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v2.5.2#115

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willbradshaw merged 89 commits intomasternaobservatory/mgs-workflow:masterfrom devnaobservatory/mgs-workflow:devCopy head branch name to clipboardNov 27, 2024

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Commits on Nov 15, 2024

• Removed redundant subsetting statement from TAXONOMY

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• Updated changelog

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• Merge pull request #98 from naobservatory/will-clean-taxonomy

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• readme: minor updates

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Commits on Nov 18, 2024

• Adding in modules for nf-test

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• Allow people to pass in RefSeq or Genbank

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• For human genome, but this can probably be removed

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• Using parameters instead of hard coded values

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Commits on Nov 19, 2024

• Updated resources to be github action friendly, and introduced the first test

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• Going to see if when I push now if the test runs

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• Hoping this works

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• testing

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• Create github-actions-demo.yml

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• Update github-actions-demo.yml

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• Misspelled workflow

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• Merge branch 'test-index' of https://github.com/naobservatory/mgs-workflow into test-index

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• Fixing

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• Hopefully verbose makes errors easier to understand?

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• Should fix issues

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• Maybe this works

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• Let's see if I can even get this running

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• Something tells me it's the base container

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• bbmap defualts to 60 gb memory causing things to fail so i manually set it low, but we'll need to programatically change this

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• Turns out that it worked, so we'll introduce everythign agian

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• Overhauled BLAST validation

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• need to confirm that this image is the issue

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• Trying container from sequera

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• Trying custom images

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• Let's try everything

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Commits on Nov 20, 2024

• Further BLAST refinements

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• Loosening trimming and filtering parameters

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• Merge branch 'master' into will-debug-bbduk

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• Merge pull request #101 from naobservatory/jefftk-readme

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• Added new containers that avoid the original base one as github actions doesn't like it

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• Turns out we can use genera, just a valid one is necessary

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• Updated bbmap_mem paramter to be passed in

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• Switched up some parameters so that they're in the config file instead of hard coded, there are still a few left, but we can get to them when we want

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• Named the test to something more general

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• Using nao-testing dir now

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• Using nao-testing dir now

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• I have a hunch

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• Trying another multiqc container

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• Remove mem constraint

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• hardcoded to lower but will need to hcange

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• Relaxed mem as well

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• Hard code lower kraken

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• Done:

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Commits on Nov 21, 2024

• Merge branch 'dev' into will-debug-bbduk

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• Updated CHANGELOG

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• Merge pull request #106 from naobservatory/will-debug-bbduk

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• Creating the a test that runs both index and run (with blast)

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• Trying sharding and splitting tests and we run out of memory on the machine

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• Removing sharding, trying correct version of nextflow

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• Throwing in a clean to see if it helps

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• Shortened first test to test out cleaning, and added cleaning to remove docker images

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• Last thing to test

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• Uncomment out

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• generate_samplesheet: add --group_across_illumina_lanes argument (#103)

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• Need to figure out a better name for this.

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• Remove hard coded mem and cpu values, turn them into profiles, and remove their references.

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• Removed unused feature

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Commits on Nov 25, 2024

• Adding all my changes to merge

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• Merging dev

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• Added run validation

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• Removed reliance on fixed cpu/mem

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• Created config file for running during test

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• Made parameters configurable

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• Updated changelog and removed old tests

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• Updated config files to have new formats

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• Everytime we update the index for the run workflow test, we must grant permission to the directory again, this was causing the current error, I just added some text to the changelog so that this co…

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• Github actions tries to use a symlink if I keep the name for index-params the same, so I change it so that it doesn't fail

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• Merge pull request #105 from naobservatory/test-index

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• Added logic to check if grouping variable matches what is in the input csv file, and added a test samplesheet with grouping

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• Turns out the other multiqc-container didn't work well, so here's a trial at another one, this one works locally, the question is if it will hold up under Github Actions.

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Commits on Nov 26, 2024

• Given that you can run the test locally, I've changed this such that the test only runs on pull requests so that we don't exhaust our limited number of hours.

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• Updated changelog

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• Updated README to reflect new testdataset and testing along with improving description for grouping

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• Fixed path

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• Update README.md

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• Added config file and script for updating lifecycle configuration

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• Updated workflows for s3 auto-cleaning

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• Added back config file for test data

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• Minor change to test-data config

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• Merge pull request #112 from naobservatory/grouping

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• Updated changelog

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Commits on Nov 27, 2024

• Merge pull request #113 from naobservatory/will-tagging

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• Moving two files to be stored in working directory rather than launch directory.

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• Merge pull request #114 from naobservatory/fix_saving_files

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• Cleaned up changelog and versioning for merge to master

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