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Damageprofiler yaxis #350

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Damageprofiler yaxis #350

wants to merge 606 commits into from

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jfy133
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@jfy133 jfy133 commented Feb 10, 2020

Simply adds an additional parameter (and default) for DamageProfiler to address #336

PR checklist

  • This comment contains a description of changes (with reason)
  • 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

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

jfy133 and others added 30 commits November 20, 2019 22:14
@jfy133
Increased base requirements to 1/4 of dev. recommendation. Updated us…
60034fe 
…age and added output docs
@jfy133
CHANGELOG.md
df50ec8
@jfy133
Linting and SexDetErrmine bump
9648b4f
@jfy133
Added sanity checks
cb300af
@jfy133
Added sanity checks and removed working comments
f358f65
@jfy133
Fixing PR template
8ab452a
@apeltzer
Merge pull request #285 from jfy133/pr_template_fix
baf56af 
Pr template fix
@apeltzer
Update environment.yml
55e13a7
@jfy133
Merge pull request #19 from nf-core/dev
7bd5ceb 
getting latest dev
@jfy133
point malt test database to nf-core as now merged
0227c60
@jfy133
Added initial attempt at MaltExtract
dd95840
@jfy133
MaltExtract now correctly runs. Can't move rma6 files in MALT process…
a751beb 
… - must copy to run
@jfy133
Added github actions test
88ae704
@jfy133
Fixed githubactions
e806f17
@jfy133
Completed MaltExtract, large docs and additional doc files
811f526
@jfy133
Linting
33db7ae
@jfy133
Moar linting
516fd04
@jfy133
Fixed MaltExtract sanity check condition typos
befe9ea
@apeltzer
Merge remote-tracking branch 'upstream/dev' into dev
792bfc7
@jfy133
Trying to find resources
2f00cbb
@jfy133
Removed duplicate MALT db download step and fixed maltextract taxon_l…
7fd4d68 
…ist retrieval
@jfy133
Bumped HOPS version after bug report fixed and removed older version …
9672855 
…of nextflow from travis
@jfy133
Revert "Bumped HOPS version after bug report fixed and removed older …
ba3788b 
…version of nextflow from travis"

This reverts commit 9672855.
@jfy133
Try again to get the taxon list downloaded
714649e
@jfy133
Apparently MaltExtract downloads sources for you, lets try it
cbf494d
@jfy133
One more attempt for the night - also add travis to find more info in…
f37ce7c 
…to failures
@jfy133
Speed up testing for maltextract resources debugging
f4c5108
@jfy133
More debugging and trying to fix travis version
e7c6b33
@jfy133
It was downloading a HTML -.-
ca68454
@jfy133
Removed tag prefixes from .collect() processes and reenabled all tests
1eb1ef3
jfy133 and others added 29 commits January 31, 2020 05:53
@jfy133
Added minimum nxf ver to README
ad2c26d
@jfy133
Change name of CI to that that I think linting wants
ba15eb5
@jfy133
Update dockerfile forl inting
960d3b5
@jfy133
Minor typo fix
c026e53
@jfy133
Merge pull request #31 from jfy133/nfcore-tools-update
ea9ef95 
Get latest Nfcore tools update
@jfy133 @maxulysse
Update CHANGELOG.md
8e0ee0b 
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
@apeltzer
Merge pull request #340 from nf-core/jfy133-patch-1
986e12e 
Added minimum nxf ver to README
@apeltzer
Merge pull request #342 from jfy133/nfcore-tools-update
0cbfb36 
Nfcore tools update
@jfy133
Merge pull request #32 from nf-core/dev
df4ee97 
Get latest changes from dev!
@jfy133
Update CHANGELOG.md
629f976
@apeltzer
Merge pull request #343 from jfy133/zcat_to_cat
271e0e1 
[Merge #342 first] Performance improvement: zcat to cat
@jfy133
Merge pull request #33 from nf-core/dev
09a045b 
Dev
@jfy133
Try ! prefix to stop NF if wrong version
3e3425a
@jfy133
Update CHANGELOG.md
c9d01d1
@jfy133
Replace with internal check
5b2b107
@jfy133
! not allowed by nf-core linting currently :(
531ce95
@maxibor
add pandas dependancies
3633960
@maxibor
Merge branch 'dev' of https://github.com/nf-core/eager into prep_kraken
6fc1949
@maxibor
add kraken dep
2856d87
@jfy133
Merge pull request #346 from maxibor/prep_kraken
ba0139d 
Add pandas and Kraken2 dependancies for adding Kraken2 to eager
@jfy133
Update usage.md
3bc8cb0
@jfy133 @maxulysse
Update docs/usage.md
d1cac40 
Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
@jfy133 @maxulysse
Update docs/usage.md
a3fdcf1 
Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
@jfy133 @maxulysse
Update docs/usage.md
fb577aa 
Co-Authored-By: Maxime Garcia <max.u.garcia@gmail.com>
@jfy133 @maxulysse
Update main.nf
a51cb06 
Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se>
@jfy133
Merge pull request #348 from nf-core/jfy133-docs-patch
66a432b 
Update usage.md
@apeltzer
Merge pull request #345 from jfy133/wrong_nf_ver_fix
da407f8 
Fix NF trying to run when old version of nextflow
@jfy133
Merge pull request #34 from nf-core/dev
498f757 
sycning
@jfy133
Added ability to set Y-axis max for damageplot and change default to …
36d0519 
…hard 0.30
@jfy133 jfy133 closed this Feb 10, 2020
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5 participants
@jfy133 @apeltzer @aidaanva @ZandraFagernas @maxibor