Update readme with GHA instructions and more detail #52
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README.md
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| ```bash | ||
| nextflow run AlexsLemonade/OpenScPCA-nf -profile batch | ||
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| For most use cases you will want to specify an output directory other than the default using the `--results_bucket` argument. |
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What are most cases? When would you want to use the default bucket?
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The default bucket is currently the results release bucket. I expect some of this to change when we get to #44, but for now it is what it is. Writing this sentence was actually what led me to file #44; I expect to add a production profile that sets the output buckets and then lock them down a bit more to avoid accidental edits, with some kind of staging location the default, but we don't have all of that set up yet.
| For most use cases you will want to specify an output directory other than the default using the `--results_bucket` argument. | |
| For most use cases you will want to use the `--results_bucket` argument to avoid writing to the default output bucket. |
| ```bash | ||
| nextflow run AlexsLemonade/OpenScPCA-nf -profile batch --results_bucket {OUTDIR} | ||
| ``` | ||
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| The workflow also has a couple of entry points other than the main workflow, for testing and creating simulated data. |
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I might make a new header for talking about entry points.
README.md
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| nextflow run AlexsLemonade/OpenScPCA-nf -profile batch -entry simulate --sim_pubdir {SIMDIR} | ||
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| To run the workflow with simulated data, you can add the `simulated` profile. |
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This is different then running the simulated entry point right? I would explicitly state that/ make a new header.
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Yes, it is different. One generates the simulated data, the other uses it. I didn't like the overlap, but since one is an entry point and one is a profile, I thought it might be okay.
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
README.md
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| ```bash | ||
| nextflow run AlexsLemonade/OpenScPCA-nf -profile batch | ||
| ``` | ||
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| For most use cases you will want to specify an output directory other than the default using the `--results_bucket` argument. |
There was a problem hiding this comment.
The default bucket is currently the results release bucket. I expect some of this to change when we get to #44, but for now it is what it is. Writing this sentence was actually what led me to file #44; I expect to add a production profile that sets the output buckets and then lock them down a bit more to avoid accidental edits, with some kind of staging location the default, but we don't have all of that set up yet.
| For most use cases you will want to specify an output directory other than the default using the `--results_bucket` argument. | |
| For most use cases you will want to use the `--results_bucket` argument to avoid writing to the default output bucket. |
README.md
Outdated
| nextflow run AlexsLemonade/OpenScPCA-nf -profile batch -entry simulate --sim_pubdir {SIMDIR} | ||
| ``` | ||
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| To run the workflow with simulated data, you can add the `simulated` profile. |
There was a problem hiding this comment.
Yes, it is different. One generates the simulated data, the other uses it. I didn't like the overlap, but since one is an entry point and one is a profile, I thought it might be okay.
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Closes #32
This PR adds more detail about running the openscpca-nf workflow, including most notably the discussion of running via GHA.