updated workflow files for imaging tutorial: Analyse HeLa fluorescence siRNA screen

[thawn]

updated the workflow files to comply with the most recent version of the tutorial Analyse HeLa fluorescence siRNA screen

updated analyze_screen.ga
updated feature_extraction.ga

[hexylena]

Thanks so much!

[shiltemann]

thanks a lot @thawn! Please feel free to add yourself as a contributor :)

[shiltemann]

@thawn there are a few issues raised by reviewdog, do you think you could address those? At least adding a license and creator (both can be done in the workflow editor of Galaxy). And if possible workflow tests would also be great to have ( instructions)

thanks!

[kostrykin]

there is a , missing at the end of the line

[thawn]

@shiltemann I created the tests as instructed in the tutorial

Now I have the following test:

    input images:
      class: Collection
      collection_type: list
      elements:
        - class: File
          identifier: B2--W00026--P00001--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00001--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00002--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00002--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00003--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00003--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00004--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00004--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00005--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00005--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00006--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00006--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00007--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00007--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00008--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00008--Z00000--T00000--dapi.tif
        - class: File
          identifier: B2--W00026--P00009--Z00000--T00000--dapi
          path: test-data/input images_B2--W00026--P00009--Z00000--T00000--dapi.tif

these images come from a zip file on zenodo: https://zenodo.org/record/3362976/files/B2.zip

Can I change the yaml file so that planemo downloads the zip from zenodo and extracts it into a collection which is then used as input?

[shiltemann]

@thawn good question, I think this is possible since recently: galaxyproject/galaxy#16014

If that doesnt work for you, a workaround could be to create a new zenodo record with the uncompressed files? ..or just add the files to a folder workflows/test-data here in the GTN

@hexylena any thoughts?

btw, thanks a lot for adding tests!

[hexylena]

these images come from a zip file on zenodo: https://zenodo.org/record/3362976/files/B2.zip

Can I change the yaml file so that planemo downloads the zip from zenodo and extracts it into a collection which is then used as input?

I don't think planemo supports that, I recommend the solution proposed by @shiltemann to create a new zenodo record and use URLs to point to those records.

 location: https://zenodo.org/record/3960260/files/004-2_1.fastq.gz

[shiltemann]

Thanks for doing all this @thawn!

I think if you rename your test files from ..-tests.yml to ..-test.yml (without the s) it will fix the linting errors

And could you add yourself to our CONTRIBUTORS.yaml file? And then also to the tutorial metadata :)