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ellisrichardj / BovTB-nf

Nextflow script for processing WGS data
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Fix inclusivity test #26

Closed ellisrichardj closed 3 years ago

ellisrichardj commented 3 years ago

The accession column was idenitcal for all rows so corrected this and removed the duplicate rows. The inclusivity tests are now passing.

afishman commented 3 years ago

Sounds excellent. Looks like you're trying to merge into the old.repo. It's annoying GitHub doesn't seem to have a way of setting the default merge branch.

On Thu, 14 Jan 2021, 11:02 pm Richard Ellis, notifications@github.com wrote:

The accession column was idenitcal for all rows so corrected this and removed the duplicate rows. The inclusivity tests are now passing.

You can view, comment on, or merge this pull request online at:

https://github.com/ellisrichardj/BovTB-nf/pull/26 Commit Summary

  • Add .circleci/config.yml
  • Update Readme.md
  • Merge pull request #1 from APHA-CSU/circleci-project-setup
  • docker build job
  • disabling docker layer caching
  • cleaning up circleci config
  • updating readme
  • testing error in dockerfile
  • touching dockerfile
  • removing error line in Dockerfile
  • updating Readme.md
  • Merge pull request #2 from APHA-CSU/docker-build
  • adding .gitignore
  • updating .gitignore
  • setting Kraken paths in Dockerfile
  • biotools path
  • embedding Install_dependancies.sh into Dockerfile
  • including kraken2 db
  • upgrading to jdk11, fixing Kraken2db path
  • Dockerfile CMD nextflow run
  • putting WGSCluster and BovPos cvs in outdir
  • assert first csv row py
  • minimal test data
  • run-pipeline-docker.sh
  • print todays results
  • renaming minimal read pair
  • validation
  • fixing config.yml
  • CIRCLE_BRANCH tag
  • setting wd on job
  • comments
  • test script as circleci replacement
  • job script
  • fixing integration tests
  • Add extra fork for VarCall process as this is the most time consuming
  • adding .gitignore
  • updating .gitignore
  • setting Kraken paths in Dockerfile
  • biotools path
  • embedding Install_dependancies.sh into Dockerfile
  • including kraken2 db
  • upgrading to jdk11, fixing Kraken2db path
  • Dockerfile CMD nextflow run
  • putting WGSCluster and BovPos cvs in outdir
  • assert first csv row py
  • minimal test data
  • run-pipeline-docker.sh
  • print todays results
  • renaming minimal read pair
  • validation
  • fixing config.yml
  • CIRCLE_BRANCH tag
  • setting wd on job
  • comments
  • test script as circleci replacement
  • job script
  • fixing integration tests
  • Update Readme.md
  • Update Readme.md
  • Update bov-tb
  • restrict memory for AssignClusterCSS process
  • Filter vcf to only descriminatory positions for cluster assignment
  • Remove dependancy location
  • Corrected poor spelling
  • Merge branch 'Restrict-Memory' of https://github.com/APHA-CSU/BovTB-nf into Restrict-Memory
  • adding second kraken2db
  • circleCI build artifacts + DRYing up minimal-test-job
  • Merge branch 'master' into Restrict-Memory to fully update
  • upgrading to Bracken 2.6.0
  • memory map on kraken2
  • circleci syntax
  • lowmem --memory-map during minimal-test
  • Dockerfile: vim, nano and updating kraken2dbs
  • sp
  • fixing merge conflicts
  • Merge pull request #4 from APHA-CSU/Restrict-Memory
  • Merge branch 'master' into kraken2-testdb
  • lowmem option bug
  • inclusivity test
  • Merge pull request #5 from APHA-CSU/IDnonbovis-lowmem
  • adding bc to Dockerfile
  • set -e on ReadStats.sh
  • testing for B6-16
  • obliterate fastq
  • updating .gitignore
  • adding work to gitignore
  • obliterate the fastq quality
  • adding bc to Dockerfile
  • adding Results to .gitignore
  • moving Dockerfile nextflow settings into nextflow.config@
  • ignoring Braken errors
  • set uniform fastq quality
  • quality test
  • quality test
  • downloading fastq files for quality data
  • quality test working
  • fixing minimal pipeline
  • adding quality test to local test runner
  • adding circleci job for quality
  • renaming files
  • tinyreads bug
  • cleaning up
  • Update Readme.md
  • Update Readme.md
  • Update tinyreads.bash
  • Update set_uniform_fastq_quality.py
  • Update tinyreads.bash
  • Update Readme.md
  • Update Readme.md
  • Merge pull request #6 from APHA-CSU/quality-test
  • input arguments to quality
  • cleaning up tests
  • circleci makes the dirs
  • setting the name
  • reducing quality code
  • nargs on filepath
  • slightly neater num reads
  • setting up aliases
  • comments
  • print todays cluster alias
  • parameterising config.yml
  • low and adequate cases
  • deleting old install files
  • debugging cleanup
  • toadys WGS cluster bug
  • fixing merge conflicts
  • nextflow test
  • moving Dockerfile into docker/
  • updating config.yml to new Dockerfile
  • referencing Dockerfile exactly
  • Merge pull request #7 from APHA-CSU/cleanup
  • Include flag for low quality sequence data
  • Add explanation comment
  • alter order of elifs
  • Explicitily call bash and use double square brackets for test
  • Change expected outcome for tiny reads test
  • Corrected comment
  • Merge pull request #8 from APHA-CSU/LowQualFlag
  • updating reads links
  • updating links for qualitytest
  • Merge pull request #9 from APHA-CSU/qualitytest-update
  • renaming bov-tb to run-pipeline
  • lod test
  • additional lod files
  • lod
  • bumping up lod level
  • Update Readme.md
  • lod
  • Merge branch 'lod' of https://github.com/APHA-CSU/BovTB-nf into lod
  • Merge pull request #10 from APHA-CSU/lod
  • Merge branch 'master' into inclusivity-test
  • single inclusivity case
  • inclusivity test
  • splitting circleci tests in two
  • lowering the number of inclusivity tests
  • touch
  • deploy function
  • DRYing up
  • DRYing up with anchors
  • Merge pull request #12 from APHA-CSU/deploy
  • using submitted ftp instead of the other one
  • Merge branch 'master' into inclusivity-test
  • deduplicate in its own process
  • removing echo
  • BASHing deduplicate
  • varCall.bash
  • execute all the things
  • trim.bash
  • map2Ref
  • mask.bash
  • ENA connection limit takin' my parallelism
  • maybe linear will make ENA happy
  • read stats and dockerfile bug
  • VCF2Consensus
  • readStats
  • assign cluster
  • idNonBovis
  • pc_aft_trim changed to proportion of uniq reads
  • pipe grep through cat to avoid notfound error, fixes #11
  • Merge pull request #13 from APHA-CSU/Thresholds
  • adding sra-toolkit to dockerfile@
  • prefetch
  • removing broken install code
  • running ln separately
  • using sra toolkit for inclusivity download cases
  • Merge branch 'master' into inclusivity-test
  • depends on tinyreads
  • Merge pull request #14 from APHA-CSU/inclusivity-test
  • fixing merge conflicts
  • bin it.
  • updating Dockerfile to make everything in bin executable@
  • Merge pull request #15 from APHA-CSU/processes
  • python unit tests
  • updating config.yml to include unit tests
  • deduplicate test job
  • Change method for counting reads, fixes #16
  • prevent no zero coverage positions error
  • removing depend_path arg
  • comment
  • Merge pull request #17 from APHA-CSU/FixReadCount
  • Merge pull request #18 from APHA-CSU/unit_tests
  • FastUniq on linux path
  • trimmomatic on path
  • bwa mem on linux path
  • docker variable
  • dropping depend_path for map2ref
  • dropping depend_path for varCall.bash
  • dropping depend_path for varCall.bash
  • bug with the trim arg
  • dropping depend_path for mask.bash
  • dropping depend_path for idnonbovis
  • dropping depend_path altogether
  • Merge pull request #19 from APHA-CSU/drop_depend_path
  • Corrected accession column and removed duplication

File Changes

Patch Links:

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