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Preprocess pipeline yaml documentation #200

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merged 11 commits into from
Mar 6, 2024
Merged

Preprocess pipeline yaml documentation #200

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b4c5085
Add pipeline.yml docs description for preprocess
Lilly-May Feb 23, 2024
9a55660
First pipeline.yml draft
Lilly-May Feb 24, 2024
31dbc57
Modified until plotting variables
Lilly-May Feb 24, 2024
3b2c6cc
Modified until Scaling
Lilly-May Feb 26, 2024
2cd2f7e
Modified until ATAC
Lilly-May Feb 27, 2024
2dc14d3
Modified entire pipeline.yml
Lilly-May Feb 27, 2024
529e251
Added links to different pipeline.yml file versions
Lilly-May Feb 27, 2024
4784a38
Added link in index.rst
Lilly-May Feb 28, 2024
c910aaf
Fixed clr norm margin options
Lilly-May Feb 29, 2024
69d8a52
Fixed clr margin options in parameter doc
Lilly-May Feb 29, 2024
5043714
Set default clr margin to 1
Lilly-May Mar 6, 2024
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1 change: 1 addition & 0 deletions docs/yaml_docs/index.rst
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Expand Up @@ -6,6 +6,7 @@ Workflows configuration files

useful_info_on_yml
pipeline_ingestion_yml
pipeline_preprocess_yml
pipeline_integration_yml
spatial_qc
spatial_preprocess
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5 changes: 3 additions & 2 deletions docs/yaml_docs/pipeline_preprocess_yml.md
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Expand Up @@ -44,6 +44,7 @@ Specified by the following three parameters:
<span class="parameter">condaenv</span> `String` (Path)<br>
Path to conda environment that should be used to run panpipes.
Leave blank if running native or your cluster automatically inherits the login node environment.
For more information on this, please refer to the detailed explanation [here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html#specifying-conda-environments-to-run-panpipes).

## General project specifications

Expand Down Expand Up @@ -328,8 +329,8 @@ Whether applying scaling or not is still a matter of debate, as stated in the [L
Parameter for CLR normalisation.
The CLR margin determines whether you normalise per cell (as you would normalise RNA data), or by feature (recommended, due to the variable nature of protein assays).
Hence, CLR margin 0 is recommended for informative qc plots in this pipeline.
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margin =1 is recommended

- 0 = normalise column-wise (per feature)
- 1 = normalise row-wise (per cell)
- 0 = normalise row-wise (per cell)
- 1 = normalise column-wise (per feature)

- <span class="parameter">background_obj</span> `String` (Path)<br>
Parameter for DSB normalisation.
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6 changes: 2 additions & 4 deletions panpipes/panpipes/pipeline_preprocess/pipeline.yml
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Expand Up @@ -15,8 +15,6 @@ resources:

condaenv:

# allows for tweaking where the jobs get submitted, in case there is a special queue for long jobs or you have access to a gpu
# leave as is if you do not want to use the alternative queues

#-------------------------------
# General project specifications
Expand Down Expand Up @@ -157,8 +155,8 @@ prot:
normalisation_methods: clr,dsb

# CLR parameters:
# 0 = normalise column-wise (per feature, recommended)
# 1 = normalise row-wise (per cell)
# 0 = normalise row-wise (per cell)
# 1 = normalise column-wise (per feature, recommended)
clr_margin: 0

# DSB parameters:
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