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LouisLeNezet committed Mar 18, 2024
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19 changes: 10 additions & 9 deletions README.md
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The **phaseimpute** pipeline is constituted of 5 main steps:

| Metro map | Modes |
|-----------|-------------|
| Metro map | Modes |
| ---------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| <img src="docs/images/metro/MetroMap.png" alt="metromap" width="800"/> | - **Pre-processing**: Phasing, QC, variant filtering, variant annotation of the reference panel <br> - **Phase**: Phasing of the target dataset on the reference panel <br> - **Simulate**: Simulation of the target dataset from high quality target data <br> - **Concordance**: Concordance between the target dataset and a truth dataset <br> - **Post-processing**: Variant filtering based on their imputation quality |

## Usage

> [!NOTE]
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Here is a short description of the different mode of the pipeline.
For more information please refer to the [documentation](https://nf-core.github.io/phaseimpute/usage/).

| Mode | Flow chart | Description |
|-------------------|-----------------------------------------------------------------|----------------------------------------------------------------------------------------|
| **Preprocessing** | <img src="docs/images/metro/PreProcessing.png" alt="phase_metro" width="600"/> | The preprocessing mode is responsible to the preparation of the multiple input file that will be used by the phasing process. <br> The main processes are : <br> - **Haplotypes phasing** of the reference panel using [**Shapeit5**](https://odelaneau.github.io/shapeit5/). <br> - **Filter** the reference panel to select only the necessary variants. <br> - **Chunking the reference panel** in a subset of region for all the chromosomes. <br> - **Extract** the positions where to perform the imputation.|
| **Phasing** | <img src="docs/images/metro/Phase.png" alt="phase_metro" width="600"/> | The phasing mode is the core mode of this pipeline. <br> It is constituted of 3 main steps: <br> - **Phasing**: Phasing of the target dataset on the reference panel using either: <br> &emsp; - [**Glimpse1**](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html) <br> &emsp; It's come with the necessety to compute the genotype likelihoods of the target dataset. <br> &emsp; This step is done using [BCFTOOLS_mpileup](https://samtools.github.io/bcftools/bcftools.html#mpileup) <br> &emsp; - [**Glimpse2**](https://odelaneau.github.io/GLIMPSE/glimpse2/index.html) For this step the reference panel is transformed to binary chunks. <br> &emsp; - [**Stitch**](https://github.com/rwdavies/stitch) <br> &emsp; - [**Quilt**](https://github.com/rwdavies/QUILT) <br> - **Ligation**: all the different chunks are merged together. <br> - **Sampling** (optional) |
| **Simulate** | <img src="docs/images/metro/Simulate.png" alt="simulate_metro" width="600"/> | The simulation mode is used to create artificial low informative genetic information from high density data. This allow to compare the imputed result to a *truth* and therefore evaluate the quality of the imputation. <br> For the moment it is possible to simulate: <br> - Low-pass data by **downsample** BAM or CRAM using [SAMTOOLS_view -s]() at different depth <br> - Genotype data by **SNP selecting** the position used by a designated SNP chip. <br> The simulation mode will also compute the **Genotype likelihoods** of the high density data. |
| **Concordance** | <img src="docs/images/metro/Concordance.png" alt="concordance_metro" width="600"/> | This mode compare two vcf together to compute a summary of the differences between them. <br> To do so it use either: <br> - [**Glimpse1**](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html) concordance process. <br> - [**Glimpse2**](https://odelaneau.github.io/GLIMPSE/glimpse2/index.html) concordance process <br> - Or convert the two vcf fill to `.zarr` using [**Scikit allele**](https://scikit-allel.readthedocs.io/en/stable/) and [**anndata**](https://anndata.readthedocs.io/en/latest/) before comparing the SNPs. |
| **Postprocessing**| <img src="docs/images/metro/PostProcessing.png" alt="postprocessing_metro" width="600"/> | This final process unable to loop the whole pipeline for increasing the performance of the imputation. To do so it filter out the best imputed position and rerun the analysis using this positions. |
| Mode | Flow chart | Description |
| ------------------ | ---------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| **Preprocessing** | <img src="docs/images/metro/PreProcessing.png" alt="phase_metro" width="600"/> | The preprocessing mode is responsible to the preparation of the multiple input file that will be used by the phasing process. <br> The main processes are : <br> - **Haplotypes phasing** of the reference panel using [**Shapeit5**](https://odelaneau.github.io/shapeit5/). <br> - **Filter** the reference panel to select only the necessary variants. <br> - **Chunking the reference panel** in a subset of region for all the chromosomes. <br> - **Extract** the positions where to perform the imputation. |
| **Phasing** | <img src="docs/images/metro/Phase.png" alt="phase_metro" width="600"/> | The phasing mode is the core mode of this pipeline. <br> It is constituted of 3 main steps: <br> - **Phasing**: Phasing of the target dataset on the reference panel using either: <br> &emsp; - [**Glimpse1**](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html) <br> &emsp; It's come with the necessety to compute the genotype likelihoods of the target dataset. <br> &emsp; This step is done using [BCFTOOLS_mpileup](https://samtools.github.io/bcftools/bcftools.html#mpileup) <br> &emsp; - [**Glimpse2**](https://odelaneau.github.io/GLIMPSE/glimpse2/index.html) For this step the reference panel is transformed to binary chunks. <br> &emsp; - [**Stitch**](https://github.com/rwdavies/stitch) <br> &emsp; - [**Quilt**](https://github.com/rwdavies/QUILT) <br> - **Ligation**: all the different chunks are merged together. <br> - **Sampling** (optional) |
| **Simulate** | <img src="docs/images/metro/Simulate.png" alt="simulate_metro" width="600"/> | The simulation mode is used to create artificial low informative genetic information from high density data. This allow to compare the imputed result to a _truth_ and therefore evaluate the quality of the imputation. <br> For the moment it is possible to simulate: <br> - Low-pass data by **downsample** BAM or CRAM using [SAMTOOLS_view -s]() at different depth <br> - Genotype data by **SNP selecting** the position used by a designated SNP chip. <br> The simulation mode will also compute the **Genotype likelihoods** of the high density data. |
| **Concordance** | <img src="docs/images/metro/Concordance.png" alt="concordance_metro" width="600"/> | This mode compare two vcf together to compute a summary of the differences between them. <br> To do so it use either: <br> - [**Glimpse1**](https://odelaneau.github.io/GLIMPSE/glimpse1/index.html) concordance process. <br> - [**Glimpse2**](https://odelaneau.github.io/GLIMPSE/glimpse2/index.html) concordance process <br> - Or convert the two vcf fill to `.zarr` using [**Scikit allele**](https://scikit-allel.readthedocs.io/en/stable/) and [**anndata**](https://anndata.readthedocs.io/en/latest/) before comparing the SNPs. |
| **Postprocessing** | <img src="docs/images/metro/PostProcessing.png" alt="postprocessing_metro" width="600"/> | This final process unable to loop the whole pipeline for increasing the performance of the imputation. To do so it filter out the best imputed position and rerun the analysis using this positions. |

## Pipeline output

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4 changes: 2 additions & 2 deletions assets/schema_input_panel.json
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"pattern": "^\\S+\\.vcf$",
"errorMessage": "Panel vcf file must be provided, cannot contain spaces and must have extension '.vcf'"
},
"index":{
"index": {
"type": "string",
"pattern": "^\\S+\\.vcf\\.(tbi|csi)$",
"errorMessage": "Panel vcf index file must be provided, cannot contain spaces and must have extension '.vcf.tbi' or '.vcf.csi'"
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"pattern": "^\\S+\\.tsv$",
"errorMessage": "Panel tsv file must be provided, cannot contain spaces and must have extension '.tsv'"
},
"legend":{
"legend": {
"type": "string",
"pattern": "^\\S+\\.legend$",
"errorMessage": "Panel legend file must be provided, cannot contain spaces and must have extension '.legend'"
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6 changes: 3 additions & 3 deletions docs/development.md
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Expand Up @@ -37,13 +37,13 @@ All channel need to be identified by a meta map as follow:
- T : tool used
- G : reference genome used (is it needed ?)


## Open questions

How to use different schema ?

- Use nf-validation
For the moment use different input / step.
In the futur, if/else logic will be added in the yml nf-core schema.
For the moment use different input / step.
In the futur, if/else logic will be added in the yml nf-core schema.

What's the use of dumpcustomsoftware ?
Will be deleted
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9 changes: 8 additions & 1 deletion docs/usage.md
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## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/phaseimpute/usage](https://nf-co.re/phaseimpute/usage)

> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/phaseimpute/usage](https://nf-co.re/phaseimpute/usage)

> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
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<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->

## Samplesheet input

<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->

## Samplesheet input
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- `apptainer`
- A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
- `conda`

- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.
If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment.

- `test`
- A profile with a complete configuration for automated testing
Expand Down Expand Up @@ -307,5 +310,9 @@ We recommend adding the following line to your environment to limit this (typica
```bash
NXF_OPTS='-Xms1g -Xmx4g'
```

NXF_OPTS='-Xms1g -Xmx4g'

```
```
2 changes: 1 addition & 1 deletion nextflow_schema.json
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}
]
},
"panel_index":{
"panel_index": {
"type": "string",
"description": "Path to the reference panel index file",
"fa_icon": "far fa-file-code",
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- singularity>=3.8
- nf-core>=2.13.0
- prettier>=3.0
- nf-test>=0.8
- nf-test>=0.8

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