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Olgabot/split kmer #29

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Olgabot/split kmer #29

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phoenixAja
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This PR will allow users the ability to use the Split Kmer Analysis package for kmer comparisons. Also includes a truncate step to subsample input fastqs with seqtk.

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/kmer-similarity 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: https://github.com/nf-core/kmer-similarity/tree/master/.github/CONTRIBUTING.md

olgabot added 30 commits April 16, 2019 21:57
@olgabot
Don't lint the pipeline for now
af7b902
@olgabot
PRs to master don't need to be from dev branch
50e6739
@olgabot
Don't change to 'test' directory
2d00479
@olgabot
Change back to original direcotry
92a6f47
@olgabot
remove sra id test for now
5bb2e52
@olgabot
Add encrypted ncbi api key
a29f6be
@olgabot
un-comment sra id for test
9bc3407
@olgabot
use small sra id
56cd63c
@olgabot
Don't compute DNA if not specified
190d49f
@olgabot
Fix not_dna flag
ed6e87c
@olgabot
Update dockerfile to use olgabot/dayhoff branch"
46843fc
@olgabot
Don't install sourmash via conda for now because of version conflicts
e4ab6b9
@olgabot
Use olgabot/dayhoff tagged docker image
a688c6b
@olgabot
Use dash instead of slash in container name
d1fe3e5
@olgabot
Use olgabot/dayhoff tagged docker image
8faa0bc
@olgabot
Use olgabot-dayhoff version
c4739cd
@olgabot
Don't specify container in main.nf
589ce92
@olgabot
Put container name in nextflow.config
c4574be
@olgabot
Use Olga's dayhoff branch on sourmash to build
7f895ad
@olgabot
Add changelog
bf45db7
@olgabot
Merge pull request #26 from czbiohub/olgabot/docker-sourmash-dayhoff
035c660 
Use olgabot/dayhoff branch to build sourmash
@olgabot
Merge branch 'dev' into olgabot/fix-tests
751dfa4
@olgabot
Merge pull request #9 from czbiohub/olgabot/fix-tests
16f5e8c 
Add ncbi authentication
@olgabot
Add summary section and single ended reads
c394f78
@olgabot
Use defulat optoins
80d3f31
@olgabot
Add test configuration
045dc49
@olgabot
Add more escaped slashes
10e3b1b
@olgabot
Add docs and changelog to make 'nf-core lint' happy
e22296b
@olgabot
demux --> nf-kmer-similarity
48f7b26
@olgabot
Add outputs for execution reports
6419235
@olgabot
Indent split kmer sketching
b0fe3e6
@olgabot
Update readme with lots of info .. maybe should be in usage/docs.md ?
13c83ea
@olgabot
Add note about divisibility by 3
276e122
@olgabot
Add bash type and remove seqtk subsampling from first example
03316d9
@olgabot
Add a bunch more explanation about split kmers
bad3510
@olgabot
Add separate ska test configuration
d0314a4
@olgabot
Add note about PRs to dev
c3f07b0
@olgabot
Use nfcore/kmermaid container
5936a60
@olgabot
Add travis matrix to separate linting, etc
e2112e8
@olgabot
Remove 'env' section since this is now covered by the matrix
d872b9a
@olgabot
Add if statement to make exit code 0 to assert --splitKmer + molecule…
7476637 
…=protein did not work
@olgabot
Use --user to install with pip
41b9e1c
@olgabot
Add markdownlint
e0de975
@olgabot
Add test_ska config to git
8f99b31
@olgabot
Don't put if statement logic into FLAGS variableg
c8e3564
@olgabot
Add PR to dev on checklist
cf58ca1
@olgabot
'script' not under a dash
0ec026e
@olgabot
Can't use 'user' in this virtualenv??
952c46e
@olgabot
Organize output directories
c26c952
@olgabot
Fix markdownlint
61892ef
@olgabot
Separate out ska and sourmash outputs
a0af972
@olgabot
Add ska to environment.yml'
c72ef56
@olgabot
Update changelog with ska, seqtk
be04112
@olgabot
Merge pull request #11 from nf-core/olgabot/add-ska-to-container
f03dd69 
Olgabot/add ska to container
@olgabot
Merge branch 'dev' into olgabot/split-kmer
622116d
@olgabot
Add ska subsampling to test suite
7767621
@olgabot
Markdownlint fixes
9d77643
@olgabot
Whitespace and capitalize
54331bd
@olgabot
Add java version back to minimum nextflow version
94e4ad7
@olgabot
Remove nf-core/tools install from non-linting stuff
fbc2556
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2 participants
@phoenixAja @olgabot