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Update pipeline_refmap_yml.md
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giuliaelgarcia authored Apr 23, 2024
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Expand Up @@ -30,22 +30,22 @@ You can download the different refmap `pipeline.yml` files here:
Computing resources to use, specifically the number of threads used for parallel jobs.
Specified by the following three parameters:
- <span class="parameter">threads_high</span> `Integer`, Default: 1<br>
Number of threads used for high intensity computing tasks.
For each thread, there must be enough memory to load all your input files at once and create the MuData object.
Number of threads used for high intensity computing tasks.
For each thread, there must be enough memory to load all your input files at once and create the MuData object.

- <span class="parameter">threads_medium</span> `Integer`, Default: 1<br>
Number of threads used for medium intensity computing tasks.
For each thread, there must be enough memory to load your mudata and do computationally light tasks.
Number of threads used for medium intensity computing tasks.
For each thread, there must be enough memory to load your mudata and do computationally light tasks.

- <span class="parameter">threads_low</span> `Integer`, Default: 1<br>
Number of threads used for low intensity computing tasks.
For each thread, there must be enough memory to load text files and do plotting, requires much less memory than the other two.
Number of threads used for low intensity computing tasks.
For each thread, there must be enough memory to load text files and do plotting, requires much less memory than the other two.

- <span class="parameter">condaenv</span> `String` (Path)<br>
Path to conda environment that should be used to run panpipes.
Path to conda environment that should be used to run panpipes.

- <span class="parameter">queues:</span> `String` (Path)<br>
In case a special queue is required for long jobs or if the user has access to a GPU-specific queue. Otherwise, leave it blank.
In case a special queue is required for long jobs or if the user has access to a GPU-specific queue. Otherwise, leave it blank.
- <span class="parameter">long:</span> `String` (Path)<br>
- <span class="parameter">gpu:</span> `String` (Path)<br>

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