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Merged
merged 2 commits into from
Mar 28, 2025
Merged

Ad missing samtools yield in bwa-mem2 #6888

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e677f10
Ad missing samtools yield in bwa-mem2
mvdbeek Mar 27, 2025
5852a26
Fix bwa-mem2 test structure
mvdbeek Mar 28, 2025
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2 changes: 0 additions & 2 deletions tools/bwa_mem2/.lint_skip
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Original file line number Diff line number Diff line change
@@ -1,3 +1 @@
ConditionalParamTypeBool
XMLOrder
TestsCaseValidation
160 changes: 108 additions & 52 deletions tools/bwa_mem2/bwa-mem2.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,10 @@
<import>read_group_macros.xml</import>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="1.21">samtools</requirement>
</expand>
<expand macro="stdio"/>
<command><![CDATA[
@pipefail@
Expand Down Expand Up @@ -282,80 +284,134 @@ bwa-mem2 mem

<tests>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
<param name="fastq_input_selector" value="single"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="single"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="rg_selector" value="set"/>
<param name="ID" value="rg1"/>
<param name="PL" value="CAPILLARY"/>
<param name="LB" value="AARDVARK-1" />
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="rg">
<param name="rg_selector" value="set"/>
<conditional name="read_group_id_conditional">
<param name="ID" value="rg1"/>
</conditional>
<conditional name="read_group_lb_conditional">
<param name="LB" value="AARDVARK-1" />
</conditional>
<param name="PL" value="CAPILLARY"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<param name="output_sort" value="unsorted"/>
<output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<param name="output_sort" value="name"/>
<output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="6" />
</test>
<test>
<param name="reference_source_selector" value="cached" />
<param name="ref_file" value="mtgenome"/>
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
<param name="analysis_type_selector" value="illumina"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="cached" />
<param name="ref_file" value="mtgenome"/>
</conditional>
<conditional name="fastq_input">
<param name="fastq_input_selector" value="paired"/>
<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
</conditional>
<conditional name="analysis_type">
<param name="analysis_type_selector" value="illumina"/>
</conditional>
<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
</test>
</tests>
Expand Down
2 changes: 1 addition & 1 deletion tools/bwa_mem2/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<import>read_group_macros.xml</import>

<token name="@TOOL_VERSION@">2.2.1</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@PROFILE_VERSION@">20.01</token>

<xml name="xrefs">
Expand Down