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Busco dev #37
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Oh yeah, this looks so much better ! Great !
I can confirm that the test profile works for me on the farm, with just this small change below.
In terms of functionality of the subworkflow, do you think it does everything it needs to do ?
added missing single quote Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Results from the Adding the following lines to
doesn't solve the problem, the following Nextflow warnings are raised:
I need to take a closer look at this, not sure which other files might be causing this error. |
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It worked, only results from
When running:
The results folder should look something like this using
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It worked, only results from
The results folder should look something like this using
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I would not worry much about publishing results to the results folder. Once the pipeline is completed we will update this with the final structure. For now as long as the code works and creates the correct output in the work folder we can move forward. |
Are there any issues with the current code besides linting? If not, let’s merge. A lot of downstream work depends on this. |
Using there
The test using |
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LGTM 👍 as long as the tests pass
Hi it looks like there's a problem with the
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It seems only the
Output:
Also the Python script you mentioned looks into each |
The archives |
@zb32 Hi. I fixed the issue you found. When running the test there should be the following file containing the
Which is the expected output (columns: "qseqid staxids bitscore qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"). |
@muffato @priyanka-surana @priyanka-surana I was not sure about merging, if you have any comments or issues that should be fixed, please let me know. |
Thank you @alxndrdiaz ! I can confirm that the Busco hit makes it way to Diamond on the unit test. I've started a full test on gfLaeSulp1.1 (and had to do a few changes, which I have added to this branch). It's a small genome, so hopefully it shouldn't take too long. I'll talk to Zaynab tomorrow morning, but I think it will be OK to merge 🤞🏼 |
Your subworkflow actually already completed on the full test. 326 Busco genes recovered across the three domains, and 280 Diamond hits. It looks fine by me 👍🏼 |
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I've ran the pipeline and it looks good :D
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).