PGP fork with nf-core's latest changes #9

Merged
merged 251 commits into from
Jan 22, 2020
Merged

Update PGP fork with nf-core's latest changes #9

merged 251 commits into from
Jan 22, 2020

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cgpu
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@cgpu cgpu commented Jan 22, 2020

PR checklist

  • This comment contains a description of changes (with reason)
  • If you've fixed a bug or added code that should be tested, add tests!
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Make sure your code lints (nf-core lint .).
  • Documentation in docs is updated
  • CHANGELOG.md is updated
  • README.md is updated

Learn more about contributing: guidelines

apeltzer and others added 30 commits September 6, 2019 11:24
@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 (nf-core#40)
5a1c386 
* remove PublishDirMode from test profile
@maxulysse
update all tools
436af40
@maxulysse
minor updates + typo fix (nf-core#42)
0dd9461 
* minor updates + typo fix
@maxulysse
Merge pull request nf-core#41 from MaxUlysse/environmentUpdate
af40f23
@maxulysse
fix VEP automated builds
9c977de
@maxulysse
Merge pull request nf-core#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 (nf-core#45)
f1483ac 
* Add workflow figure
* Include workflow figure in readme
* Update CHANGELOG
@maxulysse
Merge branch 'dev' into docs
907a75f
@maxulysse
Merge pull request nf-core#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 nf-core#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 nf-core#55 from MaxUlysse/bioconda
f0dfba4 
update tiddit to 2.8.1
@apeltzer
Use Version 98 of Mouse
0d1e56c
cgpu and others added 28 commits December 23, 2019 17:47
@cgpu
Removes java options from MarkDupesSpark
ae2800f
@cgpu
Add java-options to MarkDupesSpark; verbosity INFO->ERROR
d83907e
@cgpu
Fixes dupe --java-options; 🤦
8780b48
@cgpu
Attempt to fix MarkDupesSpark; "--lower-case"->"-CAP"; Removed tmp
db90372
@cgpu
Adds soft-coded allocation of resources to MapReads
17b84bb
@cgpu
Initialise params for MapReads split resource alloc
7f7e0c8
@cgpu
Adds neglected curlies around params
53f68a1
@cgpu
Adds neglected \ to bash vars
894a21c
@cgpu
Adds neglected \ to bash vars
7f71929
@cgpu
WIP; MapReads optimisations
b59c278
@cgpu
Implement resource alloc between bwa and samtools
c3c0b43
@cgpu
Adds max, med soft coded resource alloc
30c031d
@cgpu
Re-labels processes (from hard coded resources to soft)
d9fc37b
@cgpu
Adds extra curlies to addrees priority of eval
563b6d8
@cgpu
Add explicit declaration of maxForks/process
e922b89
@cgpu
Update med resource allocation function
7c299bd
@cgpu
Add echo true and echo of ${bwa_cpus} and ${sort_cpus}
208f61c
@cgpu
Hard code heap in MarkDuplicatesSpark at 8g
ece5cc8
@cgpu
Correct expected output bai in MarkDupes
78764c8
@cgpu
Removes Spark versions; Not stable with low resources
48e6924
@cgpu
Removes sorting; Picard might sort?
93f6f3e
@cgpu
Do not assume sorting in MarkDupes
54c92cf
@cgpu
Adds explicit --ASSUME_SORT_ORDER unsorted
ce74cf5
@cgpu
Adds missing \\
0b6321e
@cgpu
Omits -k 23
fe9bd23
@cgpu
Bringing sorted back
bd86d0c
@cgpu
Eliminating pipes in mapping step
bd2c4bb
@cgpu
Adds bwa -k 23 and GenomeChronicler as tool (#16)
d1e60c2 
- [x] Adds -k 23 (bwa mem seed length)
- [x] Exposes as params bwa_cpus, sort_cpus
- [x] Adds GenomeChronicler in tools (sarek logic)
cgpu
cgpu commented Jan 22, 2020
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Looks good to be resolved to me.

@cgpu cgpu merged commit 002277f into PGP-UK:master Jan 22, 2020
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3 participants
@cgpu @apeltzer @maxulysse