Fixed legacy parameters and cleaned up WARN due to our non-default ig…

…enomes param

.github/workflows/ci.yml

@@ -125,7 +125,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_bedtools_coverage --anno_file 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.gff3'
       - name: GENOTYPING_HC Test running GATK HaplotypeCaller
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker --run_genotyping --genotyping_tool 'hc' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker --run_genotyping --genotyping_tool 'hc' --gatk_hc_out_mode 'EMIT_ALL_ACTIVE_SITES' --gatk_hc_emitrefconf 'BP_RESOLUTION'
       - name: GENOTYPING_FB Test running FreeBayes
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'freebayes'
@@ -146,13 +146,13 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_pmdtools
       - name: GENOTYPING_UG AND MULTIVCFANALYZER Test running GATK UnifiedGenotyper and MultiVCFAnalyzer, additional VCFS
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer --additional_vcf_files 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Mammoth/vcf/JK2772_CATCAGTGAGTAGA_L008_R1_001.fastq.gz.tengrand.fq.combined.fq.mapped_rmdup.bam.unifiedgenotyper.vcf.gz' --write_allele_frequencies
       - name: COMPLEX LANE/LIBRARY MERGING Test running lane and library merging prior to GATK UnifiedGenotyper and running MultiVCFAnalyzer
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_complex,docker --run_genotyping --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP' --run_multivcfanalyzer
       - name: GENOTYPING_UG ON TRIMMED BAM Test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_genotyping --run_trim_bam --genotyping_source 'trimmed' --genotyping_tool 'ug' --gatk_ug_out_mode 'EMIT_ALL_SITES' --gatk_ug_genotype_model 'SNP'
       - name: BAM_INPUT Run the basic pipeline with the bam input profile, skip AdapterRemoval as no convertBam
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_bam,docker --skip_adapterremoval

main.nf

@@ -199,8 +199,8 @@ if (params.fasta_index && !params.fasta_index.endsWith(".fai")) {
 }
 
 // Check if genome exists in the config file. params.genomes is from igenomes.conf, params.genome specified by user
-if ( params.genome && !params.genomes.containsKey(params.genome)) {
-    exit 1, "[nf-core/eager] error: the provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}."
+if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+    exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
 }
 
 // Index files provided? Then check whether they are correct and complete

nextflow.config

@@ -24,7 +24,7 @@ params {
   //Pipeline options
   enable_conda               = false
   validate_params            = true
-  schema_ignore_params       = 'genomes'
+  schema_ignore_params       = 'genome'
   show_hidden_params         = false
 
   //Input reads
@@ -46,6 +46,10 @@ params {
   seq_dict = ''
   large_ref = false
   save_reference = false
+
+  // this is just to stop the iGenomes WARN as we set as FALSE by default. Otherwise should be overwritten by optional config load below.
+  genomes = false 
+
 
   //Skipping parts of the pipeline for impatient users
   skip_fastqc = false
@@ -346,6 +350,8 @@ profiles {
   benchmarking_human { includeConfig 'conf/benchmarking_human.config' }
   benchmarking_vikingfish { includeConfig 'conf/benchmarking_vikingfish.config' }
 }
+
+
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
   includeConfig 'conf/igenomes.config'

nextflow_schema.json

@@ -1643,4 +1643,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}