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Update FreeBayes parameters for nf-core/eager compatibility #7850

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80d626b
Update FreeBayes parameters for nf-core/eager compatibility
mertydn Mar 30, 2026
b46f999
Update FreeBayes tool version and processing logic
mertydn Mar 30, 2026
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255 changes: 187 additions & 68 deletions tools/freebayes/freebayes.xml
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@@ -1,4 +1,4 @@
<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1" profile="23.0">
<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy2" profile="23.0">
<description>bayesian genetic variant detector</description>
<macros>
<import>macros.xml</import>
Expand Down Expand Up @@ -46,6 +46,20 @@
ln -s '$options_type.optional_inputs.input_variant_type.input_variant_vcf.metadata.tabix_index' input_variant_vcf.vcf.gz.tbi &&
#end if

##If custom_discovery mode is selected, run the script directly without splitting the genome and cut the script!
#if str( $options_type.options_type_selector ) == "custom_discovery":
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@bernt-matthias bernt-matthias Mar 30, 2026

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Can this be moved down to the big if statement that we already have for the $options_type.options_type_selector cases.

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@mertydn mertydn Mar 30, 2026

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@bernt-matthias I kept this block separate on purpose. The custom_discovery mode needs to run directly, without the --region i loop. If I move it inside the main block, it will add the --region parameters and break the command. Is it okay to keep it separate to avoid the region split?

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@bernt-matthias bernt-matthias Mar 30, 2026

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How about adding a 4th mode to target_limit_type_selector. That is splitting the do_not_limit in one where sequences are processed separately in parallel and one where all sequences on a bam file are processed jointly (I think it might be important to do distinguish this anyway).

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@wm75 wm75 Mar 30, 2026

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@mertydn can you explain why this particular set of options is incompatible with splitting? I'm a bit lost.

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@mertydn mertydn Mar 30, 2026

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@wm75 I am trying to run the nf-core/eager workflow on Galaxy and get the exact same results.
In eager, this step runs all at once without splitting the data:
freebayes --bam 'b_0.bam' --fasta-reference 'localref.fa' -p 2 -C 1 -g 0

I think galaxy splits the data into pieces (--region).
But this causes changes in the vcf file, so my results do not match nextflow. I needed a way to run it without --region parametre

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@mertydn mertydn Mar 30, 2026

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I can't generate the result that only the QUAL values ​​of the Y chromosomes are different in usegalaxy. because I had changed the XML file to restrict it to only use that parameters.

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@wm75 wm75 Mar 30, 2026

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Just share one of the prior freebayes runs, or even just the inputs and the eager-produced vcf in a history and I can play with freebayes myself.

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@mertydn mertydn Mar 30, 2026

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https://usegalaxy.org/u/mert1907/h/freebayes

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@mertydn mertydn Mar 30, 2026

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@wm75 The freebayes in usegalaxy includes a large number of parameters. If you try running it by restricting it to only the parameters I mentioned, I think you will get a result showing a difference only in the Y chromosome.

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@wm75 wm75 Mar 30, 2026

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I'll investigate, thanks!

freebayes
#for $bam_count, $input_bam in enumerate( $input_bamfiles ):
--bam 'b_${bam_count}.${input_bam.ext}'
#end for
--fasta-reference '${reference_fasta_filename}'
-p $options_type.p_val
-C $options_type.c_val
-g $options_type.g_val
> '${output_vcf}' ;
exit \$? ;
#end if

##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
#if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
Expand Down Expand Up @@ -347,6 +361,7 @@
<option value="naive">3. Frequency-based pooled calling</option>
<option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
<option value="full">5. Full list of options</option>
<option value="custom_discovery">6. Custom Discovery Mode (Manual -p, -C, -g)</option>
</param>
<when value="full">

Expand Down Expand Up @@ -621,6 +636,11 @@
<when value="simple_w_filters" />
<when value="naive" />
<when value="naive_w_filters" />
<when value="custom_discovery">
<param argument="-p" name="p_val" type="integer" value="2" label="Ploidy" help="Set ploidy for the analysis. (Default: 2)" />
<param argument="-C" name="c_val" type="integer" value="1" label="Min. Alternate Count" help="Require at least this count of observations supporting an alternate allele within a single individual. (Default: 1)" />
<param argument="-g" name="g_val" type="integer" value="1" label="Min. Alternate Total" help="Require at least this count of observations supporting an alternate allele within the total population. (Default: 1)" />
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</when>
</conditional>
<conditional name="output_options">
<param name="flavor" type="select" label="Type of main output to produce" help="The tool will, by default, produce VCF output with information about sites with called variants. If you want also information (such as depth of coverage) about non-called sites, you can use the gVCF or gVCF with custom block size options. The first collapses the stats of entire blocks of consecutive non-called sites into one non-call record. The second gives you control over how many consecutive non-called sites should be combined into a non-call record.">
Expand All @@ -644,61 +664,97 @@
<filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
</data>
</outputs>

<tests>
<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
<param name="options_type_selector" value="simple"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple"/>
</conditional>
<output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
<param name="options_type_selector" value="simple" />
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple" />
</conditional>
<conditional name="output_options">
<param name="flavor" value="gvcf" />
</conditional>
<output name="output_vcf" file="freebayes-phix174.gvcf" lines_diff="4" />
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
<param name="options_type_selector" value="simple" />
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta" />
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam" />
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple" />
</conditional>
<conditional name="output_options">
<param name="flavor" value="gvcf_custom" />
</conditional>
<!-- This test produces one record per reference position
<!-- This test produces one record per reference position
so the test file only contains the first part of the expected output up to the second variant site -->
<output name="output_vcf" file="freebayes-phix174.full.sample.gvcf" compare="contains" lines_diff="2" />
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
<param name="options_type_selector" value="naive_w_filters"/>
<param name="coverage_options_selector" value="set" />
<param name="min_coverage" value="14"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="naive_w_filters"/>
</conditional>
<conditional name="coverage_options">
<param name="coverage_options_selector" value="set" />
<param name="min_coverage" value="14"/>
</conditional>
<output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
</test>
<!-- Test that user-provided (variant-input option) sites are included in output -->
<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
<param name="options_type_selector" value="full"/>
<conditional name="optional_inputs">
<param name="optional_inputs_selector" value="set" />
<conditional name="input_variant_type">
<param name="input_variant_type_selector" value="provide_vcf" />
<param name="input_variant_vcf" value="freebayes-phix174-input-sites-test3.vcf.bgzip" />
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="full"/>
<conditional name="optional_inputs">
<param name="optional_inputs_selector" value="set" />
<conditional name="input_variant_type">
<param name="input_variant_type_selector" value="provide_vcf" />
<param name="input_variant_vcf" value="freebayes-phix174-input-sites-test3.vcf.bgzip" />
</conditional>
</conditional>
</conditional>
<output name="output_vcf">
Expand All @@ -707,55 +763,118 @@
</assert_contents>
</output>
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
<param name="options_type_selector" value="full"/>
<param name="population_model_selector" value="set"/>
<param name="P" value="1"/>
<param name="trim_complex_tail" value="--trim-complex-tail"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="full"/>
<conditional name="optional_inputs">
<param name="optional_inputs_selector" value="set" />
</conditional>
<conditional name="population_model">
<param name="population_model_selector" value="set"/>
<param name="P" value="1"/>
</conditional>
</conditional>
<output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
<param name="options_type_selector" value="simple"/>
<param name="coverage_options_selector" value="set" />
<param name="min_coverage" value="250" />
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple"/>
</conditional>
<conditional name="coverage_options">
<param name="coverage_options_selector" value="set" />
<param name="min_coverage" value="250" />
</conditional>
<output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
<param name="options_type_selector" value="simple"/>
<param name="coverage_options_selector" value="set" />
<param name="limit_coverage" value="400" />
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple"/>
</conditional>
<conditional name="coverage_options">
<param name="coverage_options_selector" value="set" />
<param name="limit_coverage" value="400" />
</conditional>
<output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
</test>

<test expect_num_outputs="1">
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
<param name="options_type_selector" value="simple"/>
<param name="coverage_options_selector" value="set" />
<param name="skip_coverage" value="100" />
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple"/>
</conditional>
<conditional name="coverage_options">
<param name="coverage_options_selector" value="set" />
<param name="skip_coverage" value="100" />
</conditional>
<output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
</test>

<test expect_num_outputs="1"> <!-- Test with CRAM -->
<param name="reference_source_selector" value="history" />
<param name="processmode" value="individual" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
<param name="options_type_selector" value="simple"/>
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="simple"/>
</conditional>
<output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
</test>

<test expect_num_outputs="1">
<conditional name="reference_source">
<param name="reference_source_selector" value="history" />
<param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
<conditional name="batchmode">
<param name="processmode" value="individual" />
<param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
</conditional>
</conditional>
<conditional name="options_type">
<param name="options_type_selector" value="custom_discovery"/>
<param name="p_val" value="2"/>
<param name="c_val" value="1"/>
<param name="g_val" value="0"/>
</conditional>
<output name="output_vcf" file="freebayes-phix174-test8.vcf" lines_diff="4" />
</test>
</tests>
<help><![CDATA[
**What it does**
Expand Down
2 changes: 1 addition & 1 deletion tools/freebayes/leftalign.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0"?>
<tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@+galaxy0">
<tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@+galaxy1">
<description> indels in BAM datasets</description>
<macros>
<import>macros.xml</import>
Expand Down
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