Merge pull request #684 from nf-core/igenomes-ignore

Igenomes ignore

Author: apeltzer

CHANGELOG.md

@@ -13,7 +13,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#631](https://github.com/nf-core/eager/issues/631): - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
 - Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
 - Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data.  `
-- [#673](https://github.com/nf-core/eager/pull/673): Fix Kraken database loading when loading from directory instead of compressed file.
+- [#673](https://github.com/nf-core/eager/pull/673) - Fix Kraken database loading when loading from directory instead of compressed file.
+- [#683](https://github.com/nf-core/eager/pull/683) - Sets `--igenomes_ignore` to true by default, as rarely used by users currently and makes resolving configs less complex.
 
 ### `Dependencies`
 

nextflow.config

@@ -234,7 +234,7 @@ params {
   help = false
   igenomes_base = 's3://ngi-igenomes/igenomes/'
   tracedir = "${params.outdir}/pipeline_info"
-  igenomes_ignore = false
+  igenomes_ignore = true
   custom_config_version = 'master'
   custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
   hostnames = false

nextflow_schema.json

@@ -95,9 +95,9 @@
                 },
                 "genome": {
                     "type": "string",
-                    "description": "Name of iGenomes reference (required if not FASTA reference).",
+                    "description": "Name of iGenomes reference (required if not FASTA reference). Requires argument `--igenomes_ignore false` as iGenomes ignored by default in nf-core/eager",
                     "fa_icon": "fas fa-book",
-                    "help_text": "Alternatively to `--fasta`, the pipeline config files come bundled with paths to the Illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.\n\nThere are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.\n\nYou can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:\n\n- Human\n  - `--genome GRCh37`\n  - `--genome GRCh38`\n- Mouse *\n  - `--genome GRCm38`\n- _Drosophila_ *\n  - `--genome BDGP6`\n- _S. cerevisiae_ *\n  - `--genome 'R64-1-1'`\n\n> \\* Not bundled with nf-core eager by default.\n\nNote that you can use the same configuration setup to save sets of reference files for your own use, even if they are not part of the iGenomes resource. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for instructions on where to save such a file.\n\nThe syntax for this reference configuration is as follows:\n\n```nextflow\nparams {\n  genomes {\n    'GRCh37' {\n      fasta   = '<path to the iGenomes genome fasta file>'\n    }\n    // Any number of additional genomes, key is used with --genome\n  }\n}\n```"
+                    "help_text": "Alternatively to `--fasta`, the pipeline config files come bundled with paths to the Illumina iGenomes reference index files. If running with docker or AWS, the configuration is set up to use the [AWS-iGenomes](https://ewels.github.io/AWS-iGenomes/) resource.\n\nThere are 31 different species supported in the iGenomes references. To run the pipeline, you must specify which to use with the `--genome` flag.\n\nYou can find the keys to specify the genomes in the [iGenomes config file](../conf/igenomes.config). Common genomes that are supported are:\n\n- Human\n  - `--genome GRCh37`\n  - `--genome GRCh38`\n- Mouse *\n  - `--genome GRCm38`\n- _Drosophila_ *\n  - `--genome BDGP6`\n- _S. cerevisiae_ *\n  - `--genome 'R64-1-1'`\n\n> \\* Not bundled with nf-core eager by default.\n\nNote that you can use the same configuration setup to save sets of reference files for your own use, even if they are not part of the iGenomes resource. See the [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for instructions on where to save such a file.\n\nThe syntax for this reference configuration is as follows:\n\n```nextflow\nparams {\n  genomes {\n    'GRCh37' {\n      fasta   = '<path to the iGenomes genome fasta file>'\n    }\n    // Any number of additional genomes, key is used with --genome\n  }\n}\n**NB** Requires argument `--igenomes_ignore false` as iGenomes ignored by default in nf-core/eager\n\n```"
                 },
                 "igenomes_base": {
                     "type": "string",