Add nf-test: test_alternativepreprocessing

conf/test_alternativepreprocessing.config

@@ -24,7 +24,7 @@ params {
     config_profile_description         = "Minimal test to check the alternative short-read QC function, adapterremoval"
 
     // 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

tests/.nftignore

@@ -1,15 +1,4 @@
 .DS_Store
-bbduk/*.log
-centrifuge/*.{fastq.gz,txt}
-diamond/*/*.{tsv,log}
-fastp/*.{html,zip,json,log}
-fastqc/*_fastqc.{html,zip}
-fastqc/*/*fastqc.zip
-ganon/*/*.log
-kaiju/*/*.{tsv,txt}
-kraken2/*/*.{fastq.gz,txt}
-krona/*.html
-metaphlan/*/*.{biom,txt,sam}
 multiqc/multiqc_data/*.txt
 multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
 multiqc/multiqc_data/llms-full.txt
@@ -20,6 +9,16 @@ 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}
 pipeline_info/*.{html,json,txt,yml}
 porechop_abi/*.log