improve test script by removing redundant commands and checking missing options

Author: wdecoster

scripts/test.sh

@@ -1,3 +1,4 @@
+#!/bin/bash
 set -ev
 
 if [ -d "nanotest" ]; then
@@ -6,32 +7,39 @@ else
     git clone https://github.com/wdecoster/nanotest.git
 fi
 
+# Quick info tests (no data processing)
 NanoPlot -h
 NanoPlot --listcolors
-echo "testing figformat pdf with:"
-NanoPlot --bam nanotest/alignment.bam --verbose -o tests -o tests --format pdf --drop_outliers
-echo "testing fasta with --tsv_stats:"
-NanoPlot --fasta nanotest/reads.fa.gz --verbose --maxlength 35000 -o tests --tsv_stats
-echo "testing bam:"
-NanoPlot --bam nanotest/alignment.bam --verbose -o tests --title testing
-echo "testing bam without supplementary alignments:"
-NanoPlot --bam nanotest/alignment.bam --verbose --no_supplementary -o tests
-echo "testing summary:"
-NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose -o tests
-echo "testing fastq rich:"
-NanoPlot --fastq_rich nanotest/reads.fastq.gz --verbose --downsample 800 -o tests
-echo "testing fastq minimal:"
-NanoPlot --fastq_minimal nanotest/reads.fastq.gz --store --verbose --plots dot -o tests
-echo "testing fastq plain:"
-NanoPlot --fastq nanotest/reads.fastq.gz --verbose --minqual 4 --color red -o tests
-echo "testing fasta:"
-NanoPlot --fasta nanotest/reads.fa.gz --verbose --maxlength 35000 -o tests
-echo "testing --no_static:"
-NanoPlot --summary nanotest/sequencing_summary.txt  --verbose --maxlength 35000 -o tests --no_static
+NanoPlot --listcolormaps
+NanoPlot --version
 
+# Merged tests - combining multiple options per execution:
+
+echo "testing bam with pdf format, outlier dropping, title, and quality filtering:"
+NanoPlot --bam nanotest/alignment.bam --verbose -o tests --format pdf --drop_outliers --title "Test Run" --minqual 8
+
+echo "testing fasta with tsv_stats, length filtering, and huge mode:"
+NanoPlot --fasta nanotest/reads.fa.gz --verbose --maxlength 35000 -o tests --tsv_stats --huge
+
+echo "testing bam without supplementary, with colormap and no_static:"
+NanoPlot --bam nanotest/alignment.bam --verbose --no_supplementary -o tests --colormap Viridis --no_static
+
+echo "testing summary with loglength, N50, multiple plots, and info_in_report:"
+NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose -o tests --N50 --plots kde dot --info_in_report
+
+echo "testing fastq_rich with downsample, store, and custom prefix:"
+NanoPlot --fastq_rich nanotest/reads.fastq.gz --verbose --downsample 500 -o tests --store --prefix test_
+
+echo "testing fastq_minimal with plots, color, and threads:"
+NanoPlot --fastq_minimal nanotest/reads.fastq.gz --verbose --plots dot -o tests --color red --threads 2
+
+echo "testing cram with multiple formats, length filtering, and only_report:"
+NanoPlot --cram nanotest/alignment.cram --verbose -o tests --format png jpeg --minlength 1000 --maxlength 40000 --only_report
+
+echo "testing summary with barcoded (warning expected) and raw export:"
+NanoPlot --summary nanotest/sequencing_summary.txt --barcoded --verbose -o tests --raw
+
+# Optional legacy test (commented out due to dependency issues)
 # echo "testing legacy with summary:"
-# echo "installing seaborn and an appropriate version of numpy" # fuck this
 # pip install seaborn==0.10.1 "numpy<1.24"
-# NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose -o tests --legacy hex --raw -p prefix --plots dot
-# echo "testing legacy with multiple output formats:"
-# NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose -o tests --legacy hex --raw -p prefix --plots dot --format pdf png jpeg
+# NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose -o tests --legacy hex --raw --prefix legacy_ --plots dot --format pdf