First complete draft version of the V6 Amplicon Analysis pipeline #7
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…support for both single-end and paired-end reads
…ded new scripts to do that
…an get cleaned fastp reads for paired end reads without merging them
… primer issue for single-end primers
… with more than one detected HV region. fixed now
… make_asv_count_table script, and Krona
…ake take a joined tuple as input
…few unit tests I had forgotten
…eq nf-core module. Needed to patch some changes to add variable region output
…, removal of old cmsearch_swf and its unused modules
yeah, it should be ebi-metagenomics/amplicon-pipeline. I wouldn't include the version on the repo name |
mberacochea
requested changes
May 19, 2024
The structuer of the pipelines looks good to me, amazing work :). I've removed the nf-core/ampliconpipeline mentions in the code, this pipeline is not part of the nf-core ( it could be in the future... but not now). Tweaked the parameters, some of them were missing from then nextflow.config file. I've added `checkIfExists: true` in file() invocations, most of them should be handled by the nf-schema validation, but it's good practice to keep them. Renamed ITS_SWF to MASK_FASTA_SWF, it's not ITS specific even though that is the case for this piepline.
Every module needs a container and a VERSIONS output file.
…moduels that use the MPT (commented for now as I'm waiting to release a fix for it until later)
…ows return a version.yml, collate all the versions at the end of the pipeline and output them, refactor modules that were using shell to just use script
mberacochea
approved these changes
Jun 5, 2024
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Well. Impressive work @chrisAta. I left some comments, but I think it's good to go
…on-zero exit code added when no ASVs found, fix typo in config
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This pull request is about merging the first full draft version of the MGnify V6 Amplicon Analysis pipeline.
The pipeline has been fully refactored to use Nextflow, and contains all of the features we envisaged for it in a decent state of polish. Apart from the re-implementation of existing features, the major changes of the pipeline include:
More technical changes of the pipeline include: