Merge branch 'master' into my-new-snakemake-wrapper-paraphrase

Author: MagdalenaZZ

CHANGELOG.md

@@ -1,5 +1,51 @@
 # Changelog
 
+## [4.2.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.1...v4.2.0) (2024-08-23)
+
+
+### Features
+
+* Pcaexplorer pcaplot ([#1728](https://www.github.com/snakemake/snakemake-wrappers/issues/1728)) ([8563e88](https://www.github.com/snakemake/snakemake-wrappers/commit/8563e882e61ddad7db6386f65803d13a6c1926af))
+
+
+### Performance Improvements
+
+* autobump bio/bbtools ([#3127](https://www.github.com/snakemake/snakemake-wrappers/issues/3127)) ([a9bd6df](https://www.github.com/snakemake/snakemake-wrappers/commit/a9bd6dfdeee5692c76507148e12e81547c0c0906))
+* autobump bio/gatk3/printreads ([#3129](https://www.github.com/snakemake/snakemake-wrappers/issues/3129)) ([97b2c9d](https://www.github.com/snakemake/snakemake-wrappers/commit/97b2c9d218b120cda5991303f7b1b3d5b854bf2f))
+* autobump bio/last/lastal ([#3131](https://www.github.com/snakemake/snakemake-wrappers/issues/3131)) ([2c13329](https://www.github.com/snakemake/snakemake-wrappers/commit/2c1332948b3082438fd2021087592b47a48c8a5c))
+* autobump bio/last/lastdb ([#3130](https://www.github.com/snakemake/snakemake-wrappers/issues/3130)) ([ce9dfd4](https://www.github.com/snakemake/snakemake-wrappers/commit/ce9dfd459862a86fa0cb960708e232d21894bd60))
+* autobump bio/multiqc ([#3132](https://www.github.com/snakemake/snakemake-wrappers/issues/3132)) ([b5bb552](https://www.github.com/snakemake/snakemake-wrappers/commit/b5bb55238100f1f4c520d173323ce4c84e035cbb))
+* autobump bio/reference/ensembl-mysql-table ([#3133](https://www.github.com/snakemake/snakemake-wrappers/issues/3133)) ([065d45e](https://www.github.com/snakemake/snakemake-wrappers/commit/065d45eba68db3375213095ecf2332705b333cf0))
+
+### [4.1.1](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.1.0...v4.1.1) (2024-08-21)
+
+
+### Bug Fixes
+
+* Fix datavzrd wrapper ([#3125](https://www.github.com/snakemake/snakemake-wrappers/issues/3125)) ([5bd032c](https://www.github.com/snakemake/snakemake-wrappers/commit/5bd032cfa2a24eaa66cb7e24f5b3439fae939886))
+
+## [4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0) (2024-08-21)
+
+
+### Features
+
+* Allow outputting of rendered yte config in Datavzrd wrapper ([#3123](https://www.github.com/snakemake/snakemake-wrappers/issues/3123)) ([e74be78](https://www.github.com/snakemake/snakemake-wrappers/commit/e74be7843299478a276febfacb52825a9762500c))
+
+
+### Bug Fixes
+
+* Correctly handle non str index list for bwa-mem2/mem ([#3101](https://www.github.com/snakemake/snakemake-wrappers/issues/3101)) ([6f46508](https://www.github.com/snakemake/snakemake-wrappers/commit/6f46508aa99663930e70c82114205929aee2dfcb))
+
+
+### Performance Improvements
+
+* autobump bio/gatk3/baserecalibrator ([#3119](https://www.github.com/snakemake/snakemake-wrappers/issues/3119)) ([6c2bdfd](https://www.github.com/snakemake/snakemake-wrappers/commit/6c2bdfdca79c7037448bc601a4aeb3d578ea0980))
+* autobump bio/gatk3/realignertargetcreator ([#3118](https://www.github.com/snakemake/snakemake-wrappers/issues/3118)) ([ba219e7](https://www.github.com/snakemake/snakemake-wrappers/commit/ba219e7698eb078fe22c703a9662c8cb6deee0eb))
+* autobump bio/genomescope ([#3117](https://www.github.com/snakemake/snakemake-wrappers/issues/3117)) ([6292229](https://www.github.com/snakemake/snakemake-wrappers/commit/62922298404397c7b23dc5b8fb01bc33e445e97f))
+* autobump bio/igv-reports ([#3120](https://www.github.com/snakemake/snakemake-wrappers/issues/3120)) ([fe33c2c](https://www.github.com/snakemake/snakemake-wrappers/commit/fe33c2c27328212c528e94f995fd0bc26d7fde39))
+* autobump bio/trinity ([#3121](https://www.github.com/snakemake/snakemake-wrappers/issues/3121)) ([62b0231](https://www.github.com/snakemake/snakemake-wrappers/commit/62b0231c99920200e3fa6794f87578869cc35bd5))
+* Update Datavzrd wrapper ([#3122](https://www.github.com/snakemake/snakemake-wrappers/issues/3122)) ([5101461](https://www.github.com/snakemake/snakemake-wrappers/commit/51014613939bfc5e48e0b2ae619e283cf36bfd88))
+
 ## [4.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.14.2...v4.0.0) (2024-08-14)
 
 

bio/bbtools/environment.linux-64.pin.txt

@@ -3,42 +3,37 @@
 # platform: linux-64
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+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.3-h315aac3_2.conda#b0143a3e98136a680b728fdf9b42a258
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h46a8edc_4.conda#a7e3a62981350e232e0e7345b5aea580
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.5-h2ad013b_0_cpython.conda#9c56c4df45f6571b13111d8df2448692
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-hb711507_1.conda#4a6d410296d7e39f00bacdee7df046e9
 https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
-https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.15-h7f713cb_2.conda#9ab79924a3760f85a799f21bc99bd655
+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
-https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.5.0-hca28451_0.conda#7144d5a828e2cae218e0e3c98d8a0aeb
-https://conda.anaconda.org/conda-forge/noarch/setuptools-69.0.3-pyhd8ed1ab_0.conda#40695fdfd15a92121ed2922900d0308b
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.9.1-hdb1bdb2_0.conda#7da1d242ca3591e174a3c7d82230d3c0
+https://conda.anaconda.org/conda-forge/noarch/setuptools-72.2.0-pyhd8ed1ab_0.conda#1462aa8b243aad09ef5d0841c745eb89
 https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096
-https://conda.anaconda.org/conda-forge/noarch/wheel-0.42.0-pyhd8ed1ab_0.conda#1cdea58981c5cbc17b51973bcaddcea7
+https://conda.anaconda.org/conda-forge/noarch/wheel-0.44.0-pyhd8ed1ab_0.conda#d44e3b085abcaef02983c6305b84b584
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxfixes-5.0.3-h7f98852_1004.tar.bz2#e9a21aa4d5e3e5f1aed71e8cefd46b6a
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb
-https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f907bb958910dc404647326ca80c263e
-https://conda.anaconda.org/bioconda/linux-64/htslib-1.19.1-h81da01d_0.tar.bz2#a2b558d267544e66aef5551728b3960a
-https://conda.anaconda.org/conda-forge/noarch/pip-23.3.2-pyhd8ed1ab_0.conda#8591c748f98dcc02253003533bc2e4b1
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h7f98852_0.tar.bz2#e77615e5141cad5a2acaa043d1cf0ca5
-https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.3.0-h3d44ed6_0.conda#5a6f6c00ef982a9bc83558d9ac8f64a0
-https://conda.anaconda.org/bioconda/linux-64/samtools-1.19.2-h50ea8bc_0.tar.bz2#0150123d5e95c24ba378bf2ab645831b
-https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.3-h7f98852_1002.tar.bz2#a220b1a513e19d5cb56c1311d44f12e6
-https://conda.anaconda.org/conda-forge/linux-64/openjdk-20.0.2-hfea2f88_1.conda#3954914fc7a3b0b8f706d243fa532946
-https://conda.anaconda.org/bioconda/linux-64/bbmap-39.06-h92535d8_0.tar.bz2#23adcd1b5a326e9f1cf807f9c61ce67f
+https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-hebfffa5_3.conda#fceaedf1cdbcb02df9699a0d9b005292
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.20-h5efdd21_2.tar.bz2#f0923cdb85b44dc77bdead8018645ea9
+https://conda.anaconda.org/conda-forge/noarch/pip-24.2-pyhd8ed1ab_0.conda#6721aef6bfe5937abe70181545dd2c51
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.7.10-h4bc722e_1.conda#749baebe7e2ff3360630e069175e528b
+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-9.0.0-hda332d3_1.conda#76b32dcf243444aea9c6b804bcfa40b8
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.20-h50ea8bc_1.tar.bz2#1a4c52f8079fea1b18b3e4bd329bab3a
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.5-h4bc722e_0.conda#185159d666308204eca00295599b0a5c
+https://conda.anaconda.org/conda-forge/linux-64/openjdk-22.0.1-h8651b0f_1.conda#672153e7c3d4f70bc65993f3ee513768
+https://conda.anaconda.org/bioconda/linux-64/bbmap-39.08-h92535d8_0.tar.bz2#d44de41669589c819303092447b2454a

bio/bbtools/environment.yaml

@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bbmap =39.06
+  - bbmap =39.08
   - snakemake-wrapper-utils =0.6.2
   - pigz =2.8