Merge remote-tracking branch 'upstream/master'

CHANGELOG.md

@@ -1,5 +1,59 @@
 # Changelog
 
+### [5.2.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.2.0...v5.2.1) (2024-11-22)
+
+
+### Performance Improvements
+
+* autobump bio/biobambam2/bamsormadup ([#3480](https://www.github.com/snakemake/snakemake-wrappers/issues/3480)) ([ebdc3f3](https://www.github.com/snakemake/snakemake-wrappers/commit/ebdc3f3184a2df3d3036240a94b9abcf8d9e55be))
+* autobump bio/cnvkit/antitarget ([#3486](https://www.github.com/snakemake/snakemake-wrappers/issues/3486)) ([42b2c54](https://www.github.com/snakemake/snakemake-wrappers/commit/42b2c54c822a0766c5fc960c10f33880baaf8037))
+* autobump bio/cnvkit/batch ([#3483](https://www.github.com/snakemake/snakemake-wrappers/issues/3483)) ([3fa9e55](https://www.github.com/snakemake/snakemake-wrappers/commit/3fa9e5583bd1d53316dd1c7943715e533c061ca4))
+* autobump bio/cnvkit/call ([#3484](https://www.github.com/snakemake/snakemake-wrappers/issues/3484)) ([876f233](https://www.github.com/snakemake/snakemake-wrappers/commit/876f2337d2cbd453b7141238ec89a411e5af403e))
+* autobump bio/cnvkit/diagram ([#3487](https://www.github.com/snakemake/snakemake-wrappers/issues/3487)) ([430bfd0](https://www.github.com/snakemake/snakemake-wrappers/commit/430bfd02431dbf0619d0884209fd2ff6c5a53297))
+* autobump bio/cnvkit/export ([#3482](https://www.github.com/snakemake/snakemake-wrappers/issues/3482)) ([6880dc2](https://www.github.com/snakemake/snakemake-wrappers/commit/6880dc2a44aa4341186869c09f49e975d6f4297a))
+* autobump bio/cnvkit/target ([#3485](https://www.github.com/snakemake/snakemake-wrappers/issues/3485)) ([6494174](https://www.github.com/snakemake/snakemake-wrappers/commit/6494174a761c805ea7202029a85cd98e0270cd5d))
+* autobump bio/multiqc ([#3489](https://www.github.com/snakemake/snakemake-wrappers/issues/3489)) ([f7ff561](https://www.github.com/snakemake/snakemake-wrappers/commit/f7ff5616ce538ceb80229c72a4714e892d042998))
+* autobump bio/picard/collectinsertsizemetrics ([#3490](https://www.github.com/snakemake/snakemake-wrappers/issues/3490)) ([589d4fd](https://www.github.com/snakemake/snakemake-wrappers/commit/589d4fd402e4b36ff4c9b435151fe2c1ed046c83))
+* autobump bio/varlociraptor/call-variants ([#3495](https://www.github.com/snakemake/snakemake-wrappers/issues/3495)) ([8515079](https://www.github.com/snakemake/snakemake-wrappers/commit/8515079e43a22ded7a1de987026277476544a34f))
+* autobump bio/varlociraptor/control-fdr ([#3492](https://www.github.com/snakemake/snakemake-wrappers/issues/3492)) ([bdae3b0](https://www.github.com/snakemake/snakemake-wrappers/commit/bdae3b01c816452471aefdcacb59abe993c250d9))
+* autobump bio/varlociraptor/estimate-alignment-properties ([#3494](https://www.github.com/snakemake/snakemake-wrappers/issues/3494)) ([ca7f770](https://www.github.com/snakemake/snakemake-wrappers/commit/ca7f7708b4073f1761d50c57a08fba7b87dba0f5))
+* autobump bio/varlociraptor/preprocess-variants ([#3491](https://www.github.com/snakemake/snakemake-wrappers/issues/3491)) ([16d7bbd](https://www.github.com/snakemake/snakemake-wrappers/commit/16d7bbd84830897e23019fa6e1140cb35f28c813))
+* autobump bio/vep/cache ([#3475](https://www.github.com/snakemake/snakemake-wrappers/issues/3475)) ([af5bc47](https://www.github.com/snakemake/snakemake-wrappers/commit/af5bc477822b51f03b1235643013270246325c07))
+* autobump bio/vg/autoindex ([#3493](https://www.github.com/snakemake/snakemake-wrappers/issues/3493)) ([56d958b](https://www.github.com/snakemake/snakemake-wrappers/commit/56d958b17f81df18633457afe4f6537ed9c5f12e))
+* autobump utils/datavzrd ([#3488](https://www.github.com/snakemake/snakemake-wrappers/issues/3488)) ([b22b3e3](https://www.github.com/snakemake/snakemake-wrappers/commit/b22b3e38a45ec8d66999ab8fd25346609f176a34))
+
+## [5.2.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.1.0...v5.2.0) (2024-11-21)
+
+
+### Features
+
+* varlociraptor wrappers ([#3478](https://www.github.com/snakemake/snakemake-wrappers/issues/3478)) ([b0fa9b7](https://www.github.com/snakemake/snakemake-wrappers/commit/b0fa9b7dacf46d54239b3000a5f42587f04e19dc))
+
+
+### Performance Improvements
+
+* autobump bio/cooltools/dots ([#3456](https://www.github.com/snakemake/snakemake-wrappers/issues/3456)) ([a97cdfc](https://www.github.com/snakemake/snakemake-wrappers/commit/a97cdfc2d66700877206de2d34088c85dfa4a638))
+* autobump bio/cooltools/eigs_cis ([#3463](https://www.github.com/snakemake/snakemake-wrappers/issues/3463)) ([8f8607d](https://www.github.com/snakemake/snakemake-wrappers/commit/8f8607dc96158d82854e868c215cc75ed6f3ff14))
+* autobump bio/cooltools/eigs_trans ([#3460](https://www.github.com/snakemake/snakemake-wrappers/issues/3460)) ([745bb7b](https://www.github.com/snakemake/snakemake-wrappers/commit/745bb7bef11895aa6d648a74c8bc8b0d5acae5a1))
+* autobump bio/cooltools/expected_cis ([#3461](https://www.github.com/snakemake/snakemake-wrappers/issues/3461)) ([812e9a2](https://www.github.com/snakemake/snakemake-wrappers/commit/812e9a21582784b56a71035260dfa23e5749d972))
+* autobump bio/cooltools/expected_trans ([#3455](https://www.github.com/snakemake/snakemake-wrappers/issues/3455)) ([e91030b](https://www.github.com/snakemake/snakemake-wrappers/commit/e91030b29be6e98910b4482c36b9e7760f3f5b86))
+* autobump bio/cooltools/insulation ([#3458](https://www.github.com/snakemake/snakemake-wrappers/issues/3458)) ([4c38da3](https://www.github.com/snakemake/snakemake-wrappers/commit/4c38da3bfc3fc16ab91fc5320f22bee8ff6b8dba))
+* autobump bio/cooltools/pileup ([#3462](https://www.github.com/snakemake/snakemake-wrappers/issues/3462)) ([7177ad2](https://www.github.com/snakemake/snakemake-wrappers/commit/7177ad292a12821208c6114a24115bf5f4dd193f))
+* autobump bio/cooltools/saddle ([#3457](https://www.github.com/snakemake/snakemake-wrappers/issues/3457)) ([7fe906d](https://www.github.com/snakemake/snakemake-wrappers/commit/7fe906d7706dc50abc771f2cddf801b56401ebe1))
+* autobump bio/fastp ([#3464](https://www.github.com/snakemake/snakemake-wrappers/issues/3464)) ([beb2060](https://www.github.com/snakemake/snakemake-wrappers/commit/beb20609d58d65c831572e30bb27faa65e4403eb))
+* autobump bio/gseapy/gsea ([#3465](https://www.github.com/snakemake/snakemake-wrappers/issues/3465)) ([f8cd208](https://www.github.com/snakemake/snakemake-wrappers/commit/f8cd2084082ba140dab5eb4b3daca4bf17e23877))
+* autobump bio/merqury ([#3413](https://www.github.com/snakemake/snakemake-wrappers/issues/3413)) ([70eb542](https://www.github.com/snakemake/snakemake-wrappers/commit/70eb5424fb0f977836fb50b98872fdc576ce4c1e))
+* autobump bio/muscle ([#3466](https://www.github.com/snakemake/snakemake-wrappers/issues/3466)) ([7c89f75](https://www.github.com/snakemake/snakemake-wrappers/commit/7c89f75c54e5f370c357a7ab9c830d3001a224a3))
+* autobump bio/quast ([#3467](https://www.github.com/snakemake/snakemake-wrappers/issues/3467)) ([4167757](https://www.github.com/snakemake/snakemake-wrappers/commit/4167757bf73e5deeb507be82c8e3cec6f2189ef8))
+* autobump bio/taxonkit ([#3468](https://www.github.com/snakemake/snakemake-wrappers/issues/3468)) ([bee8a4b](https://www.github.com/snakemake/snakemake-wrappers/commit/bee8a4b7182a386eb3beb9ce34aec915bdd0fe3e))
+* autobump bio/vep/annotate ([#3470](https://www.github.com/snakemake/snakemake-wrappers/issues/3470)) ([2332600](https://www.github.com/snakemake/snakemake-wrappers/commit/23326000ef4cb5e7947e5663580d3bc82576a712))
+* autobump bio/vg/construct ([#3472](https://www.github.com/snakemake/snakemake-wrappers/issues/3472)) ([09986e1](https://www.github.com/snakemake/snakemake-wrappers/commit/09986e164c36f13cfe40c5737ceeec1c8102712d))
+* autobump bio/vg/ids ([#3469](https://www.github.com/snakemake/snakemake-wrappers/issues/3469)) ([f9889f7](https://www.github.com/snakemake/snakemake-wrappers/commit/f9889f7bccf9c357ac4918ff377ddebb51466ed6))
+* autobump bio/vg/kmers ([#3474](https://www.github.com/snakemake/snakemake-wrappers/issues/3474)) ([555b73a](https://www.github.com/snakemake/snakemake-wrappers/commit/555b73a92343ce7125665a2d5c437729feb13bf1))
+* autobump bio/vg/merge ([#3473](https://www.github.com/snakemake/snakemake-wrappers/issues/3473)) ([61ae4e0](https://www.github.com/snakemake/snakemake-wrappers/commit/61ae4e078ca2e0231ca67d83a7126a658022941f))
+* autobump bio/vg/prune ([#3471](https://www.github.com/snakemake/snakemake-wrappers/issues/3471)) ([421ae43](https://www.github.com/snakemake/snakemake-wrappers/commit/421ae437e005f35d25818e57927dfa1676a2dd01))
+* autobump bio/vg/sim ([#3476](https://www.github.com/snakemake/snakemake-wrappers/issues/3476)) ([722f872](https://www.github.com/snakemake/snakemake-wrappers/commit/722f872d92e0a5003a141dda499df4ff8d8d9942))
+
 ## [5.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.0.2...v5.1.0) (2024-11-14)
 
 

bio/biobambam2/bamsormadup/environment.linux-64.pin.txt

@@ -1,33 +1,41 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
+# created-by: conda 24.9.2
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.7.22-hbcca054_0.conda#a73ecd2988327ad4c8f2c331482917f2
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h7e041cc_2.conda#9172c297304f2a20134fc56c97fbe229
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_2.conda#e2042154faafe61969556f28bade94b9
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
+https://conda.anaconda.org/conda-forge/linux-64/libboost-headers-1.85.0-ha770c72_4.conda#00e4848983222729ccb7c69f1039f4b9
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#cc3573974587f12dda90d96e3e55a702
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_2.conda#c28003b0be0494f9a7664389146716ff
-https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54
-https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.20.1-hd590300_1.conda#2facbaf5ee1a56967aecaee89799160e
-https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda#3cb76c3f10d3bc7f1105b2fc9db984df
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.3-heb4867d_0.conda#09a6c610d002e54e18353c06ef61a253
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553
 https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
-https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda#1635570038840ee3f9c71d22aa5b8b6d
-https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3
-https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
-https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-h59595ed_1.conda#e05410383ad9c39aaa76675a7661db24
-https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.4-hd590300_0.conda#412ba6938c3e2abaca8b1129ea82e238
-https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.8-he1b5a44_3.tar.bz2#83f1dc295c711bdbaf97e1f3bedf2f52
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda#30fd6e37fe21f86f4bd26d6ee73eeec7
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-14.2.0-h4852527_1.conda#8371ac6457591af2cf6159439c1fd051
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe
+https://conda.anaconda.org/conda-forge/linux-64/nettle-3.9.1-h7ab15ed_0.conda#2bf1915cc107738811368afcb0993a59
 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda#c94a5994ef49749880a8139cf9afcbe1
+https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3
 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
-https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.55.1-h47da74e_0.conda#a802251d1eaeeae041c867faf0f94fa8
-https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
-https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
-https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
-https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.78.0-h2c5509c_4.conda#417a9d724dc4b651f4a711d3aa3694e3
-https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.4.0-hca28451_0.conda#1158ac1d2613b28685644931f11ee807
-https://conda.anaconda.org/conda-forge/linux-64/curl-8.4.0-hca28451_0.conda#2bcf7689cae931dd35d9a45626f49fce
-https://conda.anaconda.org/bioconda/linux-64/staden_io_lib-1.14.14-h0191234_7.tar.bz2#6e0d09d5ed6b77a78c48e5be30d70d02
-https://conda.anaconda.org/bioconda/linux-64/libmaus2-2.0.810-h05617a9_4.tar.bz2#1a01fbd9922fa10056eca9816ab894a2
-https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.183-h4ac6f70_3.tar.bz2#679768a5b2b79a198cc0a57e4ac427d2
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.64.0-h161d5f1_0.conda#19e57602824042dfd0446292ef90488b
+https://conda.anaconda.org/conda-forge/linux-64/snappy-1.1.8-he1b5a44_3.tar.bz2#83f1dc295c711bdbaf97e1f3bedf2f52
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
+https://conda.anaconda.org/conda-forge/linux-64/libboost-1.85.0-h0ccab89_4.conda#4da1690badd566fc1041f91cd5655727
+https://conda.anaconda.org/conda-forge/linux-64/xerces-c-3.2.5-h988505b_2.conda#9dda9667feba914e0e80b95b82f7402b
+https://conda.anaconda.org/conda-forge/linux-64/libboost-devel-1.85.0-h00ab1b0_4.conda#ded76b8670cb505006c891c4d45844a5
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.10.1-hbbe4b11_0.conda#6e801c50a40301f6978c53976917b277
+https://conda.anaconda.org/conda-forge/linux-64/boost-cpp-1.85.0-h3c6214e_4.conda#cc4533eabf5caa8b4fbb56418d1617a9
+https://conda.anaconda.org/bioconda/linux-64/staden_io_lib-1.15.0-hbc8f6b7_1.tar.bz2#f4fb988b2e07e9425b74e12d2e1b049a
+https://conda.anaconda.org/bioconda/linux-64/libmaus2-2.0.813-heefa079_0.tar.bz2#62d380c07b389b74c301580cff0912c2
+https://conda.anaconda.org/bioconda/linux-64/biobambam-2.0.185-h02148a2_0.tar.bz2#aaa114d0dc3f75f6984cdcd32f4ebe9c

bio/biobambam2/bamsormadup/environment.yaml

@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - biobambam =2.0.183
+  - biobambam =2.0.185