added validation catch of nonmerging of PE + metagenomics

nf-core · Aug 9, 2024 · 7b32ebd · 7b32ebd
1 parent 634435c
commit 7b32ebd
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -145,15 +145,15 @@ params {
     metagenomics_profiling_tool                  = null
     metagenomics_profiling_database              = null
     metagenomics_krakenuniq_ramchunksize         = "16G"
-    metagenomics_kraken2_savereads                = false
-    metagenomics_kraken2_savereadclassifications  = false
+    metagenomics_kraken2_savereads               = false
+    metagenomics_kraken2_savereadclassifications = false
     metagenomics_kraken2_saveminimizers          = false
     metagenomics_malt_mode                       = 'BlastN'
     metagenomics_malt_alignmentmode              = 'SemiGlobal'
     metagenomics_malt_savereads                  = false
     metagenomics_malt_minsupportmode             = 'percent'
     metagenomics_malt_minsupportpercent          = 0.01
-    metagenomics_malt_minsupportreads                 = 1
+    metagenomics_malt_minsupportreads            = 1
     metagenomics_malt_minpercentidentity         = 85
     metagenomics_malt_toppercent                 = 1
     metagenomics_malt_maxqueries                 = 100

diff --git a/subworkflows/local/utils_nfcore_eager_pipeline/main.nf b/subworkflows/local/utils_nfcore_eager_pipeline/main.nf
@@ -225,6 +225,7 @@ def validateInputParameters() {
     if ( params.metagenomics_complexity_tool == 'prinseq'  && params.metagenomics_prinseq_mode == 'entropy' && params.metagenomics_prinseq_dustscore != 0.5 ) {
         if (params.metagenomics_complexity_entropy == 0.3) { exit 1, ("[nf-core/eager] ERROR: Metagenomics: You picked PRINSEQ++ with 'entropy' mode but provided a dust score. Please specify an entropy filter threshold using the --metagenomics_complexity_entropy flag") }
     }
+    if ( params.run_metagenomics && params.preprocessing_skippairmerging ) { exit 1, ("[nf-core/eager] ERROR: Metagenomics: Currently no support for unmerged paired end reads inputs into Metagenomics subworkflow. Please rerun without --preprocessing_skippairmerging.") }
     if ( params.run_genotyping                        && ! params.genotyping_tool                ) { exit 1, ("[nf-core/eager] ERROR: --run_genotyping was specified, but no --genotyping_tool was specified.") }
     if ( params.run_genotyping                        && ! params.genotyping_source              ) { exit 1, ("[nf-core/eager] ERROR: --run_genotyping was specified, but no --genotyping_source was specified.") }
     if ( params.genotyping_source == 'trimmed'        && ! params.run_trim_bam                   ) { exit 1, ("[nf-core/eager] ERROR: --genotyping_source cannot be 'trimmed' unless BAM trimming is turned on with `--run_trim_bam`.") }