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Olgabot/split kmer#29

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phoenixAja wants to merge 143 commits intomasterolgabot/nf-kmer-similarity:masterfrom olgabot/split-kmerolgabot/nf-kmer-similarity:olgabot/split-kmerCopy head branch name to clipboard

+517-249

Commits

Commits on Apr 17, 2019

• Don't lint the pipeline for now

  olgabot

  committed
  af7b902

• PRs to master don't need to be from dev branch

  olgabot

  committed
  50e6739

• Don't change to 'test' directory

  olgabot

  committed
  2d00479

• Change back to original direcotry

  olgabot

  committed
  92a6f47

• remove sra id test for now

  olgabot

  committed
  5bb2e52

• Add encrypted ncbi api key

  olgabot

  committed
  a29f6be

• un-comment sra id for test

  olgabot

  committed
  9bc3407

• use small sra id

  olgabot

  committed
  56cd63c

Commits on Jul 1, 2019

• Don't compute DNA if not specified

  olgabot

  committed
  190d49f

• Fix not_dna flag

  olgabot

  committed
  ed6e87c

• Update dockerfile to use olgabot/dayhoff branch"

  olgabot

  committed
  46843fc

• Don't install sourmash via conda for now because of version conflicts

  olgabot

  committed
  e4ab6b9

• Use olgabot/dayhoff tagged docker image

  olgabot

  committed
  a688c6b

• Use dash instead of slash in container name

  olgabot

  committed
  d1fe3e5

• Use olgabot/dayhoff tagged docker image

  olgabot

  committed
  8faa0bc

Commits on Jul 4, 2019

• Use olgabot-dayhoff version

  olgabot

  committed
  c4739cd

• Don't specify container in main.nf

  olgabot

  committed
  589ce92

• Put container name in nextflow.config

  olgabot

  committed
  c4574be

Commits on Jul 5, 2019

• Use Olga's dayhoff branch on sourmash to build

  olgabot

  committed
  7f895ad

• Add changelog

  olgabot

  committed
  bf45db7

• Merge pull request #26 from czbiohub/olgabot/docker-sourmash-dayhoff

  Show description for 035c660
  olgabot

  authored
  035c660

• Merge branch 'dev' into olgabot/fix-tests

  olgabot

  authored
  751dfa4

• Merge pull request #9 from czbiohub/olgabot/fix-tests

  Show description for 16f5e8c
  olgabot

  authored
  16f5e8c

• Add summary section and single ended reads

  olgabot

  committed
  c394f78

• Use defulat optoins

  olgabot

  committed
  80d3f31

• Add test configuration

  olgabot

  committed
  045dc49

• Add more escaped slashes

  olgabot

  committed
  10e3b1b

• Add docs and changelog to make 'nf-core lint' happy

  olgabot

  committed
  e22296b

• demux --> nf-kmer-similarity

  olgabot

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  48f7b26

• Add outputs for execution reports

  olgabot

  committed
  6419235

• Add date from initial commit

  olgabot

  committed
  ee85dff

• Don't lint for now

  olgabot

  committed
  55054c7

• Add .github folder

  olgabot

  committed
  eec23be

• Rename to nf-kmer-similarity

  olgabot

  committed
  342294c

• Allow PRs to master from anywhere

  olgabot

  committed
  7e0b63a

• Fix sample input processing

  olgabot

  committed
  0fd88d3

• Add comment about read_paths

  olgabot

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  902cb10

• Add a bunch of documentatin

  olgabot

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  02760aa

• Add default value for log2_sketch_size"

  olgabot

  committed
  3b1ca28

• Use dev tag on docker image (Makefile)

  olgabot

  committed
  b629b89

• Move timeline to later

  olgabot

  committed
  d38a6a0

• Use reorganizedd inputs

  olgabot

  committed
  fd76e43

• Re-add PRs to master only from dev restriction

  olgabot

  committed
  2859209

• No docker push for now

  olgabot

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  268f3cd

• Actually let's keep docker_push for now

  olgabot

  committed
  a1e766e

• Add workflow.onComplete from rnaseq

  olgabot

  committed
  df4b424

• Add code of conduct

  olgabot

  committed
  1b6bcd7

• reduce test size

  olgabot

  committed
  f4b3eee

• fix test data reading

  olgabot

  committed
  87142a9

• Don't use dayhoff encoding yet

  olgabot

  committed
  065fd28

• Fix default parameters'

  olgabot

  committed
  e1da42d

• Remove samples_*

  olgabot

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  71c7cec

• No reference genome for this summary

  olgabot

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  d9eedc7

• Remove makeHISATIndex

  olgabot

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  eeac91d

• Add scrape_software_versions

  olgabot

  committed
  47dd5bb

• Remove biohub-specific aws configuration and add manifest

  olgabot

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  6934a41

• Ignore pycache

  olgabot

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  d0eeb5c

• Add assets

  olgabot

  committed
  1abe9f2

• Remove read_paths_singles line"

  olgabot

  committed
  f6d4fe9

• Add molecule, kmer size, log2 sketch size to summary

  olgabot

  committed
  2682612

• Add one_signature_per_record to Summary

  olgabot

  committed
  45eb47c

• Remove rnaseq-specific checks in workflow.onComplete

  olgabot

  committed
  344412a

• Use dev tag on docker image

  olgabot

  committed
  3b17c09

• Use dash instead of slash in container name

  olgabot

  committed
  8d6faf6

Commits on Jul 9, 2019

• Remove trace dir stuff from beginning of nextflow.config

  olgabot

  committed
  edfb9d6

• Print name of file when reporting it isn't found

  olgabot

  committed
  31ee9f1

• Use 8GB for low memory

  olgabot

  committed
  e0e6270

• Use base config labels for memory resources

  olgabot

  committed
  df36fd7

Commits on Jul 15, 2019

• Use awsbatch and test configs

  olgabot

  committed
  a5a5022

• Remove git cruft

  olgabot

  committed
  47f8398

• Use more traditional nf-core dockerfiel

  olgabot

  committed
  46ae6e5

• Double escape sourmash compute commands

  olgabot

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  9bc14ed

Commits on Jul 17, 2019

• Actually attach custom configs

  olgabot

  committed
  13ed6b6

• Actually activate conda environment

  olgabot

  committed
  955fb45

• Add splitKmer field and start writing split kmer analysis

  olgabot

  committed
  204cd05

• Add splitKmer test configuration

  olgabot

  committed
  07349ce

• Output ska splitkmer vs sourmash sketches to separate directories

  olgabot

  committed
  598c182

• Wrap compare into splitKmer if/else

  olgabot

  committed
  41032c1

• Use separate channels for ska vs sourmash sketches

  olgabot

  committed
  e1968a8

Commits on Jul 18, 2019

• Docker still not building :(

  olgabot

  committed
  1a64c42

• Remove } and don't have docker enabled by default

  olgabot

  committed
  6095a3c

• Get .travis.yml from olgabot/dayhoff

  olgabot

  committed
  055215a

• Use nf-core dockerfile

  olgabot

  committed
  837b738

• remove manual sourmash installs

  olgabot

  committed
  9e17b66

Commits on Jul 22, 2019

• Use apt to install gcc and friends

  olgabot

  committed
  adee8cd

Commits on Jul 24, 2019

• Tests finally work!!!

  olgabot

  committed
  6c169ea

Commits on Jul 26, 2019

• with compare sketches

  phoenixAja

  committed
  832e945

Commits on Jul 30, 2019

• better outdir naming

  phoenixAja

  committed
  ee63906

Commits on Aug 1, 2019

• no pipefail

  olgabot

  committed
  2688ee9

• Comment out process shell

  olgabot

  committed
  86e5070

• Merge branch 'dev' into olgabot/dayhoff

  olgabot

  authored
  d2191dc

Commits on Aug 2, 2019

• split kmer with different ksizes

  phoenixAja

  committed
  6bd3594

Commits on Aug 4, 2019

• fixed comparisons step for multiple ksizes

  phoenixAja

  committed
  e97e72a

• changed publishDir path in comparisons to be conistant with sketch publishDir

  phoenixAja

  committed
  a8ed8f1

Commits on Aug 5, 2019

• multiple ska output files included

  phoenixAja

  committed
  3de12e9

Commits on Aug 6, 2019

• added truncate process if fastqs are too large

  phoenixAja

  committed
  3274ea0

Commits on Aug 23, 2019

• Merge pull request #1 from czbiohub/olgabot/dayhoff

  Show description for 55ac8a6
  olgabot

  authored
  55ac8a6

Commits on Aug 26, 2019

• Increase max time to 16h

  olgabot

  committed
  a574c35

Commits on Sep 10, 2019

• added docker run options

  phoenixAja

  committed
  7aa217a

• changed truncate step to use seqtk

  phoenixAja

  committed
  ea758fd

• added params.truncate to info

  phoenixAja

  committed
  9d74582

• readme and changelog updates

  phoenixAja

  committed
  992d547

• Dockerfile and environment.yml for ska portion of pipeline

  phoenixAja

  committed
  ba75d41

Commits on Sep 15, 2019

• remove scratch files to avoid confusion

  olgabot

  committed
  bce840e

Commits on Sep 18, 2019

• Build Docker image with environment

  olgabot

  committed
  8c1da07

Commits on Sep 19, 2019

• Remove docker enabled and set default kmer sizes

  olgabot

  committed
  4f5f60c

• Rename truncate --> subsample

  olgabot

  committed
  b2e2224

• Don't allow for 'protein' molecule specified when --splitKmer is set

  olgabot

  committed
  373a742

• Don't set default ksizes in nextflow config as it changes when splitkmer is set

  olgabot

  committed
  a1d70b2

• Add default value for subsampling the fastq files

  olgabot

  committed
  5069e2c

• Don't specify container in main.nf

  olgabot

  committed
  13a2103

• Remove commented code

  olgabot

  committed
  27f6df4

• Remove commented test-y stuff

  olgabot

  committed
  a1df8e4

• Indent split kmer sketching

  olgabot

  committed
  b0fe3e6

• Update readme with lots of info .. maybe should be in usage/docs.md ?

  olgabot

  committed
  13c83ea

Commits on Oct 8, 2019

• Add note about divisibility by 3

  olgabot

  committed
  276e122

• Add bash type and remove seqtk subsampling from first example

  olgabot

  committed
  03316d9

• Add a bunch more explanation about split kmers

  olgabot

  committed
  bad3510

• Add separate ska test configuration

  olgabot

  committed
  d0314a4

• Add note about PRs to dev

  olgabot

  committed
  c3f07b0

• Use nfcore/kmermaid container

  olgabot

  committed
  5936a60

• Add travis matrix to separate linting, etc

  olgabot

  committed
  e2112e8

• Remove 'env' section since this is now covered by the matrix

  olgabot

  committed
  d872b9a

• Add if statement to make exit code 0 to assert --splitKmer + molecule=protein did not work

  olgabot

  committed
  7476637

• Use --user to install with pip

  olgabot

  committed
  41b9e1c

• Add markdownlint

  olgabot

  committed
  e0de975

• Add test_ska config to git

  olgabot

  committed
  8f99b31

• Don't put if statement logic into FLAGS variableg

  olgabot

  committed
  c8e3564

• Add PR to dev on checklist

  olgabot

  committed
  cf58ca1

• 'script' not under a dash

  olgabot

  committed
  0ec026e

• Can't use 'user' in this virtualenv??

  olgabot

  committed
  952c46e

• Organize output directories

  olgabot

  committed
  c26c952

• Fix markdownlint

  olgabot

  committed
  61892ef

• Separate out ska and sourmash outputs

  olgabot

  committed
  a0af972

Commits on Oct 20, 2019

• Add ska to environment.yml'

  olgabot

  committed
  c72ef56

• Update changelog with ska, seqtk

  olgabot

  committed
  be04112

• Merge pull request #11 from nf-core/olgabot/add-ska-to-container

  Show description for f03dd69
  olgabot

  authored
  f03dd69

• Merge branch 'dev' into olgabot/split-kmer

  olgabot

  authored
  622116d

• Add ska subsampling to test suite

  olgabot

  committed
  7767621

• Markdownlint fixes

  olgabot

  committed
  9d77643

• Whitespace and capitalize

  olgabot

  committed
  54331bd

• Add java version back to minimum nextflow version

  olgabot

  committed
  94e4ad7

• Remove nf-core/tools install from non-linting stuff

  olgabot

  committed
  fbc2556