Merge remote-tracking branch 'upstream/master'

tdayris · Jan 7, 2025 · 973bf15 · 973bf15
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,68 @@
 # Changelog
 
+## [5.5.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.4.0...v5.5.0) (2024-12-10)
+
+
+### Features
+
+* NGSCheckMate ([#3498](https://www.github.com/snakemake/snakemake-wrappers/issues/3498)) ([df7fe5b](https://www.github.com/snakemake/snakemake-wrappers/commit/df7fe5bcb5fe737e4d4bd958caec4445ce1f6748))
+
+
+### Performance Improvements
+
+* Update datavzrd wrapper to latest yte version ([#3537](https://www.github.com/snakemake/snakemake-wrappers/issues/3537)) ([336079b](https://www.github.com/snakemake/snakemake-wrappers/commit/336079be7c46dad737227dd02bc6e3b498af87f5))
+
+## [5.4.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.3.0...v5.4.0) (2024-12-06)
+
+
+### Features
+
+* NGS-bits SampleAncestry ([#3502](https://www.github.com/snakemake/snakemake-wrappers/issues/3502)) ([8600d44](https://www.github.com/snakemake/snakemake-wrappers/commit/8600d44e79ae4dafa181d3b06eed6e3db0c7a2df))
+* NGS-bits SampleSimilarity ([#3500](https://www.github.com/snakemake/snakemake-wrappers/issues/3500)) ([710597c](https://www.github.com/snakemake/snakemake-wrappers/commit/710597cdc4e7f518d1fda2ec246bb6a7e0e29ba9))
+* NGSCheckMate make pattern ([#3499](https://www.github.com/snakemake/snakemake-wrappers/issues/3499)) ([3b96cc1](https://www.github.com/snakemake/snakemake-wrappers/commit/3b96cc18b5a7ce8643fc3f8a492333d8f339e4c5))
+* Sex.DetERRmine ([#3497](https://www.github.com/snakemake/snakemake-wrappers/issues/3497)) ([3919f2e](https://www.github.com/snakemake/snakemake-wrappers/commit/3919f2e4b6fae381cf92c921e6f17086819de345))
+
+
+### Performance Improvements
+
+* autobump bio/bbtools ([#3507](https://www.github.com/snakemake/snakemake-wrappers/issues/3507)) ([19d027d](https://www.github.com/snakemake/snakemake-wrappers/commit/19d027d176bfa5da7ec2d75b9222547b0fd2b919))
+* autobump bio/busco ([#3506](https://www.github.com/snakemake/snakemake-wrappers/issues/3506)) ([aad4b56](https://www.github.com/snakemake/snakemake-wrappers/commit/aad4b56df0ca427a0a12dba67bcf0edef51d545b))
+* autobump bio/busco ([#3519](https://www.github.com/snakemake/snakemake-wrappers/issues/3519)) ([6af2e11](https://www.github.com/snakemake/snakemake-wrappers/commit/6af2e11535a6407a0a60eaa18f7e15548e4a4a01))
+* autobump bio/encode_fastq_downloader ([#3521](https://www.github.com/snakemake/snakemake-wrappers/issues/3521)) ([cbf06d2](https://www.github.com/snakemake/snakemake-wrappers/commit/cbf06d227d2cece579b1bdff413d09036e2d976f))
+* autobump bio/freebayes ([#3509](https://www.github.com/snakemake/snakemake-wrappers/issues/3509)) ([12b8b3c](https://www.github.com/snakemake/snakemake-wrappers/commit/12b8b3ce9d5be65a2165b4ca3e0403935b950237))
+* autobump bio/gatk3/baserecalibrator ([#3523](https://www.github.com/snakemake/snakemake-wrappers/issues/3523)) ([7a7518e](https://www.github.com/snakemake/snakemake-wrappers/commit/7a7518e63e0c6eac8d7cb935808b8692e4e688ff))
+* autobump bio/gatk3/indelrealigner ([#3525](https://www.github.com/snakemake/snakemake-wrappers/issues/3525)) ([a0d913c](https://www.github.com/snakemake/snakemake-wrappers/commit/a0d913ce81ceb45aeff0eeee8e1e92e63bda786c))
+* autobump bio/gatk3/printreads ([#3524](https://www.github.com/snakemake/snakemake-wrappers/issues/3524)) ([67af9a6](https://www.github.com/snakemake/snakemake-wrappers/commit/67af9a6899872a5e2e8cabc58572aa31d51a43cc))
+* autobump bio/gatk3/realignertargetcreator ([#3522](https://www.github.com/snakemake/snakemake-wrappers/issues/3522)) ([5f8ffe7](https://www.github.com/snakemake/snakemake-wrappers/commit/5f8ffe7349ab24d55d45e1811519b2b9e9985068))
+* autobump bio/hifiasm ([#3510](https://www.github.com/snakemake/snakemake-wrappers/issues/3510)) ([2b1b9f2](https://www.github.com/snakemake/snakemake-wrappers/commit/2b1b9f265231a3f3bc121dd9d4f34111b15d4486))
+* autobump bio/mapdamage2 ([#3526](https://www.github.com/snakemake/snakemake-wrappers/issues/3526)) ([92da252](https://www.github.com/snakemake/snakemake-wrappers/commit/92da252bcafd05a0187b635b1938593aa4268c3b))
+* autobump bio/mosdepth ([#3511](https://www.github.com/snakemake/snakemake-wrappers/issues/3511)) ([762b273](https://www.github.com/snakemake/snakemake-wrappers/commit/762b273800120519ffd2bc2f670ae93be6187cac))
+* autobump bio/mtnucratio ([#3512](https://www.github.com/snakemake/snakemake-wrappers/issues/3512)) ([7f6a3b0](https://www.github.com/snakemake/snakemake-wrappers/commit/7f6a3b07cc2bae16fb30c097e783b70e87ad58f1))
+* autobump bio/ngsbits/sampleancestry ([#3527](https://www.github.com/snakemake/snakemake-wrappers/issues/3527)) ([2abf38c](https://www.github.com/snakemake/snakemake-wrappers/commit/2abf38c30e541dd45563ee7ec3959ccf43802fab))
+* autobump bio/ngsbits/samplesimilarity ([#3529](https://www.github.com/snakemake/snakemake-wrappers/issues/3529)) ([c91ce10](https://www.github.com/snakemake/snakemake-wrappers/commit/c91ce1075792f231d833a89298e88353c96973b1))
+* autobump bio/ngscheckmate/makesnvpattern ([#3528](https://www.github.com/snakemake/snakemake-wrappers/issues/3528)) ([ff9a81d](https://www.github.com/snakemake/snakemake-wrappers/commit/ff9a81d923b8efc807f0054400d03c6277777cb8))
+* autobump bio/reference/ensembl-mysql-table ([#3513](https://www.github.com/snakemake/snakemake-wrappers/issues/3513)) ([6b5c545](https://www.github.com/snakemake/snakemake-wrappers/commit/6b5c5454e86cfd393e5fa55b86566e60ef43dd5c))
+* autobump bio/sexdeterrmine ([#3514](https://www.github.com/snakemake/snakemake-wrappers/issues/3514)) ([2b18309](https://www.github.com/snakemake/snakemake-wrappers/commit/2b183092fd31225462490d43df5916e678ea5f83))
+* autobump bio/spades/metaspades ([#3530](https://www.github.com/snakemake/snakemake-wrappers/issues/3530)) ([070b9b6](https://www.github.com/snakemake/snakemake-wrappers/commit/070b9b62af3cc79f7a4fe1500963892631f8d752))
+* autobump bio/varlociraptor/call-variants ([#3533](https://www.github.com/snakemake/snakemake-wrappers/issues/3533)) ([8c563f1](https://www.github.com/snakemake/snakemake-wrappers/commit/8c563f18f02f3f06760f2f25ad85383f9d776b2d))
+* autobump bio/varlociraptor/control-fdr ([#3532](https://www.github.com/snakemake/snakemake-wrappers/issues/3532)) ([ce7d1b0](https://www.github.com/snakemake/snakemake-wrappers/commit/ce7d1b00bdf6a856ffe5ed6bac7258ca970cde4a))
+* autobump bio/varlociraptor/estimate-alignment-properties ([#3531](https://www.github.com/snakemake/snakemake-wrappers/issues/3531)) ([0b5ac04](https://www.github.com/snakemake/snakemake-wrappers/commit/0b5ac04792bcd54984ea6b0e6af41efa33fba126))
+* autobump bio/varlociraptor/preprocess-variants ([#3534](https://www.github.com/snakemake/snakemake-wrappers/issues/3534)) ([56a8933](https://www.github.com/snakemake/snakemake-wrappers/commit/56a8933de936e20e0068bd1d8cb6bbea3826f655))
+* autobump bio/vep/annotate ([#3515](https://www.github.com/snakemake/snakemake-wrappers/issues/3515)) ([2609900](https://www.github.com/snakemake/snakemake-wrappers/commit/26099008485dbf5a8054f3284a1892dd1245ac8a))
+* autobump bio/vep/cache ([#3516](https://www.github.com/snakemake/snakemake-wrappers/issues/3516)) ([f46427c](https://www.github.com/snakemake/snakemake-wrappers/commit/f46427c7951ad1a2ccd142b74698aac3009b2c66))
+* autobump bio/vep/plugins ([#3535](https://www.github.com/snakemake/snakemake-wrappers/issues/3535)) ([9a6ccc3](https://www.github.com/snakemake/snakemake-wrappers/commit/9a6ccc34ce5db38c419076d7f707321bf69357dc))
+* autobump bio/vg/giraffe ([#3517](https://www.github.com/snakemake/snakemake-wrappers/issues/3517)) ([6fffdd6](https://www.github.com/snakemake/snakemake-wrappers/commit/6fffdd6caec48f099b6140dd113a295f7202fa63))
+* autobump utils/csvtk ([#3508](https://www.github.com/snakemake/snakemake-wrappers/issues/3508)) ([41e8545](https://www.github.com/snakemake/snakemake-wrappers/commit/41e8545b5663c91d6b13b5acd2c126a6b42a9a92))
+* autobump utils/csvtk ([#3520](https://www.github.com/snakemake/snakemake-wrappers/issues/3520)) ([d4a52e5](https://www.github.com/snakemake/snakemake-wrappers/commit/d4a52e5e900aa16cad66ebbea1b22fb27d3709ea))
+
+## [5.3.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.2.1...v5.3.0) (2024-11-27)
+
+
+### Features
+
+* Add vg giraffe ([#3302](https://www.github.com/snakemake/snakemake-wrappers/issues/3302)) ([fbf806d](https://www.github.com/snakemake/snakemake-wrappers/commit/fbf806d97336b23caa443b9063b0042e97712d28))
+* MtNucRatioCalculator ([#3496](https://www.github.com/snakemake/snakemake-wrappers/issues/3496)) ([b221057](https://www.github.com/snakemake/snakemake-wrappers/commit/b2210576f75be6a90569b676688b476c4aaba7a8))
+
 ### [5.2.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v5.2.0...v5.2.1) (2024-11-22)
 
 

diff --git a/bio/bbtools/environment.linux-64.pin.txt b/bio/bbtools/environment.linux-64.pin.txt
@@ -1,7 +1,7 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
-# created-by: conda 24.9.0
+# 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-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244
@@ -17,12 +17,12 @@ https://conda.anaconda.org/conda-forge/linux-64/libgomp-14.2.0-h77fa898_1.conda#
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
 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-1.34.2-heb4867d_0.conda#2b780c0338fc0ffa678ac82c54af51fd
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.3-hb9d3cd8_1.conda#ee228789a85f961d14567252a03e725f
 https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c
 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-3.3.2-hb9d3cd8_0.conda#4d638782050ab6faa27275bed57e9b4e
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9
 https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda#b3c17d95b5a10c6e64a21fa17573e70e
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hb9d3cd8_1.conda#19608a9656912805b2b9a2f6bd257b04
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hb9d3cd8_1.conda#77cbc488235ebbaab2b6e912d3934bae
@@ -40,7 +40,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.c
 https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda#aeb98fdeb2e8f25d43ef71fbacbeec80
 https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.44-hadc24fc_0.conda#f4cc49d7aa68316213e4b12be35308d1
 https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda#b6f02b52a174e612e89548f4663ce56a
-https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hf672d98_0.conda#be2de152d8073ef1c01b7728475f2fe7
 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/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
 https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
@@ -66,11 +66,11 @@ https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.con
 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
 https://conda.anaconda.org/conda-forge/linux-64/libglib-2.82.2-h2ff4ddf_0.conda#13e8e54035ddd2b91875ba399f0f7c04
 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.0-h6565414_0.conda#80eaf80d84668fa5620ac9ec1b4bf56f
-https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_100_cp313.conda#08e9aef080f33daeb192b2ddc7e4721f
+https://conda.anaconda.org/conda-forge/linux-64/python-3.13.0-h9ebbce0_101_cp313.conda#f4fea9d5bb3f2e61a39950a7ab70ee4e
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.6-hb9d3cd8_0.conda#febbab7d15033c913d53c7a2c102309d
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-6.0.1-hb9d3cd8_0.conda#4bdb303603e9821baf5fe5fdff1dc8f8
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hb9d3cd8_1.conda#a7a49a8b85122b49214798321e2e96b4
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hb9d3cd8_2.conda#d8602724ac0d276c380b97e9eb0f814b
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.1-hb9d3cd8_0.conda#279b0de5f6ba95457190a1c459a64e31
 https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292
 https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5
 https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3
@@ -83,4 +83,4 @@ https://conda.anaconda.org/bioconda/linux-64/htslib-1.21-h5efdd21_0.tar.bz2#06b9
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.5-hb9d3cd8_3.conda#7bbe9a0cc0df0ac5f5a8ad6d6a11af2f
 https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768
 https://conda.anaconda.org/bioconda/linux-64/samtools-1.21-h50ea8bc_0.tar.bz2#4a7fe11223f61cb2d950ed54e20c12ce
-https://conda.anaconda.org/bioconda/linux-64/bbmap-39.11-h92535d8_0.tar.bz2#3a3efec1dc3f0d40d0354a6a9ef2ad77
+https://conda.anaconda.org/bioconda/linux-64/bbmap-39.13-h92535d8_0.tar.bz2#cf1b6aad444683743e7eb26f474a6ec5
diff --git a/bio/bbtools/environment.yaml b/bio/bbtools/environment.yaml
@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bbmap =39.11
+  - bbmap =39.13
   - snakemake-wrapper-utils =0.6.2
   - pigz =2.8