From 50a44d037bb86703f405c5903ffa944222ce0052 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 9 Apr 2020 17:02:36 +0200 Subject: [PATCH 1/2] better docs and organisation of giles --- README.md | 12 ++++++++++-- conf/pipeline/viralrecon/genomes.config | 16 ++++++++++++++++ docs/pipeline/viralrecon/genomes.md | 9 +++++++++ pipeline/viralrecon.config | 11 +---------- 4 files changed, 36 insertions(+), 12 deletions(-) create mode 100644 conf/pipeline/viralrecon/genomes.config create mode 100644 docs/pipeline/viralrecon/genomes.md diff --git a/README.md b/README.md index 49283ed..17ce78c 100644 --- a/README.md +++ b/README.md @@ -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/` repository.** diff --git a/conf/pipeline/viralrecon/genomes.config b/conf/pipeline/viralrecon/genomes.config new file mode 100644 index 0000000..45c8247 --- /dev/null +++ b/conf/pipeline/viralrecon/genomes.config @@ -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" + } + } +} diff --git a/docs/pipeline/viralrecon/genomes.md b/docs/pipeline/viralrecon/genomes.md new file mode 100644 index 0000000..9577434 --- /dev/null +++ b/docs/pipeline/viralrecon/genomes.md @@ -0,0 +1,9 @@ +# 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. diff --git a/pipeline/viralrecon.config b/pipeline/viralrecon.config index 45c8247..25d93c4 100644 --- a/pipeline/viralrecon.config +++ b/pipeline/viralrecon.config @@ -2,15 +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/NC_045512.2.fasta.gz" - gff = "https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/NC_045512.2.gff.gz" - } - } -} +includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config" } \ No newline at end of file From 5678494e45eb098cdc59a05b83c71d6d9d1d63ab Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 9 Apr 2020 17:13:19 +0200 Subject: [PATCH 2/2] fix typo --- pipeline/viralrecon.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipeline/viralrecon.config b/pipeline/viralrecon.config index 25d93c4..3a79bef 100644 --- a/pipeline/viralrecon.config +++ b/pipeline/viralrecon.config @@ -4,4 +4,4 @@ * ------------------------------------------------- */ -includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config" } \ No newline at end of file +includeConfig "${params.custom_config_base}/conf/pipeline/viralrecon/genomes.config" \ No newline at end of file