update local modules to nf-core structure#89
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huh, I didn't notice this PR before sorry for that. Nice work!
The latest CAGEr release includes changes we need, I am not sure how hard is it to make a container with it. Last time I made the container from dev, I assume that since then bioconductor should have released their latest container (3.22) which includes the necessary changes in CAGEr.
I see that I had a bit of a misunderstanding with the usage of "genome", so that's nice to have fixed.
I also see that the nf-core way of including scripts is neat, but the many parameters can get confusing and it would be nice to add docs to each module about these too.
I think that was basically all I caught. Very nice to have nf-tests, thanks again!
| } | ||
| process { | ||
| """ | ||
| input[0] = file("${projectDir}/modules/local/cager/report/tests/fixtures/dummy.Rmd") |
| */ | ||
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| params { | ||
| pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/customcage/' |
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this should change to cageseq/v2, right?
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yup, at least this path breaks at the moment
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| setup { | ||
| run("GTF2TXDB") { | ||
| script "modules/local/gtf2txdb/main.nf" |
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i think this has been ran already, we could upload an example txdb file instead. Unless this is like this to keep the dependencies between tests intact
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we can use https://nf-co.re/docs/tutorials/nf-core_components/using_seqera_containers for cager container |
| } | ||
| }, | ||
| "required": ["gtf", "genome"] | ||
| "required": ["gtf"] |
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@mashehu I see that this is towards the nf-test-and-fix-dev branch. I can merge dev into that branch if that's ok? |
# Conflicts: # conf/base.config
move script to template and move all logic into the script
…latest template version
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@mashehu I committed some local changes, which were supposed to be only adding annotations for inputs, but it seems to be way more, but mostly updates which should have been there already. I hope I didn't revert back changes. Can you check? |
| ch_fasta = ch_genome_name.combine(ch_pre_fa) | ||
| ch_index = channel.empty() | ||
| } else { | ||
| ch_fasta = channel.empty() |
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fail if ch_fasta is empty, because we need it for chromosome size
| } else { | ||
| ch_fasta = channel.empty() | ||
| } | ||
| } else if (params.genome) { |
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in the nextflow_schema.json require either genome or fasta to be present
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(cherry picked from commit 88774ac08b8ca77fcab7de2ac349777dedf6d0d1)
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continuation of #87
mainly doing a partial template update and converting the local modules to an nf-core structure (mainly adding an environment.yml and full container syntax to allow conda, docker and singularity, as well as tests, where possible).