Merging template updates #90
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The remaining issues/improvements regarding input parameters and completing the pipeline schema will be tackled with separate PRs if the reviewers agree. |
ggabernet
reviewed
Aug 3, 2020
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I just had some comments, and one comment to usage.md: I think you forgot to remove this from the toc:
* [Main arguments](#main-arguments)
* [`-profile`](#-profile) * [`-profile`](#-profile)
* [`--reads`](#--reads) * [`--reads`](#--reads)
* [`--single_end`](#--single_end) * [`--single_end`](#--single_end)
As now the pipeline specific parameters will be directly parsed from the nextflow.config file.
ggabernet
reviewed
Aug 3, 2020
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
ggabernet
reviewed
Aug 4, 2020
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I think the usage.md still needs some edits. Here is the template version: https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/docs/usage.md
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Many thanks to contributing to nf-core/hlatyping!
Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).
PR checklist
nextflow run . -profile test,docker).nf-core lint .).docsis updatedCHANGELOG.mdis updatedREADME.mdis updatedLearn more about contributing: https://github.com/nf-core/hlatyping/tree/master/.github/CONTRIBUTING.md