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Update diamond module #738

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b29a2e7
Update diamond module
Apr 22, 2026
a64f650
Update diamond dependency version to 2.1.24
sofstam Apr 22, 2026
1eac009
Merge branch 'update_diamond' of https://github.com/sofstam/taxprofil…
Apr 22, 2026
970df3f
Prettier
Apr 22, 2026
3b5132c
Remove versions for diamond/blastx
Apr 22, 2026
167dc11
Update test datasets
Apr 27, 2026
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5 changes: 3 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -15,8 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Dependencies`

| Tool | Previous version | New version |
| ---- | ---------------- | ----------- |
| Tool | Previous version | New version |
| ------- | ---------------- | ----------- |
| diamond | 2.1.12 | 2.1.24 |

## v2.0.0 - [2026-04-15]

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2 changes: 1 addition & 1 deletion conf/test.config
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Expand Up @@ -24,7 +24,7 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.1.csv'
perform_shortread_qc = true
perform_longread_qc = true
perform_shortread_redundancyestimation = true
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2 changes: 1 addition & 1 deletion conf/test_alternativepreprocessing.config
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Expand Up @@ -25,7 +25,7 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_shortreadfastqpairsonly.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.1.csv'
perform_shortread_qc = true
perform_longread_qc = true
shortread_qc_tool = 'adapterremoval'
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2 changes: 1 addition & 1 deletion conf/test_falcobbduk.config
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Expand Up @@ -25,7 +25,7 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_shortreadfastqpairsonly.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.1.csv'
preprocessing_qc_tool = 'falco'
perform_shortread_qc = true
perform_longread_qc = false
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2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -14,7 +14,7 @@ params {

// Input data for full size test
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_full.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_full_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_full_v2.1.csv'

// Genome references
hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz'
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2 changes: 1 addition & 1 deletion conf/test_malt.config
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Expand Up @@ -29,7 +29,7 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet_malt.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.1.csv'
perform_shortread_qc = false
perform_longread_qc = false
perform_shortread_redundancyestimation = false
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2 changes: 1 addition & 1 deletion conf/test_minimal.config
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Expand Up @@ -25,7 +25,7 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.1.csv'
perform_shortread_qc = false
perform_longread_qc = false
perform_shortread_redundancyestimation = false
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2 changes: 1 addition & 1 deletion conf/test_nopreprocessing.config
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Expand Up @@ -25,7 +25,7 @@ params {

// Input data
input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.0.csv'
databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v2.1.csv'
perform_shortread_qc = false
perform_longread_qc = false
perform_shortread_redundancyestimation = false
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -52,7 +52,7 @@
},
"diamond/blastx": {
"branch": "master",
"git_sha": "c44e4bb090eb4c9136f6d3f786285e4a9000f38f",
"git_sha": "1b534ad2336876dbe82e9fea2773334cb624b426",
"installed_by": ["modules"]
},
"falco": {
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2 changes: 1 addition & 1 deletion modules/nf-core/diamond/blastx/environment.yml
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82 changes: 43 additions & 39 deletions modules/nf-core/diamond/blastx/main.nf
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35 changes: 26 additions & 9 deletions modules/nf-core/diamond/blastx/meta.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/diamond/blastx/tests/main.nf.test
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36 changes: 24 additions & 12 deletions modules/nf-core/diamond/blastx/tests/main.nf.test.snap
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2 changes: 1 addition & 1 deletion subworkflows/local/profiling/main.nf
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Expand Up @@ -323,7 +323,7 @@ workflow PROFILING {
ch_diamond_reads_format = params.diamond_save_reads ? 'sam' : params.diamond_output_format

DIAMOND_BLASTX(ch_input_for_diamond.reads, ch_input_for_diamond.db, ch_diamond_reads_format, [])
ch_versions = ch_versions.mix(DIAMOND_BLASTX.out.versions.first())
//ch_versions = ch_versions.mix(DIAMOND_BLASTX.out.versions.first())
ch_raw_profiles = ch_raw_profiles.mix(DIAMOND_BLASTX.out.tsv)
ch_multiqc_files = ch_multiqc_files.mix(DIAMOND_BLASTX.out.log)
}
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