Doc fix (patch 0.10.1)

.nf-core.yml

@@ -43,4 +43,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.10.0
+  version: 0.10.1

CHANGELOG.md

@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[0.10.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.1)] – Onix (patch 1) – [2026-03-30]
+
+### Enhancements & fixes
+
+- Updated the instructions for building the Uniprot Reference Proteomes
+  database to accommodate duplicated sequences
+
 ## [[0.10.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.0)] – Onix – [2026-02-12]
 
 ### Enhancements & fixes

CITATION.cff

@@ -69,13 +69,13 @@ authors:
     orcid: https://orcid.org/0000-0003-1658-1762
     website: https://github.com/BethYates
 cff-version: 1.2.0
-date-released: "2026-02-12"
+date-released: "2026-03-30"
 doi: 10.5281/zenodo.7949058
 license: MIT
 message: If you use this software, please cite it using the metadata from this file
   and all references from CITATIONS.md .
 repository-code: https://github.com/sanger-tol/blobtoolkit
-title: sanger-tol/blobtoolkit v0.10.0 - Onix
+title: sanger-tol/blobtoolkit v0.10.1 - Onix (patch 1)
 type: software
 url: https://pipelines.tol.sanger.ac.uk/blobtoolkit
-version: 0.10.0
+version: 0.10.1

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.0" target="_blank">sanger-tol/blobtoolkit</a>
+  This report has been generated by the <a href="https://github.com/sanger-tol/blobtoolkit/releases/tag/0.10.1" target="_blank">sanger-tol/blobtoolkit</a>
   analysis pipeline.
 report_section_order:
   "sanger-tol-blobtoolkit-methods-description":

docs/usage.md

@@ -233,12 +233,16 @@ mkdir extract
 curl -L $EBI_URL/$(curl -vs $EBI_URL 2>&1 | awk '/tar.gz/ {print $9}') | \
   tar -xzf - -C extract
 
-# Create a single fasta file with all the fasta files from each subdirectory:
-find extract -type f -name '*.fasta.gz' ! -name '*_DNA.fasta.gz' ! -name '*_additional.fasta.gz' -exec cat '{}' '+' > reference_proteomes.fasta.gz
-
-# create the accession-to-taxid map for all reference proteome sequences:
-find extract -type f -name '*.idmapping.gz' -exec zcat {} + | \
-  awk 'BEGIN {OFS="\t"; print "accession", "accession.version", "taxid", "gi"} $2=="NCBI_TaxID" {print $1, $1, $3, 0}' > reference_proteomes.taxid_map
+# Create a single fasta file with all the unique sequences (determined by their accession) from the fasta
+# files from each subdirectory. It needs up to 32 GB RAM !
+find extract -type f -name '*.fasta.gz' ! -name '*_DNA.fasta.gz' ! -name '*_additional.fasta.gz' -exec zcat '{}' '+' \
+| awk '{ if (/^>/) { if ($1 in seen) {skip=1} else {skip=0; print}; seen[$1]=1 } else { if (!skip) {print} } }' \
+| gzip --best > reference_proteomes.fasta.gz
+
+# create the accession-to-taxid map for all reference proteome sequences, again removing duplicates:
+find extract -type f -name '*.idmapping.gz' -exec zcat {} + \
+| awk 'BEGIN {OFS="\t"; print "accession", "accession.version", "taxid", "gi"} $2=="NCBI_TaxID" {print $1, $1, $3, 0}' \
+| sort -u > reference_proteomes.taxid_map
 
 # create the taxon aware diamond blast database
 diamond makedb -p 16 --in reference_proteomes.fasta.gz --taxonmap reference_proteomes.taxid_map --taxonnodes $TAXDUMP/nodes.dmp --taxonnames $TAXDUMP/names.dmp -d reference_proteomes.dmnd

nextflow.config

@@ -363,7 +363,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '0.10.0'
+    version         = '0.10.1'
     doi             = '10.5281/zenodo.7949058'
 }
 

ro-crate-metadata.json

@@ -183,10 +183,10 @@
             },
             "url": [
                 "https://github.com/sanger-tol/blobtoolkit",
-                "https://pipelines.tol.sanger.ac.uk//blobtoolkit/0.10.0/"
+                "https://pipelines.tol.sanger.ac.uk//blobtoolkit/0.10.1/"
             ],
             "version": [
-                "0.10.0"
+                "0.10.1"
             ]
         },
         {

tests/default.nf.test.snap

@@ -81,7 +81,7 @@
                     "windowstats_input.py": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/blobtoolkit": "v0.10.0"
+                    "sanger-tol/blobtoolkit": "v0.10.1"
                 }
             },
             [

tests/nobusco.nf.test.snap

@@ -81,7 +81,7 @@
                     "windowstats_input.py": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/blobtoolkit": "v0.10.0"
+                    "sanger-tol/blobtoolkit": "v0.10.1"
                 }
             },
             [

tests/raw.nf.test.snap

@@ -86,7 +86,7 @@
                     "windowstats_input.py": "1.0.0"
                 },
                 "Workflow": {
-                    "sanger-tol/blobtoolkit": "v0.10.0"
+                    "sanger-tol/blobtoolkit": "v0.10.1"
                 }
             },
             [