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Merge pull request #149 from MaxUlysse/viralreconupdate

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Viralreconupdate
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Harshil Patel 2020-04-09 18:22:06 +01:00 committed by GitHub
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README.md
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@ -15,6 +15,7 @@ A repository for hosting Nextflow configuration files containing custom paramete
* [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
* [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
* [Pipeline-specific documentation](#pipeline-specific-documentation)
* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
@ -159,9 +160,9 @@ Each configuration file will add new params and overwrite the params already exi
Note that pipeline-specific configs are not required and should only be added if needed.
### Pipeline-specific documentation
### Pipeline-specific institutional documentation
Currently documentation is available for the following pipeline within the specific profile:
Currently documentation is available for the following pipelines within specific profiles:
* ampliseq
* [BINAC](docs/pipeline/ampliseq/binac.md)
@ -174,6 +175,13 @@ Currently documentation is available for the following pipeline within the speci
* [MUNIN](docs/pipeline/sarek/munin.md)
* [UPPMAX](docs/pipeline/sarek/uppmax.md)
### Pipeline-specific documentation
Currently documentation is available for the following pipeline:
* viralrecon
* [genomes](docs/pipeline/viralrecon/genomes.md)
### Enabling pipeline-specific configs within a pipeline
:warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**

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conf/pipeline/viralrecon/genomes.config Normal file
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@ -0,0 +1,16 @@
/*
* -------------------------------------------------
* nfcore/viralrecon custom profile Nextflow config file
* -------------------------------------------------
* Defines viral reference genomes for all environments.
*/
params {
// Genome reference file paths
genomes {
'NC_045512.2' {
fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.fasta.gz"
gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.gff.gz"
}
}
}

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docs/pipeline/viralrecon/genomes.md Normal file
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# nf-core/configs: viralrecon specific configuration
Extra specific configuration for viralrecon pipeline
## Usage
Will be used automatically when running the pipeline with the shared configs in the nf-core/configs repository
This will download and launch the viralrecon specific [`viralrecon.config`](../../../conf/pipeline/viralrecon/genomes.config) which has been pre-configured with custom genomes.

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pipeline/viralrecon.config
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@ -2,19 +2,6 @@
* -------------------------------------------------
* nfcore/viralrecon custom profile Nextflow config file
* -------------------------------------------------
* Defines viral reference genomes for all environments.
*/
params {
// Genome reference file paths
genomes {
'NC_045512.2' {
fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz"
gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz"
}
'MN908947.3' {
fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz"
gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
}
}
}
includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config"