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Merge pull request #149 from MaxUlysse/viralreconupdate
Viralreconupdate
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4 changed files with 37 additions and 17 deletions
12
README.md
12
README.md
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@ -15,6 +15,7 @@ A repository for hosting Nextflow configuration files containing custom paramete
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config)
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* [Pipeline-specific institutional documentation](#pipeline-specific-institutional-documentation)
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* [Pipeline-specific documentation](#pipeline-specific-documentation)
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* [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline)
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* [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files)
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@ -159,9 +160,9 @@ Each configuration file will add new params and overwrite the params already exi
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Note that pipeline-specific configs are not required and should only be added if needed.
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### Pipeline-specific documentation
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### Pipeline-specific institutional documentation
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Currently documentation is available for the following pipeline within the specific profile:
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Currently documentation is available for the following pipelines within specific profiles:
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* ampliseq
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* [BINAC](docs/pipeline/ampliseq/binac.md)
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@ -174,6 +175,13 @@ Currently documentation is available for the following pipeline within the speci
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* [UPPMAX](docs/pipeline/sarek/uppmax.md)
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### Pipeline-specific documentation
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Currently documentation is available for the following pipeline:
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* viralrecon
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* [genomes](docs/pipeline/viralrecon/genomes.md)
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### Enabling pipeline-specific configs within a pipeline
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:warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
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16
conf/pipeline/viralrecon/genomes.config
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conf/pipeline/viralrecon/genomes.config
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/*
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* -------------------------------------------------
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* nfcore/viralrecon custom profile Nextflow config file
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* -------------------------------------------------
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* Defines viral reference genomes for all environments.
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*/
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params {
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// Genome reference file paths
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genomes {
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'NC_045512.2' {
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.fasta.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.gff.gz"
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}
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}
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}
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docs/pipeline/viralrecon/genomes.md
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docs/pipeline/viralrecon/genomes.md
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# nf-core/configs: viralrecon specific configuration
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Extra specific configuration for viralrecon pipeline
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## Usage
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Will be used automatically when running the pipeline with the shared configs in the nf-core/configs repository
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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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* -------------------------------------------------
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* nfcore/viralrecon custom profile Nextflow config file
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* -------------------------------------------------
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* Defines viral reference genomes for all environments.
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*/
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params {
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// Genome reference file paths
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genomes {
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'NC_045512.2' {
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.gff.gz"
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}
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'MN908947.3' {
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fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.fna.gz"
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gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz"
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}
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}
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}
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includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config"
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