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Update README.md
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johausmann authored Oct 26, 2023
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33 changes: 33 additions & 0 deletions README.md
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Expand Up @@ -186,6 +186,9 @@ As well as an organism name for the SnpEff annotation:
When a custom reference genome is provided, the pipeline automatically generates a bwa-mem2 index
in the case of fastq input and a custom SnpEff database for functional annotations using the steps
described below. The steps are listed here for documentation purposes and should __not be performed manually__.
If the indexes should be reused for multiple runs, they can be generated permanently with the
--reference_generate option. Afterwards the generated references can either be set in the
nextflow.config file or set via command line arguments of the workflow.

The reference genome FASTA needs to be indexed for different components of the pipeline.
bwa-mem2 indices, .fai index and a .dict index can be generated with the following three commands:
Expand Down Expand Up @@ -236,6 +239,12 @@ Other low quality mutations are removed from the output.
The VAF thresholds can be changed with the parameters `--low_frequency_variant_threshold`,
`--subclonal_variant_threshold` and `--low_quality_clonal_variant_threshold`.

### Lineage only mode

At some point, it might be desirable to run only the lineage determination to obtain the pangolin calls
of a sample. To solve this problem, we have implemented the lineage-only mode, which can be executed by specifying the option
"--lineage_mode" option. Please note that this mode can only be used with FASTA or VCF as input.

## How to run

### Requirements
Expand Down Expand Up @@ -387,6 +396,29 @@ path to BAM and path to BAI.
| ... | ... | ... |


For lineage-only:
```
nextflow run tron-bioinformatics/covigator-ngs-pipeline \
[-r v0.10.0] \
[-profile conda] \
--fasta <FASTA_FILE> \
--name example_run \
--output <OUTPUT_FOLDER> \
--lineage_mode
```

For preparation of custom references:
```
nextflow run tron-bioinformatics/covigator-ngs-pipeline \
[-r v0.10.0] \
[-profile conda] \
--reference <path_to_reference>/<custom_genome>.fasta \
--gff <path_to_reference>/<custom_genome_annotation>.gff3
--output <OUTPUT_FOLDER> \
--snpeff_organism <name_of_organism>
--reference_generate
```


### Getting help

Expand Down Expand Up @@ -417,6 +449,7 @@ Optional input only required to use a custom reference:
* --snpeff_data: path to the SnpEff data folder, it will be useful to use the pipeline on other virus than SARS-CoV-2
* --snpeff_config: path to the SnpEff config file, it will be useful to use the pipeline on other virus than SARS-CoV-2
* --snpeff_organism: organism to annotate with SnpEff, it will be useful to use the pipeline on other virus than SARS-CoV-2
* --reference_generate: Run reference generate to prepare reusable custom reference
Optional input:
* --fastq2: the second input FASTQ file
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -103,6 +103,7 @@ Optional input only required to use a custom reference:
* --snpeff_data: path to the SnpEff data folder, it will be useful to use the pipeline on other virus than SARS-CoV-2
* --snpeff_config: path to the SnpEff config file, it will be useful to use the pipeline on other virus than SARS-CoV-2
* --snpeff_organism: organism to annotate with SnpEff, it will be useful to use the pipeline on other virus than SARS-CoV-2
* --reference_generate: Run reference generate to prepare a reusable custom reference
Optional input:
* --fastq2: the second input FASTQ file
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