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Fix containerized merqury #5945

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merged 7 commits into from
Apr 13, 2024
Merged

Fix containerized merqury #5945

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e6a94e9
Fix containerized merqury
mvdbeek Apr 12, 2024
17b6dd4
remove upstream deps
bgruening Apr 12, 2024
8a30c13
fix container init
bgruening Apr 13, 2024
a9bbe10
update test data, its a bit concerning why this has changed
bgruening Apr 13, 2024
d4116f3
fix last test
bgruening Apr 13, 2024
0db03a9
fix last tests
bgruening Apr 13, 2024
e5fa216
Update macros.xml
bgruening Apr 13, 2024
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2 changes: 1 addition & 1 deletion tools/merqury/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
<requirement type="package" version="@TOOL_VERSION@">merqury</requirement>
<requirement type="package" version="1.34">tar</requirement>
<requirement type="package" version="4.6.0">findutils</requirement>
<requirement type="package" version="8.32">coreutils</requirement>
<requirement type="package" version="9.5">coreutils</requirement>
</requirements>
</xml>
<xml name="citations">
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12 changes: 6 additions & 6 deletions tools/merqury/merqury.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -236,32 +236,32 @@
<output_collection name="png_files" type="list" count="6">
<element name="output_02.assembly.spectra-cn.fl">
<assert_contents>
<has_size value="71874" delta="100"/>
<has_size value="74570" delta="100"/>
</assert_contents>
</element>
<element name="output_02.assembly.spectra-cn.ln">
<assert_contents>
<has_size value="71888" delta="100"/>
<has_size value="74476" delta="100"/>
</assert_contents>
</element>
<element name="output_02.assembly.spectra-cn.st">
<assert_contents>
<has_size value="71123" delta="100"/>
<has_size value="74205" delta="100"/>
</assert_contents>
</element>
<element name="output_02.spectra-asm.fl">
<assert_contents>
<has_size value="47245" delta="100"/>
<has_size value="48524" delta="100"/>
</assert_contents>
</element>
<element name="output_02.spectra-asm.ln">
<assert_contents>
<has_size value="46896" delta="100"/>
<has_size value="48028" delta="100"/>
</assert_contents>
</element>
<element name="output_02.spectra-asm.st">
<assert_contents>
<has_size value="45945" delta="100"/>
<has_size value="47447" delta="100"/>
</assert_contents>
</element>
</output_collection>
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2 changes: 1 addition & 1 deletion tools/merqury/merqury_plot_CN.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,9 @@
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<version_command>merqury --version</version_command>

<command detect_errors="exit_code"><![CDATA[
mkdir -p output_files/ &&
export MERQURY="\$(dirname \$(which merqury.sh))/../share/merqury" &&
\$MERQURY/plot/plot_spectra_cn.R
-f '$input1'
-o output_files/merqury_plot
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2 changes: 1 addition & 1 deletion tools/merqury/test-data/output_02_qv.tabular
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
assembly 0 1037953
assembly 0 1037953 +inf 0
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It's normal that this changes, it just means that the bug is fixed. The problem is that the test data was wrong initially.

6 changes: 3 additions & 3 deletions tools/merqury/test-data/output_03_qv.tabular
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
assembly_01 0 1037953
assembly_02 0 1037953
Both 0 2075906
assembly_01 0 1037953 +inf 0
assembly_02 0 1037953 +inf 0
Both 0 2075906 +inf 0
2 changes: 1 addition & 1 deletion tools/merqury/test-data/output_06_qv.tabular
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
assembly unique k-mers common k-mers QV error rate
assembly 0 1037953
assembly 0 1037953 +inf 0