Updates the amrfinderplus/run module into the pipeline
Update the usage docs as to how to supply a local database (removed the NCBI download part because that alone did not work. The user would have to index/create blast database files, which seems more complicated (skimming through the code from AMRFinderPlus amrfinder_index.cpp file). So just using the update command from conda seems more reasonable.
This also solves #328
PR checklist
[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/funcscan branch on the nf-core/test-datasets repository.
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,singularity --outdir <OUTDIR>).
[x] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
amrfinderplus/run
module into the pipelineThis also solves #328
PR checklist
nf-core lint
).nextflow run . -profile test,singularity --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).