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test data
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sumanm99 committed Aug 22, 2024
1 parent 3b67261 commit c390238
Showing 6 changed files with 76 additions and 41 deletions.
1 change: 0 additions & 1 deletion src/nanoplot/config.vsh.yaml
Original file line number Diff line number Diff line change
@@ -15,7 +15,6 @@ argument_groups:
- name: --fastq
type: file
description: Data is in one or more default fastq file(s).
# default: "src/nanoplot/test_data/test1.fastq"
example: read.fq
direction: input
multiple: true
2 changes: 1 addition & 1 deletion src/nanoplot/script.sh
Original file line number Diff line number Diff line change
@@ -102,7 +102,7 @@ if [[ -n "$par_statsum" ]]; then
base_name=$(echo "$par_statsum" | sed 's/\*.*//')
# Make a folder with the extracted string as the name
mkdir -p "$base_name"
mv "$par_temp"/*.txt "$base_name"
mv *.txt "$base_name"
# else
# mkdir -p "$par_output"
# mv *.txt "$par_output"
40 changes: 40 additions & 0 deletions src/nanoplot/test.sh
Original file line number Diff line number Diff line change
@@ -210,4 +210,44 @@ echo "Test 4 succeeded."

###########################################################################

# Test 5: Run NanoPlot with different input

# Check if HTML file is generated
if ! ls target/result/*.html 1> /dev/null 2>&1; then
echo "Output HTML file not found"
exit 1
fi

# Check if summary file is generated
if ! ls target/result/*.txt 1> /dev/null 2>&1; then
echo "NanoPlot summary file not found"
exit 1
fi

# Check if plots are generated
if ! ls target/result/*.png 1> /dev/null 2>&1; then
echo "Plots are not found"
exit 1
fi

# Check if files are empty
if find target/result -name "*.html" -type f -size 0 | grep -q .; then
echo "At least one HTML file is empty."
exit 1
fi
if find target/result -name "*.png" -type f -size 0 | grep -q .; then
echo "At least one plot is empty."
exit 1
fi
if find target/result -name "*.txt" -type f -size 0 | grep -q .; then
echo "NanoPlot summary file is empty."
exit 1
fi

# rm -f target/result/* # Clear output

echo "Test 5 succeeded."

###########################################################################

echo "All tests successfully completed!"
6 changes: 1 addition & 5 deletions src/nanoplot/test_data/script.sh
Original file line number Diff line number Diff line change
@@ -68,8 +68,4 @@ cp -r /tmp/snakemake-wrappers/bio/assembly-stats/test/*.fasta src/nanoplot/test_
#########################################################################################

## Bam file ##
cp -r /tmp/snakemake-wrappers/bio/arriba/test/A.bam src/nanoplot/test_data/test.bam

#########

## Cram file ##
cp -r /tmp/snakemake-wrappers/bio/arriba/test/A.bam src/nanoplot/test_data/test.bam
40 changes: 20 additions & 20 deletions src/nanoplot/test_data/test1.fastq
Original file line number Diff line number Diff line change
@@ -1,50 +1,50 @@
@read_1
AAACGCATCTGCAATACCATCGGGTCAGTATGTATTCACTTA
ATACAACCGACCTTTTCGGTCCGAATGCAGGCGCGTCAGAGGAAACTATCC
+
111111111111111111111111111111111111111111
888888888888888888888888888888888888888888888888888

@read_2
GCGTGGTGTACCGGTGGTCTATGTTATCTAGCTTGGACCGTAGAGCACCGTTTTCCAAGGCGTAAAGTGAAAAGGGAAAACGCTGGATGCCACCCTGGCA
GCCGGAGTAAACAATGCTCTTAACGTACTTCCCACCTAAAGGTACTACAAAACTTGATCTCAACTG
+
))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))
GGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

@read_3
TCGAGCAGTTAGACAGGTGTACCCGGACATCTTCCTAATTGGGGTTCTCTGAAAACTCTTAAGGTGCTAGGCCTGATTTAGAGACGTAT
ACCTGCACACGGAGAGCATCTCAAAATATCGGCCCTGGGAATCGTATCTCGTCGACGCGGAAAGTTTAGCCGGTTCTG
+
LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
..............................................................................

@read_4
ATTCCCCGTCAAATACCCTCCATGCGTCTAGGCTGCGATCCTAGACAAATCGTCGGCATGCGCACATTCCTTCGCTGTTCTTTTGAA
GCTAACCTGGGAAAGCCTGCAGAGAAGGGTGAATCCACAAACTTGGGAACG
+
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHKKKKKKKKKKKKKKKKKKKKK
888888888888888888888888888888888888888888888888888

@read_5
AGACAACATACGACCATCCATGATACCTTTGACTTCGAGATGCCTTCGTGGCAGCAAAAACGTAATGGGGCTACGGTACCCGCGCTAAGGTTTTATGAGA
TTCGCTGAAGGGCGTAGCTACCTATCTCGGCGGCAACCAGCTCACATGGGCAAAGGGAGGGTACCGTTTTCCCCGGATACGATCTTCCCTTGCCGTCA
+
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM

@read_6
CGTCCGACCCAAGCTGACCCAGGGCCAACCTTCGAGATTTCGAAATGGGGTTGGAAGTATGCTTCCCCCCACGC
GCAGTATTGATTAACGTGGGGCAAAGTACGTAGGACGTACCTCCTGTTGCGTGCTCACCCACAGGCCGTTACCCCG
+
((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((
4444444444444444444444444444444444444444444444444444444444444444444444444444

@read_7
GTGTGTTAATACATCTATCGCTCGGAGAATTCAGCTCCAACACGGTTTTGTAGAGAGTCGAGA
CTCAGCTGAGTGGCGGAGGGCTATGGGTCCGTCCGACTCTAT
+
???????????????????????????????????????????????????????????????
HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH

@read_8
GGAACTAGTCGGACGATTCAGCTTCGCTGTCATT
CCGCGATATGCGTGATGCTAATTTATCCAAAGTAATCACACCTCC
+
0000000000000000000000000000000000
444444444444444444444444444444444444444444444

@read_9
CGACATCACGAGAATGTACCTCGCGACCCCCGTTTACTCATTCATGCGGGT
TTTCCCCGGTTATGGGGTAGCCTTTTGGGCGACATGTCCGCGTGGACGCAGGAAGTACCTCCCGTATGTTAGG
+
888888888888888888888888888888888888888888888888888
%%%%%%%%%%%%%%%%%%%%%%%%#################################################

@read_10
AAAACCCTAGGACAGGGCACTGCCACAGCGTAATGCCCACGCTTATGTGGACCGTGATGTAAGGATTACATCCCAGCTAA
ATCGAGGGAATTTGATTCTTCTCGCAAAGCCGCGTTGACTAGGCTACCCAGTACAGCTTAAAGACCTGAAAATTAGTTATCAGTCCTCTCT
+
--------------------------------------------------------------------------------
BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

28 changes: 14 additions & 14 deletions src/nanoplot/test_data/test2.fastq
Original file line number Diff line number Diff line change
@@ -1,35 +1,35 @@
@read_1
CCTACGGAACAAATACATTCTGGAAGAAGATTGCCGAAAGATGCCC
AATCCAAAAGTGATTGCACCAAGCCAGAATACC
+
----------------------------------------------
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

@read_2
ATTATAGCGAAGAGTGGATACATCATGGAAGTCAAGTGCC
TGGATAATCCATCGATATCTATAGAAATACCGCCATATGGGCCCCTACGGCCAGCCGGATATCAATGGATGACTAAC
+
OOOOOOOOOOOOOOONNNNNNNNNNNNNNNNNNNNNNNNN
.............................................................................

@read_3
TGATAAGGTCCGGTGGACTAGCCCGTGTCGGCTCACCTCGTTAATGATGTGTGTGAACTCGTACAATACA
CCTTAAGTCGCATACCATTGTCCGTGGGAGTTCATACAAATACGCGTTACTGAAGCCTCGCTCTGTATAGTAAATTAAGTTCTTATGACA
+
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

@read_4
TGTATCACGCGGGGACCGCACGCAATCTGTTAACTGCTCTAGGTTTTAACCTGTTCCCCCCACGCCGCCG
TGCAAAGGCCCCCGGCTTCATCCTC
+
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
0000000000000000000000000

@read_5
TTTCGTCATGTAACCGATAACATGCAGTGCGAAGTTTCGCGAGTTCACCTAAACGGTAGTTTAGACGGTCTAAA
TGTCAGTAATGCTACTCTTGTTGCGAGCCGGGGTATCCTAA
+
CHANGELOG.md CONTRIBUTING.md LICENSE out output README.md README.qmd src target _viash.yaml
)))))))))))))))))))))))))))))))))))))))))

@read_6
GTGCCTAGAACCCTAGACGTATAGCAAGACTGGACTCGGCGTCGAAAACCAGGCCTGTCCCTGAG
ATATACGTGACCTTTTATTTTAGACGCTAGCTGGTATACATTTCAATTCTCGGCTATTGTGTCCGGC
+
KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK
))))))))))))))))))))))))))))))))))))))))))))))---------------------

@read_7
TTCTCTTGAGAGGTTATCGGCGC
TTCGATAATTCATACCTCAC
+
'''''''''''''''''''''''
JJJJJJJJJJJJJJJJJJJJ

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