This PR adds the sourmash compare nf-core module to the workflow. sourmash compare produces a similarity matrix for samples. The output csv for test data looks like this:
~#8 should be merged to dev and this branch synced before this PR is evaluated~ done
The next step after this PR is integrating visualizations for the gather and compare outputs. After this PR is merged, I would be able to assess whether fastq files are high enough quality to post to the SRA, but I wouldn't expect anyone else to be able to yet bc there aren't enough docs or visualizations.
PR checklist
[x] This comment contains a description of changes (with reason).
[x] If you've fixed a bug or added code that should be tested, add tests!
[x] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] ~Usage Documentation in docs/usage.md is updated.~
[ ] ~Output Documentation in docs/output.md is updated.~
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).
This PR adds the
sourmash compare
nf-core module to the workflow.sourmash compare
produces a similarity matrix for samples. The output csv for test data looks like this:~#8 should be merged to
dev
and this branch synced before this PR is evaluated~ doneThe next step after this PR is integrating visualizations for the gather and compare outputs. After this PR is merged, I would be able to assess whether fastq files are high enough quality to post to the SRA, but I wouldn't expect anyone else to be able to yet bc there aren't enough docs or visualizations.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --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).