From 64dd812fadba5221884b7ab9136283c6391704a0 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 28 Nov 2018 16:58:09 +0000 Subject: [PATCH] Bit of restructuring --- docs/configuration/reference_genomes.md | 49 ------------------------- docs/{configuration => }/crick.md | 0 2 files changed, 49 deletions(-) delete mode 100755 docs/configuration/reference_genomes.md rename docs/{configuration => }/crick.md (100%) diff --git a/docs/configuration/reference_genomes.md b/docs/configuration/reference_genomes.md deleted file mode 100755 index 7327253..0000000 --- a/docs/configuration/reference_genomes.md +++ /dev/null @@ -1,49 +0,0 @@ -# nf-core/atacseq: Reference Genomes Configuration - -The nf-core/atacseq pipeline needs a reference genome for alignment and annotation. - -These paths can be supplied on the command line at run time (see the [usage docs](../usage.md)), -but for convenience it's often better to save these paths in a nextflow config file. -See below for instructions on how to do this. -Read [Adding your own system](adding_your_own.md) to find out how to set up custom config files. - -## Adding paths to a config file -Specifying long paths every time you run the pipeline is a pain. -To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline. - -Note that this genome key can also be specified in a config file if you always use the same genome. - -To use this system, add paths to your config file using the following template: - -```nextflow -params { - genomes { - 'YOUR-ID' { - fasta = '/genome.fa' - } - 'OTHER-GENOME' { - // [..] - } - } - // Optional - default genome. Ignored if --genome 'OTHER-GENOME' specified on command line - genome = 'YOUR-ID' -} -``` - -You can add as many genomes as you like as long as they have unique IDs. - -## illumina iGenomes -To make the use of reference genomes easier, illumina has developed a centralised resource called [iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html). -Multiple reference index types are held together with consistent structure for multiple genomes. - -We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default. -The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon. -The pipeline will automatically download the required reference files when you run the pipeline. -For more information about the AWS iGenomes, see https://ewels.github.io/AWS-iGenomes/ - -Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource. -Once downloaded, you can customise the variable `params.igenomes_base` in your custom configuration file to point to the reference location. -For example: -```nextflow -params.igenomes_base = '/path/to/data/igenomes/' -``` diff --git a/docs/configuration/crick.md b/docs/crick.md similarity index 100% rename from docs/configuration/crick.md rename to docs/crick.md