Added schema back in and removed all trace of attribute and hostname (45122bcf) · Commits · Chaos / Cutandrun

lib/WorkflowMain.groovy

+2 −6

Original line number	Diff line number	Diff line
		@@ -82,9 +82,7 @@ class WorkflowMain {
		//
		public static String getGenomeAttribute(params, attribute) {
		def val = ''
		if (params.attribute) {
		val = params.attribute
		} else if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
		if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
		if (params.genomes[ params.genome ].containsKey(attribute)) {
		val = params.genomes[ params.genome ][ attribute ]
		}
		@@ -97,9 +95,7 @@ class WorkflowMain {
		//
		public static String getGenomeAttributeSpikeIn(params, attribute) {
		def val = ''
		if (params.attribute) {
		val = params.attribute
		} else if (params.genomes && params.spikein_genome && params.genomes.containsKey(params.spikein_genome)) {
		if (params.genomes && params.spikein_genome && params.genomes.containsKey(params.spikein_genome)) {
		if (params.genomes[ params.spikein_genome ].containsKey(attribute)) {
		val = params.genomes[ params.spikein_genome ][ attribute ]
		}

+0 −2

Original line number	Diff line number	Diff line
		@@ -91,12 +91,10 @@ params {
		schema_ignore_params = 'genomes'
		enable_conda = false
		singularity_pull_docker_container = false
		attribute = null

		// Config options
		custom_config_version = "master"
		custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
		hostnames = [:]
		config_profile_name = null
		config_profile_description = null
		config_profile_contact = null

+23 −0

Original line number	Diff line number	Diff line
		@@ -419,6 +419,22 @@
		"fa_icon": "fas fa-question-circle",
		"hidden": true
		},
		"publish_dir_mode": {
		"type": "string",
		"default": "copy",
		"description": "Method used to save pipeline results to output directory.",
		"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
		"fa_icon": "fas fa-copy",
		"enum": [
		"symlink",
		"rellink",
		"link",
		"copy",
		"copyNoFollow",
		"move"
		],
		"hidden": true
		},
		"email_on_fail": {
		"type": "string",
		"description": "Email address for completion summary, only when pipeline fails.",
		@@ -479,6 +495,13 @@
		"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
		"hidden": true,
		"fa_icon": "fas fa-bacon"
		},
		"singularity_pull_docker_container": {
		"type": "boolean",
		"description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
		"hidden": true,
		"fa_icon": "fas fa-toolbox",
		"help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
		}
		}
		}