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Merge pull request #5 from OpenOmics/dev
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Version 2 Update
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chenv3 authored Apr 19, 2024
2 parents 5b5f374 + 7cf901b commit 6e5cc43
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2 changes: 1 addition & 1 deletion .github/workflows/main.yaml
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Expand Up @@ -23,7 +23,7 @@ jobs:
/opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \
/opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
/opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \
--output /opt2/output --genome hg38 --version gex --mode local --dry-run
--output /opt2/output --genome hg38 --pipeline gex --cellranger 8.0.0 --mode local --dry-run
- name: View the pipeline config file
run: |
echo "Generated config file for pipeline...." && cat $PWD/output/config.json
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -17,6 +17,7 @@ Welcome to cell-seek! Before getting started, we highly recommend reading throug
The **`./cell-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

* [<code>cell-seek <b>run</b></code>](https://openomics.github.io/cell-seek/usage/run/): Run the cell-seek pipeline with your input files.
* [<code>cell-seek <b>genome</b></code>](https://openomics.github.io/cell-seek/usage/genome/): Create a custom genome reference file that can be used with the pipeline.
* [<code>cell-seek <b>unlock</b></code>](https://openomics.github.io/cell-seek/usage/unlock/): Unlocks a previous runs output directory.
* [<code>cell-seek <b>cache</b></code>](https://openomics.github.io/cell-seek/usage/cache/): Cache remote resources locally, coming soon!

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2 changes: 1 addition & 1 deletion VERSION
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1.0.0
2.0.0
320 changes: 300 additions & 20 deletions cell-seek

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10 changes: 10 additions & 0 deletions config/genome.json
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"atac_ref": "/data/NCBR/references/cellranger_references/refdata-cellranger-arc-mm10-2020-A-2.0.0",
"vdj_ref": "/data/NCBR/references/cellranger_references/refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0/",
"arc_ref": "/data/NCBR/references/cellranger_references/refdata-cellranger-arc-mm10-2020-A-2.0.0"
},
"hg2024": {
"gex_transcriptome": "/data/OpenOmics/references/cell-seek/human/refdata-gex-GRCh38-2024-A",
"cite_transcriptome": "/data/OpenOmics/references/cell-seek/human/refdata-gex-GRCh38-2024-A",
"vdj_ref": "/data/NCBR/references/cellranger_references/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0/"
},
"mm2024": {
"gex_transcriptome": "/data/OpenOmics/references/cell-seek/mouse/refdata-gex-GRCm39-2024-A",
"cite_transcriptome": "/data/OpenOmics/references/cell-seek/mouse/refdata-gex-GRCm39-2024-A",
"vdj_ref": "/data/NCBR/references/cellranger_references/refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0/"
}
}
}
2 changes: 1 addition & 1 deletion config/modules.json
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{
"tools": {
"cellranger": "cellranger/7.1.0",
"cellranger": {"7.1.0": "cellranger/7.1.0", "7.2.0": "cellranger/7.2.0", "8.0.0": "cellranger/8.0.0"},
"cellranger-atac": "cellranger-atac/2.1.0",
"cellranger-arc": "cellranger-arc/2.0.1",
"python2": "python/2.7",
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7 changes: 4 additions & 3 deletions docs/index.md
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## Overview
Welcome to cell-seek's documentation! This guide is the main source of documentation for users that are getting started with [cell-seek](https://github.com/OpenOmics/cell-seek/).
Welcome to cell-seek's documentation! This guide is the main source of documentation for users that are getting started with [cell-seek](https://github.com/OpenOmics/cell-seek/).

The **`./cell-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:
The **`./cell-seek`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions:

* [<code>cell-seek <b>run</b></code>](usage/run.md): Run the cell-seek pipeline with your input files.
* [<code>cell-seek <b>genome</b></code>](usage/genome.md): Create a custom genome reference file that can be used with the pipeline.
* [<code>cell-seek <b>unlock</b></code>](usage/unlock.md): Unlocks a previous runs output directory.
* [<code>cell-seek <b>cache</b></code>](usage/cache.md): Cache remote resources locally, coming soon!

Expand All @@ -49,7 +50,7 @@ Before getting started, we highly recommend reading through the [usage](usage/ru

For more information about issues or trouble-shooting a problem, please checkout our [FAQ](faq/questions.md) prior to [opening an issue on Github](https://github.com/OpenOmics/cell-seek/issues).

## Contribute
## Contribute

This site is a living document, created for and by members like you. cell-seek is maintained by the members of NCBR and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository :octicons-heart-fill-24:{ .heart }](https://github.com/OpenOmics/cell-seek).

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94 changes: 94 additions & 0 deletions docs/usage/genome.md
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# <code>cell-seek <b>genome</b></code>

## 1. About
The `cell-seek` executable is composed of several inter-related sub commands. Please see `cell-seek -h` for all available options.

This part of the documentation describes options and concepts for <code>cell-seek <b>genome</b></code> sub command in more detail. With minimal configuration, the **`genome`** sub command enables you to create a custom reference genome JSON file that can be used in the **`run`** sub command.

If a reference genome that does not come with the pipeline, then a custom json file needs to be provided to run.

Creating a custom reference genome file is fast and easy! In its most basic form, <code>cell-seek <b>genome</b></code> only has *one required input* with the optional arguments supplying the reference paths.

## 2. Synopsis
```text
$ ./cell-seek genome [-h] \
[--gex GEX_PATH] [--vdj VDJ_PATH] \
[--atac ATAC_PATH] [--multiome MULTIOME_PATH] \
--name NAME
```

The synopsis for this command shows its parameters and their usage. Optional parameters are shown in square brackets.

A user **must** provide the name of the reference via `--name` argument. After running the genome sub command, you can use the generated json file as the reference when running the pipeline.

Use you can always use the `-h` option for information on a specific command.

### 2.1 Required Arguments

`--name NAME`
> **Name of the reference.**
> *type: string*
>
> The name of the reference, which will also be used as the name of the generated reference file.
> ***Example:*** `--name NAME`
### 2.2 Reference Options

Each of the following arguments are optional and do not need to be provided. At least one needs to be used for a reference path to be included in the generated file.

`--gex GEX_PATH`
> **Path to the gene expression reference.**
> *type: path*
>
> This reference is the same one used for the gene expression capture for the GEX, CITE, and MULTI pipelines. This flag is the only one needed to supply the value for all three pipelines.
>
> ***Example:*** `--gex /data/GEX_PATH`
---
`--vdj VDJ_PATH`
> **Path to the vdj reference.**
> *type: path*
>
> This reference is the one used for the VDJ capture for the VDJ and MULTI pipelines. This flag is the only one needed to supply the value for the two pipelines.
>
> ***Example:*** `--vdj /data/VDJ_PATH`
---
`--atac ATAC_PATH`
> **Path to the atac reference.**
> *type: path*
>
> This reference is used in the ATAC pipeline.
>
> ***Example:*** `--atac /data/ATAC_PATH`
---
`--multiome MULTIOME_PATH`
> **Path to the multiome reference.**
> *type: path*
>
> This reference is used in the multiome pipeline.
>
> ***Example:*** `--multiome /data/MULTIOME_PATH`
### 2.3 Miscellaneous Options
Each of the following arguments are optional, and do not need to be provided.

`-h, --help`
> **Display Help.**
> *type: boolean*
>
> Shows command's synopsis, help message, and an example command
>
> ***Example:*** `--help`
## 3. Example
```bash
# Step 0.) Grab an interactive node (do not run on head node)
srun -N 1 -n 1 --time=12:00:00 -p interactive --mem=8gb --cpus-per-task=4 --pty bash
module purge
module load singularity snakemake

# Step 1.) Create a custom NAME.json file with provided reference(s)
cell-seek genome --name NAME --gex /data/GEX_PATH
```
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