add "refs/tags" for GitHub references

Formula/ale.rb

@@ -2,7 +2,7 @@ class Ale < Formula
   # cite Clark_2013: "https://doi.org/10.1093/bioinformatics/bts723"
   desc "Assembly Likelihood Estimator"
   homepage "https://github.com/sc932/ALE"
-  url "https://github.com/sc932/ALE/archive/20220503.tar.gz"
+  url "https://github.com/sc932/ALE/archive/refs/tags/20220503.tar.gz"
   sha256 "b04a047fd3b11c0e84718bea20fe7d03f50f80a542d3b18e66c5b95983b9e559"
   head "https://github.com/sc932/ALE.git"
 

Formula/andi.rb

@@ -2,7 +2,7 @@ class Andi < Formula
   # cite Hauboid_2015: "https://doi.org/10.1093/bioinformatics/btu815"
   desc "Estimate evolutionary distance between similar genomes"
   homepage "https://github.com/EvolBioInf/andi"
-  url "https://github.com/EvolBioInf/andi/archive/v0.14.tar.gz"
+  url "https://github.com/EvolBioInf/andi/archive/refs/tags/v0.14.tar.gz"
   sha256 "2c9e11524f38e74fe3f981e6acd9527c1a1ca30994a30c5e86808ba5165a25b7"
   license "GPL-3.0-or-later"
 

Formula/any2fasta.rb

@@ -1,7 +1,7 @@
 class Any2fasta < Formula
   desc "Convert various sequence formats to FASTA"
   homepage "https://github.com/tseemann/any2fasta"
-  url "https://github.com/tseemann/any2fasta/archive/v0.4.2.tar.gz"
+  url "https://github.com/tseemann/any2fasta/archive/refs/tags/v0.4.2.tar.gz"
   sha256 "e4cb2ddccda6298f5b0aee0c10184a75307a08b584d2abbfbf0d59d37b197e73"
   license "GPL-3.0"
 

Formula/arks.rb

@@ -2,7 +2,7 @@ class Arks < Formula
   # cite Coombe_2018: "https://doi.org/10.1186/s12859-018-2243-x"
   desc "Scaffold genome assemblies with 10x Genomics Chromium reads"
   homepage "https://github.com/bcgsc/arks"
-  url "https://github.com/bcgsc/arks/archive/v1.0.4.tar.gz"
+  url "https://github.com/bcgsc/arks/archive/refs/tags/v1.0.4.tar.gz"
   sha256 "bb99a2e2adc988605a19b2f1cfcd6300ba392ac9697efc22c2b2b77de2b13711"
   head "https://github.com/bcgsc/arks.git"
 

Formula/astral.rb

@@ -2,7 +2,7 @@ class Astral < Formula
   # cite Zhang_2017: "https://doi.org/10.1007/978-3-319-67979-2_4"
   desc "Estimate species tree given set of unrooted gene trees"
   homepage "https://github.com/smirarab/ASTRAL"
-  url "https://github.com/smirarab/ASTRAL/archive/v5.7.1.tar.gz"
+  url "https://github.com/smirarab/ASTRAL/archive/refs/tags/v5.7.1.tar.gz"
   sha256 "8aa6fd4324efca325d3dde432517090fac314bea95f407b1dd59977181fec77e"
   license "Apache-2.0"
   head "https://github.com/smirarab/ASTRAL.git"

Formula/autodock-vina.rb

@@ -4,7 +4,7 @@ class AutodockVina < Formula
   include Language::Python::Virtualenv
   desc "Docking and virtual screening program"
   homepage "https://github.com/ccsb-scripps/AutoDock-Vina/"
-  url "https://github.com/ccsb-scripps/AutoDock-Vina/archive/v1.2.5.tar.gz"
+  url "https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v1.2.5.tar.gz"
   sha256 "38aec306bff0e47522ca8f581095ace9303ae98f6a64031495a9ff1e4b2ff712"
   license "Apache-2.0"
   head "https://github.com/ccsb-scripps/AutoDock-Vina.git", branch: "develop"

Formula/bamm.rb

@@ -2,7 +2,7 @@ class Bamm < Formula
   # cite Rabosky_2014: "https://doi.org/10.1371/journal.pone.0089543"
   desc "Bayesian analysis of macroevolutionary mixture models on phylogenies"
   homepage "http://bamm-project.org"
-  url "https://github.com/macroevolution/bamm/archive/v2.5.0.tar.gz"
+  url "https://github.com/macroevolution/bamm/archive/refs/tags/v2.5.0.tar.gz"
   sha256 "526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4"
   license "GPL-2.0"
   head "https://github.com/macroevolution/bamm.git"

Formula/barrnap.rb

@@ -1,7 +1,7 @@
 class Barrnap < Formula
   desc "BAsic Rapid Ribosomal RNA Predictor"
   homepage "https://github.com/tseemann/barrnap"
-  url "https://github.com/tseemann/barrnap/archive/0.9.tar.gz"
+  url "https://github.com/tseemann/barrnap/archive/refs/tags/0.9.tar.gz"
   sha256 "36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15"
 
   bottle do

Formula/beast2.rb

@@ -2,7 +2,7 @@ class Beast2 < Formula
   # cite Bouckaert_2014: "https://doi.org/10.1371/journal.pcbi.1003537"
   desc "Bayesian evolutionary analysis by sampling trees"
   homepage "https://www.beast2.org/"
-  url "https://github.com/CompEvol/beast2/archive/v2.6.3.tar.gz"
+  url "https://github.com/CompEvol/beast2/archive/refs/tags/v2.6.3.tar.gz"
   sha256 "7528d3f4732bd2066079eb9001161deda20afc59424ec58fca844e56785dc6a9"
   license "LGPL-2.1"
 

Formula/berokka.rb

@@ -1,7 +1,7 @@
 class Berokka < Formula
   desc "Trim, circularise, and orient long read assemblies"
   homepage "https://github.com/tseemann/berokka"
-  url "https://github.com/tseemann/berokka/archive/v0.2.3.tar.gz"
+  url "https://github.com/tseemann/berokka/archive/refs/tags/v0.2.3.tar.gz"
   sha256 "460f4272768e205008aa8aa885d1df5bab9af2c5b404c261e00573c6a30a641f"
   license "GPL-3.0"
   revision 1

Formula/bifrost.rb

@@ -2,7 +2,7 @@ class Bifrost < Formula
   # cite Holley_2019: "https://doi.org/10.1101/695338"
   desc "Construction, indexing and querying of colored/compacted de Bruijn graphs"
   homepage "https://github.com/pmelsted/bifrost"
-  url "https://github.com/pmelsted/bifrost/archive/v1.0.5.tar.gz"
+  url "https://github.com/pmelsted/bifrost/archive/refs/tags/v1.0.5.tar.gz"
   sha256 "47360fe757b4aeec438deb38449dcaad607fc7421e7d6bf819112c8ed58c0d5d"
   license "BSD-2-Clause"
 

Formula/biomake.rb

@@ -2,7 +2,7 @@ class Biomake < Formula
   # cite Holmes_2016: "https://doi.org/10.1101/093245"
   desc "GNU-Make-like utility for managing builds and complex workflows"
   homepage "https://github.com/evoldoers/biomake"
-  url "https://github.com/evoldoers/biomake/archive/v0.1.5.tar.gz"
+  url "https://github.com/evoldoers/biomake/archive/refs/tags/v0.1.5.tar.gz"
   sha256 "630009c52472b97dfb22304330fe809abd5e038e8b0b6aa084c7fc437b8cd6a0"
   license "BSD-3-Clause"
 

Formula/bmdca.rb

@@ -3,7 +3,7 @@ class Bmdca < Formula
   # cite Russ_2020: "https://doi.org/10.1126/science.aba3304"
   desc "Boltzmann-machine Direct Coupling Analysis"
   homepage "https://github.com/ranganathanlab/bmDCA/"
-  url "https://github.com/ranganathanlab/bmDCA/archive/v0.8.12.tar.gz"
+  url "https://github.com/ranganathanlab/bmDCA/archive/refs/tags/v0.8.12.tar.gz"
   sha256 "542991c51ba1e9d74b500e09e80d43f716fe4214a24d71f580a24df667762049"
   license "GPL-3.0-only"
 

Formula/bonsai.rb

@@ -1,7 +1,7 @@
 class Bonsai < Formula
   desc "Ultrafast, flexible taxonomic analysis and classification"
   homepage "https://github.com/dnbaker/bonsai"
-  url "https://github.com/dnbaker/bonsai/archive/v0.3.tar.gz"
+  url "https://github.com/dnbaker/bonsai/archive/refs/tags/v0.3.tar.gz"
   sha256 "f89efdf87c4d4a20bf3b8d4e9a11120b44b2b6b3055698c1e48d7790088618b3"
   license "MIT"
 

Formula/bracken.rb

@@ -2,7 +2,7 @@ class Bracken < Formula
   # cite Lu_2017: "https://doi.org/10.7717/peerj-cs.104"
   desc "Bayesian estimation species abundances from Kraken output"
   homepage "https://ccb.jhu.edu/software/bracken/index.shtml"
-  url "https://github.com/jenniferlu717/Bracken/archive/v2.6.0.tar.gz"
+  url "https://github.com/jenniferlu717/Bracken/archive/refs/tags/v2.6.0.tar.gz"
   sha256 "fb1837d6f32b8f8c87353b9dc8a23d3418c348b00824a7064eb58f9bab11ea68"
   license "GPL-3.0"
 

Formula/canu.rb

@@ -2,7 +2,7 @@ class Canu < Formula
   # cite Koren_2017: "https://doi.org/10.1101/gr.215087.116"
   desc "Single molecule sequence assembler"
   homepage "https://canu.readthedocs.io/en/latest/"
-  url "https://github.com/marbl/canu/archive/v1.9.tar.gz"
+  url "https://github.com/marbl/canu/archive/refs/tags/v1.9.tar.gz"
   sha256 "6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385"
   head "https://github.com/marbl/canu.git"
 

Formula/cd-hit.rb

@@ -2,7 +2,7 @@ class CdHit < Formula
   # cite Li_2006: "https://doi.org/10.1093/bioinformatics/btl158"
   desc "Cluster and compare protein or nucleotide sequences"
   homepage "http://cd-hit.org"
-  url "https://github.com/weizhongli/cdhit/archive/V4.8.1.tar.gz"
+  url "https://github.com/weizhongli/cdhit/archive/refs/tags/V4.8.1.tar.gz"
   sha256 "f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70"
   license "GPL-2.0-or-later"
   revision 1

Formula/centrifuge.rb

@@ -2,7 +2,7 @@ class Centrifuge < Formula
   # cite Kim_2016: "https://doi.org/10.1101/gr.210641.116"
   desc "Rapid sensitive classification of metagenomic sequences"
   homepage "http://www.ccb.jhu.edu/software/centrifuge"
-  url "https://github.com/infphilo/centrifuge/archive/v1.0.3.tar.gz"
+  url "https://github.com/infphilo/centrifuge/archive/refs/tags/v1.0.3.tar.gz"
   sha256 "71340f5c0c20dd4f7c4d98ea87f9edcbb1443fff8434e816a5465cbebaca9343"
   license "GPL-3.0"
 

Formula/circlator.rb

@@ -5,7 +5,7 @@ class Circlator < Formula
 
   desc "Tool to circularize genome assemblies"
   homepage "https://sanger-pathogens.github.io/circlator/"
-  url "https://github.com/sanger-pathogens/circlator/archive/v1.5.5.tar.gz"
+  url "https://github.com/sanger-pathogens/circlator/archive/refs/tags/v1.5.5.tar.gz"
   sha256 "927b6c156bfba6fa02db0c1173e280f85373320814c51e084170df583e604a2a"
   license "GPL-3.0"
 
@@ -62,7 +62,7 @@ class Circlator < Formula
   end
 
   resource "pysam" do
-    url "https://github.com/pysam-developers/pysam/archive/v0.15.0.1.tar.gz"
+    url "https://github.com/pysam-developers/pysam/archive/refs/tags/v0.15.0.1.tar.gz"
     sha256 "b169ffbe0efb39fd193779e5982da1de86e392dfe66c6bc49d79aa34fe58b46b"
   end
 

Formula/clonalframeml.rb

@@ -2,7 +2,7 @@ class Clonalframeml < Formula
   # cite Didelot_2015: "https://doi.org/10.1371/journal.pcbi.1004041"
   desc "Efficient Inference of Recombination in Bacterial Genomes"
   homepage "https://github.com/xavierdidelot/ClonalFrameML"
-  url "https://github.com/xavierdidelot/ClonalFrameML/archive/v1.12.tar.gz"
+  url "https://github.com/xavierdidelot/ClonalFrameML/archive/refs/tags/v1.12.tar.gz"
   sha256 "ef76705c1a0f1343184f956cd0bdc96c2cfdbb998177330b09b6df84c74c2de6"
   license "GPL-3.0"
   head "https://github.com/xavierdidelot/ClonalFrameML.git"

Formula/das_tool.rb

@@ -2,7 +2,7 @@ class DasTool < Formula
   # cite Sieber_2018: "https://doi.org/10.1038/s41564-018-0171-1"
   desc "Genomic binning refiner"
   homepage "https://github.com/cmks/DAS_Tool"
-  url "https://github.com/cmks/DAS_Tool/archive/1.1.2.tar.gz"
+  url "https://github.com/cmks/DAS_Tool/archive/refs/tags/1.1.2.tar.gz"
   sha256 "0cb13aadb8727a7a1fd08b25336d59f742f6a6384a8bff894cb79b6a5661c613"
   head "https://github.com/cmks/DAS_Tool.git"
 

Formula/dehomopolymerate.rb

@@ -1,7 +1,7 @@
 class Dehomopolymerate < Formula
   desc "Collapse homopolymer runs in FASTQ files"
   homepage "https://github.com/tseemann/dehomopolymerate"
-  url "https://github.com/tseemann/dehomopolymerate/archive/v0.4.0.tar.gz"
+  url "https://github.com/tseemann/dehomopolymerate/archive/refs/tags/v0.4.0.tar.gz"
   sha256 "89b825e8092600cd8a81c81db6b40c1f206ea6b0f1853a15185aefaf24d02383"
   license "GPL-3.0"
 

Formula/disty.rb

@@ -1,7 +1,7 @@
 class Disty < Formula
   desc "Compute a distance matrix from a core genome alignment file"
   homepage "https://github.com/c2-d2/disty"
-  url "https://github.com/c2-d2/disty/archive/0.1.0.tar.gz"
+  url "https://github.com/c2-d2/disty/archive/refs/tags/0.1.0.tar.gz"
   sha256 "4fe8a37e1545904af226ffc7c38e3776d6b1fe7640b792fad6d9d3b30abc7bd2"
   license "MIT"
   head "https://github.com/c2-d2/disty.git"

Formula/e-mem.rb

@@ -2,7 +2,7 @@ class EMem < Formula
   # cite Khiste_2015: "https://doi.org/10.1093/bioinformatics/btu687"
   desc "Efficiently compute MEMs between large genomes"
   homepage "https://www.csd.uwo.ca/~ilie/E-MEM/"
-  url "https://github.com/lucian-ilie/E-MEM/archive/v1.0.1.tar.gz"
+  url "https://github.com/lucian-ilie/E-MEM/archive/refs/tags/v1.0.1.tar.gz"
   sha256 "70a5a1e8b4e190d117b8629fff3493a4762708c8c0fe9eae84da918136ceafea"
   license "GPL-3.0-or-later"
   revision 1

Formula/easel.rb

@@ -1,7 +1,7 @@
 class Easel < Formula
   desc "Multiple sequence alignment toolset"
   homepage "https://github.com/EddyRivasLab/easel"
-  url "https://github.com/EddyRivasLab/easel/archive/easel-0.46.tar.gz"
+  url "https://github.com/EddyRivasLab/easel/archive/refs/tags/easel-0.46.tar.gz"
   sha256 "6648ab45346c2cef4a5d4086de8e43e44f0c0f367cf92df08f4f9c88c179da42"
 
   livecheck do

Formula/epa-ng.rb

@@ -2,7 +2,7 @@ class EpaNg < Formula
   # cite Barbera_2018: "https://doi.org/10.1093/sysbio/syy054"
   desc "Massively parallel phylogenetic placement of genetic sequences"
   homepage "https://github.com/Pbdas/epa-ng"
-  url "https://github.com/Pbdas/epa-ng/archive/v0.3.8.tar.gz"
+  url "https://github.com/Pbdas/epa-ng/archive/refs/tags/v0.3.8.tar.gz"
   sha256 "d1db23919f49cfad202b18623e5eb30c3d6cedcc1705b944221daea8131cbb74"
   license "AGPL-3.0"
   head "https://github.com/Pbdas/epa-ng.git"

Formula/express.rb

@@ -2,7 +2,7 @@ class Express < Formula
   # cite Roberts_2012: "https://doi.org/10.1038/nmeth.2251"
   desc "Streaming quantification for sequencing"
   homepage "http://bio.math.berkeley.edu/eXpress/"
-  url "https://github.com/adarob/eXpress/archive/1.5.3.tar.gz"
+  url "https://github.com/adarob/eXpress/archive/refs/tags/1.5.3.tar.gz"
   sha256 "1c09fa067672ba2ccbac6901602f3e2d9b5e514ff1fe87f54163e94af69ff022"
   license "Artistic-2.0"
   head "https://github.com/adarob/eXpress.git"

Formula/faqcs.rb

@@ -2,7 +2,7 @@ class Faqcs < Formula
   # cite Lo_2014: "https://doi.org/10.1186/s12859-014-0366-2"
   desc "Quality Control of Next Generation Sequencing Data"
   homepage "https://github.com/LANL-Bioinformatics/FaQCs"
-  url "https://github.com/LANL-Bioinformatics/FaQCs/archive/2.10.tar.gz"
+  url "https://github.com/LANL-Bioinformatics/FaQCs/archive/refs/tags/2.10.tar.gz"
   sha256 "0458e3500adab5257ba11d1db5402adfc52feb936da39c0a26089cbfc1007832"
   license "GPL-3.0-or-later"
 

Formula/fasta.rb

@@ -2,7 +2,7 @@ class Fasta < Formula
   # cite Pearson_1990: "https://doi.org/10.1016/0076-6879(90)83007-V"
   desc "Classic FASTA sequence alignment suite"
   homepage "https://faculty.virginia.edu/wrpearson/fasta/"
-  url "https://github.com/wrpearson/fasta36/archive/v36.3.8h_11-Feb-2020.tar.gz"
+  url "https://github.com/wrpearson/fasta36/archive/refs/tags/v36.3.8h_11-Feb-2020.tar.gz"
   version "36.3.8h"
   sha256 "916b327ac996151c808bd7066dea59c4ecb6035fc27c27fa8f011d49548867d6"
 

Formula/fastani.rb

@@ -2,7 +2,7 @@ class Fastani < Formula
   # cite Jain_2017: "https://doi.org/10.1101/225342"
   desc "Fast Whole-Genome Similarity (ANI) Estimation"
   homepage "https://github.com/ParBLiSS/FastANI"
-  url "https://github.com/ParBLiSS/FastANI/archive/v1.32.tar.gz"
+  url "https://github.com/ParBLiSS/FastANI/archive/refs/tags/v1.32.tar.gz"
   sha256 "f66b3bb5b272aa3db4deae782e47020fa9aae63eecbbd6fd93df876237d3b2e5"
   license "Apache-2.0"
   revision 1

Formula/fastp.rb

@@ -2,7 +2,7 @@ class Fastp < Formula
   # cite Chen_2018: "https://doi.org/10.1101/274100"
   desc "Ultrafast all-in-one FASTQ preprocessor"
   homepage "https://github.com/OpenGene/fastp"
-  url "https://github.com/OpenGene/fastp/archive/v0.20.1.tar.gz"
+  url "https://github.com/OpenGene/fastp/archive/refs/tags/v0.20.1.tar.gz"
   sha256 "e1b663717850bed7cb560c0c540e9a05dd9448ec76978faaf853a6959fd5b1b3"
   license "MIT"
   head "https://github.com/OpenGene/fastp.git"

Formula/fastq-pair.rb

@@ -2,7 +2,7 @@ class FastqPair < Formula
   # cite Edwards_2019: "https://doi.org/10.1101/552885"
   desc "Fast efficient re-pairing of FASTQ files"
   homepage "https://github.com/linsalrob/fastq-pair"
-  url "https://github.com/linsalrob/fastq-pair/archive/v1.0.tar.gz"
+  url "https://github.com/linsalrob/fastq-pair/archive/refs/tags/v1.0.tar.gz"
   sha256 "74fd5bae4d85cc02245ff1b03f31fa3788c50966d829b107076a806ae061da3b"
   license "MIT"
   head "https://github.com/linsalrob/fastq-pair.git"

Formula/fermi-lite.rb

@@ -2,7 +2,7 @@ class FermiLite < Formula
   # cite Li_2012: "https://doi.org/10.1093/bioinformatics/bts280"
   desc "Assembling Illumina short reads in small regions"
   homepage "https://github.com/lh3/fermi-lite"
-  url "https://github.com/lh3/fermi-lite/archive/v0.1.tar.gz"
+  url "https://github.com/lh3/fermi-lite/archive/refs/tags/v0.1.tar.gz"
   sha256 "661053bc7213b575912fc7be9cdfebc1c92a10319594a8e8f18542c9e2adda6e"
   license "MIT"
 

Formula/filtlong.rb

@@ -1,7 +1,7 @@
 class Filtlong < Formula
   desc "Quality filtering of long noisy DNA sequencing reads"
   homepage "https://github.com/rrwick/Filtlong"
-  url "https://github.com/rrwick/Filtlong/archive/v0.2.0.tar.gz"
+  url "https://github.com/rrwick/Filtlong/archive/refs/tags/v0.2.0.tar.gz"
   sha256 "a4afb925d7ced8d083be12ca58911bb16d5348754e7c2f6431127138338ee02a"
   license "GPL-3.0"
 

Formula/flowcraft.rb

@@ -1,7 +1,7 @@
 class Flowcraft < Formula
   desc "Nextflow pipeline assembler for genomics"
   homepage "https://github.com/assemblerflow/flowcraft"
-  url "https://github.com/assemblerflow/flowcraft/archive/1.4.1.tar.gz"
+  url "https://github.com/assemblerflow/flowcraft/archive/refs/tags/1.4.1.tar.gz"
   sha256 "ca5f698f286b6bcc6fc15cb7767ae903e06f6b7af11183917845b1be4304f11f"
   license "GPL-3.0"
   revision 2

Formula/foldseek.rb

@@ -2,7 +2,7 @@ class Foldseek < Formula
   # cite van Kempen_2023: "https://doi.org/10.1038/s41587-023-01773-0"
   desc "Fast and sensitive comparisons of large protein structure sets"
   homepage "https://github.com/steineggerlab/foldseek"
-  url "https://github.com/steineggerlab/foldseek/archive/8-ef4e960.tar.gz"
+  url "https://github.com/steineggerlab/foldseek/archive/refs/tags/8-ef4e960.tar.gz"
   version "8-ef4e960"
   sha256 "c74d02c4924d20275cc567783b56fff10e76ed67f3d642f53c283f67c4180a1e"
   license "GPL-3.0-or-later"

Formula/fwdpp.rb

@@ -2,7 +2,7 @@ class Fwdpp < Formula
   # cite Thornton_2014: "https://doi.org/10.1534/genetics.114.165019"
   desc "C++ template library for forward-time population genetic simulations"
   homepage "https://molpopgen.github.io/fwdpp/"
-  url "https://github.com/molpopgen/fwdpp/archive/0.8.1.tar.gz"
+  url "https://github.com/molpopgen/fwdpp/archive/refs/tags/0.8.1.tar.gz"
   sha256 "63392c05afb46161186e462c5fbbe0610d261fadcac41b17f6e037011affdbbe"
   license "GPL-3.0"
   head "https://github.com/molpopgen/fwdpp.git"

Formula/gemma.rb

@@ -2,7 +2,7 @@ class Gemma < Formula
   # cite Zhou_2012: "http://dx.doi.org/10.1038/ng.2310"
   desc "Linear mixed models (LMMs) for genome-wide association (GWA)"
   homepage "https://github.com/genetics-statistics/gemma"
-  url "https://github.com/genetics-statistics/GEMMA/archive/v0.98.4.tar.gz"
+  url "https://github.com/genetics-statistics/GEMMA/archive/refs/tags/v0.98.4.tar.gz"
   sha256 "4f57a045d3289afaf31f818bf411ac46c5ee6f78ff8c9c4117963ca54e0bb9f0"
   license "GPL-3.0"
 

Formula/gemmi.rb

@@ -1,7 +1,7 @@
 class Gemmi < Formula
   desc "Macromolecular crystallography library and utilities"
   homepage "https://project-gemmi.github.io/"
-  url "https://github.com/project-gemmi/gemmi/archive/v0.6.3.tar.gz"
+  url "https://github.com/project-gemmi/gemmi/archive/refs/tags/v0.6.3.tar.gz"
   sha256 "d7fa5e2a96f2093900a8ceaf835d2761562b5c42403e3f4cc98d32bb94f6a091"
   license "MPL-2.0"
   head "https://github.com/project-gemmi/gemmi.git", branch: "master"

Formula/genome-painter.rb

@@ -1,7 +1,7 @@
 class GenomePainter < Formula
   desc "Paint genomes with taxa-specific k-mer probabilities"
   homepage "https://github.com/scwatts/genome_painter"
-  url "https://github.com/scwatts/genome_painter/archive/v0.0.8.tar.gz"
+  url "https://github.com/scwatts/genome_painter/archive/refs/tags/v0.0.8.tar.gz"
   sha256 "434d81b4ed301f14aa3e9a55fdeeefab295264aa82410482abda23655e7a18bd"
   license "GPL-3.0-or-later"
   revision 1

Formula/gfakluge.rb

@@ -2,7 +2,7 @@ class Gfakluge < Formula
   # cite Dawson_2019: "https://doi.org/10.21105/joss.01083"
   desc "C++ library and utilities for Graphical Fragment Assembly (GFA)"
   homepage "https://github.com/edawson/gfakluge"
-  url "https://github.com/edawson/gfakluge/archive/1.1.2.tar.gz"
+  url "https://github.com/edawson/gfakluge/archive/refs/tags/1.1.2.tar.gz"
   sha256 "4b9e2d358d87a8a0b8508b6ae076af7657f8bb5c823a73f912917c5689f72121"
   license "MIT"
   head "https://github.com/edawson/gfakluge.git"

Formula/harvest-tools.rb

@@ -2,7 +2,7 @@ class HarvestTools < Formula
   # cite Treangen_2014: "https://doi.org/10.1186/s13059-014-0524-x"
   desc "Utility for creating and interfacing with Gingr files"
   homepage "https://github.com/marbl/harvest-tools"
-  url "https://github.com/marbl/harvest-tools/archive/v1.3.tar.gz"
+  url "https://github.com/marbl/harvest-tools/archive/refs/tags/v1.3.tar.gz"
   sha256 "ffbcf0a115c74507695fd6cee4a9d5ba27a700db36b32d226521ef8dd3309264"
   head "https://github.com/marbl/harvest-tools.git"
 

Formula/hh-suite.rb

@@ -2,7 +2,7 @@ class HhSuite < Formula
   # cite Steinegger_2019: "https://doi.org/10.1186/s12859-019-3019-7"
   desc "Remote protein homology detection suite"
   homepage "https://github.com/soedinglab/hh-suite"
-  url "https://github.com/soedinglab/hh-suite/archive/v3.3.0.tar.gz"
+  url "https://github.com/soedinglab/hh-suite/archive/refs/tags/v3.3.0.tar.gz"
   sha256 "dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964"
   license "GPL-3.0-or-later"
   revision 2