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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

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Commits

Commits on Apr 17, 2019

• Don't lint the pipeline for now

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

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• Don't change to 'test' directory

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• Change back to original direcotry

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• remove sra id test for now

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• Add encrypted ncbi api key

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• un-comment sra id for test

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• use small sra id

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Commits on Jul 1, 2019

• Don't compute DNA if not specified

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• Fix not_dna flag

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• Update dockerfile to use olgabot/dayhoff branch"

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

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• Use olgabot/dayhoff tagged docker image

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• Use dash instead of slash in container name

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• Use olgabot/dayhoff tagged docker image

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Commits on Jul 4, 2019

• Use olgabot-dayhoff version

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• Don't specify container in main.nf

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• Put container name in nextflow.config

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Commits on Jul 5, 2019

• Use Olga's dayhoff branch on sourmash to build

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• Add changelog

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

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

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

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• Add summary section and single ended reads

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• Use defulat optoins

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• Add test configuration

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• Add more escaped slashes

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

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• demux --> nf-kmer-similarity

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• Add outputs for execution reports

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• Add date from initial commit

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• Don't lint for now

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• Add .github folder

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• Rename to nf-kmer-similarity

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• Allow PRs to master from anywhere

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  7e0b63a

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• Fix sample input processing

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• Add comment about read_paths

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• Add a bunch of documentatin

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• Add default value for log2_sketch_size"

  olgabot

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• Use dev tag on docker image (Makefile)

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• Move timeline to later

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• Use reorganizedd inputs

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• Re-add PRs to master only from dev restriction

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• No docker push for now

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• Actually let's keep docker_push for now

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• Add workflow.onComplete from rnaseq

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• Add code of conduct

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  1b6bcd7

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• reduce test size

  olgabot

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  f4b3eee

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• fix test data reading

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• Don't use dayhoff encoding yet

  olgabot

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• Fix default parameters'

  olgabot

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• Remove samples_*

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• No reference genome for this summary

  olgabot

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• Remove makeHISATIndex

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• Add scrape_software_versions

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• Remove biohub-specific aws configuration and add manifest

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• Ignore pycache

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• Add assets

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• Remove read_paths_singles line"

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

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• Add one_signature_per_record to Summary

  olgabot

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• Remove rnaseq-specific checks in workflow.onComplete

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• Use dev tag on docker image

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• Use dash instead of slash in container name

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Commits on Jul 9, 2019

• Remove trace dir stuff from beginning of nextflow.config

  olgabot

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

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• Use 8GB for low memory

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• Use base config labels for memory resources

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Commits on Jul 15, 2019

• Use awsbatch and test configs

  olgabot

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• Remove git cruft

  olgabot

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• Use more traditional nf-core dockerfiel

  olgabot

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• Double escape sourmash compute commands

  olgabot

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Commits on Jul 17, 2019

• Actually attach custom configs

  olgabot

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• Actually activate conda environment

  olgabot

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  955fb45

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• Add splitKmer field and start writing split kmer analysis

  olgabot

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• Add splitKmer test configuration

  olgabot

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• Output ska splitkmer vs sourmash sketches to separate directories

  olgabot

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• Wrap compare into splitKmer if/else

  olgabot

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• Use separate channels for ska vs sourmash sketches

  olgabot

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Commits on Jul 18, 2019

• Docker still not building :(

  olgabot

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

  olgabot

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• Get .travis.yml from olgabot/dayhoff

  olgabot

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• Use nf-core dockerfile

  olgabot

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• remove manual sourmash installs

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Commits on Jul 22, 2019

• Use apt to install gcc and friends

  olgabot

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Commits on Jul 24, 2019

• Tests finally work!!!

  olgabot

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Commits on Jul 26, 2019

• with compare sketches

  phoenixAja

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Commits on Jul 30, 2019

• better outdir naming

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Commits on Aug 1, 2019

• no pipefail

  olgabot

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• Comment out process shell

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• Merge branch 'dev' into olgabot/dayhoff

  olgabot

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Commits on Aug 2, 2019

• split kmer with different ksizes

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Commits on Aug 4, 2019

• fixed comparisons step for multiple ksizes

  phoenixAja

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

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Commits on Aug 5, 2019

• multiple ska output files included

  phoenixAja

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Commits on Aug 6, 2019

• added truncate process if fastqs are too large

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Commits on Aug 23, 2019

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

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Commits on Aug 26, 2019

• Increase max time to 16h

  olgabot

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Commits on Sep 10, 2019

• added docker run options

  phoenixAja

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• changed truncate step to use seqtk

  phoenixAja

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• added params.truncate to info

  phoenixAja

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• readme and changelog updates

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• Dockerfile and environment.yml for ska portion of pipeline

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Commits on Sep 15, 2019

• remove scratch files to avoid confusion

  olgabot

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Commits on Sep 18, 2019

• Build Docker image with environment

  olgabot

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Commits on Sep 19, 2019

• Remove docker enabled and set default kmer sizes

  olgabot

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• Rename truncate --> subsample

  olgabot

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

  olgabot

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

  olgabot

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• Add default value for subsampling the fastq files

  olgabot

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• Don't specify container in main.nf

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• Remove commented code

  olgabot

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• Remove commented test-y stuff

  olgabot

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• Indent split kmer sketching

  olgabot

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

  olgabot

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Commits on Oct 8, 2019

• Add note about divisibility by 3

  olgabot

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• Add bash type and remove seqtk subsampling from first example

  olgabot

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• Add a bunch more explanation about split kmers

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• Add separate ska test configuration

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• Add note about PRs to dev

  olgabot

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• Use nfcore/kmermaid container

  olgabot

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• Add travis matrix to separate linting, etc

  olgabot

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

  olgabot

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

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• Use --user to install with pip

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• Add markdownlint

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• Add test_ska config to git

  olgabot

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• Don't put if statement logic into FLAGS variableg

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• Add PR to dev on checklist

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• 'script' not under a dash

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

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• Organize output directories

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• Fix markdownlint

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• Separate out ska and sourmash outputs

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Commits on Oct 20, 2019

• Add ska to environment.yml'

  olgabot

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• Update changelog with ska, seqtk

  olgabot

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

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

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• Add ska subsampling to test suite

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• Markdownlint fixes

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• Whitespace and capitalize

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• Add java version back to minimum nextflow version

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

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