diff --git a/main.nf b/main.nf index 3b6635e..921aef7 100644 --- a/main.nf +++ b/main.nf @@ -29,7 +29,7 @@ version = '2.0.0' * Input parameters: */ -params.resume = false +// params.resume = false log_main = """ @@ -82,9 +82,7 @@ reclustered gene orthology file : ${params.sub_orthologs} """ -include { paramsHelp; paramsSummaryMap; validateParameters } from 'plugin/nf-schema' - -if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)" +include { paramsHelp; validateParameters } from 'plugin/nf-schema' // if( !workflow.resume ) { // println "Removing the output folder" @@ -101,11 +99,9 @@ include { SCORE } from "${LOCAL_SUBWORKFLOWS}/score.nf" include { PLOT } from "${WORKFLOWS}/plot.nf" -// println paramsSummaryMap(workflow) - workflow { - // validateParameters() + validateParameters() if (params.wf == "plot" ) { log.info(log_plot) diff --git a/nextflow_schema.json b/nextflow_schema.json index dab100b..3dcd0be 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -11,10 +11,6 @@ "description": "", "default": "", "properties": { - "resume": { - "type": "string", - "description": "Convenient param for detecting resume mistake" - }, "wf": { "type": "string", "description": "Workflow to be run, by default the main one. Alternative is plot", @@ -35,13 +31,13 @@ "annotations": { "type": "string", "description": "Path to GTF annotation files", - "format": "file-path", + "format": "file-path-pattern", "default": "./test/GTF/*_annot-subsetted.gtf.gz" }, "genomes": { "type": "string", "description": "Path to fasta genome files", - "format": "file-path", + "format": "file-path-pattern", "default": "./test/GENOMES/*_gDNA-subsetted.fasta.gz" }, "cluster": { @@ -128,7 +124,7 @@ } }, "plot_parameters": { - "title": "Plot parameters", + "title": "Plot Parameters", "type": "object", "description": "Specific parameters for generating plots", "default": "", @@ -161,7 +157,7 @@ "output_plot": { "type": "string", "description": "Path where to store resulting plot", - "format": "file-path", + "format": "directory-path", "default": "./output_plot" } } @@ -173,8 +169,7 @@ "email": { "type": "string", "description": "Email for notification", - "format": "email", - "default": "yourmail@yourdomain.xyz" + "format": "email" } } } diff --git a/params.config.test b/params.config.test index a061ba0..29cbe0c 100644 --- a/params.config.test +++ b/params.config.test @@ -14,7 +14,7 @@ params { short_dist = "2,0.50,0.60,0.25" prevaln = null output = "$projectDir/output_test" - email = "yourmail@yourdomain.xyz" + email = null geneID = "ENSG00000159055" output_plot = "$projectDir/output_plot" relevant_exs = "chr21:32274830-32274896"