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Updating tb-profiler to 6.4.0 #6543

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merged 6 commits into from
Nov 16, 2024
Merged

Updating tb-profiler to 6.4.0 #6543

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fb94337
Updating to 6.4.0
emarinier Nov 8, 2024
4913122
Testing adding prefix to file output.
emarinier Nov 8, 2024
8853f3a
Debugging
emarinier Nov 12, 2024
89cee99
Testing fixing delly version.
emarinier Nov 12, 2024
f7d0517
delly 1.2.6
emarinier Nov 12, 2024
7113e37
Removing debug code.
emarinier Nov 12, 2024
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15 changes: 8 additions & 7 deletions tools/tb-profiler/tb_profiler_profile.xml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy1" profile="20.09" license="AGPL-3.0-or-later">
<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09" license="AGPL-3.0-or-later">
<description>Infer strain types and drug resistance markers from sequences</description>
<macros>
<token name="@TOOL_VERSION@">6.2.1</token>
<token name="@TOOL_VERSION@">6.4.0</token>
</macros>
<xrefs>
<xref type="bio.tools">tb-profiler</xref>
</xrefs>
<requirements>
<requirement type="package" version="1.2.6">delly</requirement>
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If this is true, we should maybe fix the conda package.

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Oh delly is not even a dependency of tb-profiler. https://github.com/bioconda/bioconda-recipes/blob/master/recipes/tb-profiler/meta.yaml

It is a dependency of https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pathogen-profiler/meta.yaml

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I guess then we leave it like it is.

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Coming to this late - pathogen-profiler is the underlying tool that tb-profiler uses. It depends on delly 1.2.6. The tb-profiler 4.6.0 in bioconda depends on pathogen-profiler 4.5.0 which has exactly this dependency (delly 1.2.6). I don't understand why an extra requirement is needed in the tool wrapper?

<requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
Expand Down Expand Up @@ -67,7 +68,7 @@
#if str($fastq_or_bam.input_select) != "bam"
&& mv bam/tbprofiler.bam '${output_bam}'
#end if
&& bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.vcf.gz
&& bcftools view -Ov -o '${output_vcf}' vcf/tbprofiler.targets.vcf.gz
#if $output_format == "pdf"
&& mv results/tbprofiler.results.pdf '${output_pdf}'
#else if $output_format == "txt"
Expand Down Expand Up @@ -189,7 +190,7 @@
<has_line line="Drug-resistance: RR-TB" />
<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
<has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
</assert_contents>
</output>
</test>
Expand All @@ -204,7 +205,7 @@
<has_line line="Drug-resistance: RR-TB" />
<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
<has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
</assert_contents>
</output>
</test>
Expand All @@ -223,7 +224,7 @@
<output name="output_txt">
<assert_contents>
<has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;43&#009;1.000&#009;rifampicin&#009;Assoc w R" />
</assert_contents>
</output>
<output name="results_json">
Expand All @@ -244,7 +245,7 @@
<has_line line="Octal: 000000000000771" />
<has_line line="Drug-resistance: RR-TB" />
<has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
<has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;35&#009;1.000&#009;rifampicin&#009;Assoc w R" />
</assert_contents>
</output>
</test>
Expand Down