Add nf-test: test_alternativepreprocessing

conf/test_alternativepreprocessing.config

@@ -20,18 +20,19 @@ process {
 }
 
 params {
-    config_profile_name                = 'Test profile for adapterremoval'
-    config_profile_description         = "Minimal test to check the alternative short-read QC function, adapterremoval"
+    config_profile_name                = 'Test profile for alternative preprocessing tools'
+    config_profile_description         = "Minimal test to check the alternative short-read and long-read processing and QC tools"
 
     // Input data
-    input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
+    input                              = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_shortreadfastqpairsonly.csv'
     databases                          = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.3.csv'
     perform_shortread_qc               = true
     perform_longread_qc                = true
     shortread_qc_tool                  = 'adapterremoval'
     longread_adapterremoval_tool       = 'porechop'
     longread_filter_tool               = 'filtlong'
     perform_shortread_complexityfilter = true
+    shortread_complexityfilter_tool    = 'prinseqplusplus'
     perform_shortread_hostremoval      = true
     perform_longread_hostremoval       = true
     perform_runmerging                 = true

nextflow.config

@@ -355,9 +355,6 @@ profiles {
     test_falcobbduk {
         includeConfig 'conf/test_falcobbduk.config'
     }
-    test_prinseqplusplus {
-        includeConfig 'conf/test_prinseqplusplus.config'
-    }
     metaval {
         includeConfig 'conf/metaval.config'
     }

tests/.nftignore

@@ -23,6 +23,16 @@ multiqc/multiqc_data/multiqc_software_versions.txt
 multiqc/multiqc_data/multiqc_sources.txt
 multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
 multiqc/multiqc_report.html
+bbduk/*.log
+centrifuge/*.{fastq.gz,txt}
+diamond/*/*.{tsv,log}
+fastp/*.{html,zip,json,log}
+fastqc/*/*_fastqc.{html,zip}
+ganon/*/*.log
+kaiju/*/*.{tsv,txt}
+kraken2/*/*.{fastq.gz,txt}
+krona/*.html
+metaphlan/*/*.{biom,txt,sam}
 nonpareil/*.{npa,npc,npl,npo,png,csv,json,pdf}
 nonpareil/nonpareil_all_samples.tsv
 pipeline_info/*.{html,json,txt,yml}