Added Busco to run in protein mode

SandraBabirye commented 2 months ago

PR checklist

[ ] Edited the annotation_statistics subworkflow: added the gffread nfcore module to obtain the protein.fasta file and hard coded the busco to run in protein mode
[ ] Edited the extract annotatistics local module bby adding a new input channel for the Busco statistics
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

SandraBabirye commented 2 months ago

Hi @BethYates and @tkchafin , Kindly review my commits towards solving issue 141. Thank you

github-actions[bot] commented 2 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 067833c

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.1.0'`` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-genomenote_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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BethYates commented 2 months ago

We need to pass an argument -y to the GFFREAD process to tell it to output protein fasta sequences, to do this you need to add the following to the process block in modules.config withName: GFFREAD { ext.args = "-y" }

BethYates commented 1 month ago

We will need to add a block to base.config to set memory, cpus and time for BUSCOPROTEINS. The meta for the input channel to BUSCOPROTEINS doesn't have a value for genome_size so we can't use the same black as we do for BUSCO run in genome mode. Something like this should work , but feel free to adjust the values as you see fit withName: BUSCOPROTEINS { memory = { check_max( 4.GB * task.attempt, 'memory' ) } cpus = { log_increase_cpus(2, 2*task.attempt, 1, 2) } time = { check_max( 2.h * task.attempt, 'time') } }

sanger-tol / genomenote