nf-core
bioformats2raw module
PR checklist
Closes #7422
- [x] This comment contains a description of changes (with reason).
- [x] If you've added a new tool - have you followed the module conventions in the contribution docs
- [x] Remove all TODO statements.
- [x] Emit the
versions.ymlfile. - [x] Follow the naming conventions.
- [x] Follow the parameters requirements.
- [x] Follow the input/output options guidelines.
- [x] Add a resource
label - [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
new modules: bioformats2raw
I used now a seqera container: community.wave.seqera.io/library/bioformats2raw:0.9.4--3eec45888b3759e5
- not sure if this is correct in the module main.nf
- nf-test passes with docker
The tool is not in conda-forge or bioconda but from the ome channel ( open microscopy environment ) and i get errors from linting:
The environment.yml of the module bioformats2raw is not valid: 'ome' is not one of ['bioconda', 'conda-forge'].
so i added the changes :) Thank you so much for your help @camlloyd , i added the process_high label because of the max_workers argument. I am not sure which one of the process labels would be better.
The linter has a problem with the ome conda channel:
The tool is not in conda-forge or bioconda but from the ome channel ( open microscopy environment ) and i get errors from linting: The environment.yml of the module bioformats2raw is not valid: 'ome' is not one of ['bioconda', 'conda-forge'].
But then i guess it would be ready for review again. :)
so i added the changes :) Thank you so much for your help @camlloyd , i added the process_high label because of the max_workers argument. I am not sure which one of the process labels would be better.
The linter has a problem with the ome conda channel:
The tool is not in conda-forge or bioconda but from the ome channel ( open microscopy environment ) and i get errors from linting: The environment.yml of the module bioformats2raw is not valid: 'ome' is not one of ['bioconda', 'conda-forge'].
But then i guess it would be ready for review again. :)
Added an action point regarding the emitted versions. I will open an issue regarding the linting error.
so i added the changes :) Thank you so much for your help @camlloyd , i added the process_high label because of the max_workers argument. I am not sure which one of the process labels would be better. The linter has a problem with the ome conda channel:
The tool is not in conda-forge or bioconda but from the ome channel ( open microscopy environment ) and i get errors from linting: The environment.yml of the module bioformats2raw is not valid: 'ome' is not one of ['bioconda', 'conda-forge'].
But then i guess it would be ready for review again. :)
Added an action point regarding the emitted versions. I will open an issue regarding the linting error.
@CaroAMN you can ignore this specific linting issue for now (thanks @mirpedrol!)
the vcf produced seems to be unstable, can you try using the nft-vcf plugin to check them out?
the vcf produced seems to be unstable, can you try using the nft-vcf plugin to check them out?
mh not sure what is happening but the tests failing are for Test Process CNVNATOR_CONVERT2VCF which is not my module... 😱
the vcf produced seems to be unstable, can you try using the nft-vcf plugin to check them out?
mh not sure what is happening but the tests failing are for
Test Process CNVNATOR_CONVERT2VCFwhich is not my module... 😱
ok never mind, issue resolved
I think there's an issue for this somewhere... https://github.com/nf-core/modules/blob/5dd32197158306d66ab90958ea1c3588bba172ec/modules/nf-core/ale/environment.yml
I think there's an issue for this somewhere... https://github.com/nf-core/modules/blob/5dd32197158306d66ab90958ea1c3588bba172ec/modules/nf-core/ale/environment.yml
ale is on bioconda, no?
For me this is similar to the idea with pip (cf https://github.com/nf-core/tools/issues/3461). Aka we need to allow more stuff. An issue has been created for that one in particular already: https://github.com/nf-core/tools/issues/3499