perf: autobump conda envs

Author: johanneskoester

workflow/envs/arriba.linux-64.pin.txt

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - arriba =2.5
+  - arriba =2.5.1

workflow/envs/arriba.yaml

@@ -0,0 +1,20 @@
+# 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/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+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-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.25.1-h3f43e3d_1.conda#3b0d184bc9404516d418d4509e418bdc
+https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.25.1-h3f43e3d_1.conda#2f4de899028319b27eb7a4023be5dfd2
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-h4852527_7.conda#f627678cf829bd70bccf141a19c3ad3e
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda#c94a5994ef49749880a8139cf9afcbe1
+https://conda.anaconda.org/conda-forge/linux-64/mpfr-4.2.1-h90cbb55_3.conda#2eeb50cab6652538eee8fc0bc3340c81
+https://conda.anaconda.org/conda-forge/linux-64/gawk-5.3.1-hcd3d067_0.conda#91d4414ab699180b2b0b10b8112c5a2f

workflow/envs/awk.linux-64.pin.txt

@@ -1,4 +1,4 @@
 channels:
   - conda-forge
 dependencies:
-  - gawk =5.1
+  - gawk =5.3.1

workflow/envs/awk.yaml

@@ -0,0 +1,38 @@
+# 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/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+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-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda#f7f0d6cc2dc986d42ac2689ec88192be
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda#915f5995e94f60e9a4826e0b0920ee88
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
+https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-h13024bc_3.tar.bz2#99c4e90e82db906439e00beafb343d16
+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.25.1-h3f43e3d_1.conda#3b0d184bc9404516d418d4509e418bdc
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.25.1-h3f43e3d_1.conda#2f4de899028319b27eb7a4023be5dfd2
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hcf80075_0.conda#eecce068c7e4eddeb169591baac20ac4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-h4852527_7.conda#f627678cf829bd70bccf141a19c3ad3e
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
+https://conda.anaconda.org/conda-forge/linux-64/gmp-6.3.0-hac33072_2.conda#c94a5994ef49749880a8139cf9afcbe1
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.67.0-had1ee68_0.conda#b499ce4b026493a13774bcf0f4c33849
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.14.1-h332b0f4_0.conda#45f6713cb00f124af300342512219182
+https://conda.anaconda.org/conda-forge/linux-64/mpfr-4.2.1-h90cbb55_3.conda#2eeb50cab6652538eee8fc0bc3340c81
+https://conda.anaconda.org/conda-forge/linux-64/gawk-5.3.1-hcd3d067_0.conda#91d4414ab699180b2b0b10b8112c5a2f
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.22.1-h566b1c6_0.tar.bz2#646b491ab86e0ab7173d35eb3a5f3241
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.22.1-h96c455f_0.tar.bz2#7088984cee084e606b2826b1fc3b5906

workflow/envs/awk_bedtools.linux-64.pin.txt

@@ -2,6 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bedtools =2.30
-  - gawk =5.1
-  - samtools =1.15
+  - bedtools =2.31.1
+  - gawk =5.3.1
+  - samtools =1.22.1

workflow/envs/awk_bedtools.yaml

@@ -0,0 +1,38 @@
+# 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/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+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-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda#f7f0d6cc2dc986d42ac2689ec88192be
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-hcd61629_7.conda#f116940d825ffc9104400f0d7f1a4551
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_7.conda#8621a450add4e231f676646880703f49
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hcf80075_0.conda#eecce068c7e4eddeb169591baac20ac4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-h4852527_7.conda#f627678cf829bd70bccf141a19c3ad3e
+https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.67.0-had1ee68_0.conda#b499ce4b026493a13774bcf0f4c33849
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_2.conda#dfc5aae7b043d9f56ba99514d5e60625
+https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda#f2cfec9406850991f4e3d960cc9e3321
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-37_h4a7cf45_openblas.conda#8bc098f29d8a7e3517bac5b25aab39b1
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.14.1-h332b0f4_0.conda#45f6713cb00f124af300342512219182
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.22.1-h566b1c6_0.tar.bz2#646b491ab86e0ab7173d35eb3a5f3241
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-37_h0358290_openblas.conda#3794858d4d6910a7fc3c181519e0b77a
+https://conda.anaconda.org/conda-forge/linux-64/gsl-2.7-he838d99_0.tar.bz2#fec079ba39c9cca093bf4c00001825de
+https://conda.anaconda.org/bioconda/linux-64/bcftools-1.22-h3a4d415_1.tar.bz2#ffd6659738d1b06f8d3fa5a3b0604703

workflow/envs/bcftools.linux-64.pin.txt

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bcftools =1.19
+  - bcftools =1.22

workflow/envs/bcftools.yaml

@@ -0,0 +1,31 @@
+# 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/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
+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-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda#51a19bba1b8ebfb60df25cde030b7ebc
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda#f7f0d6cc2dc986d42ac2689ec88192be
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
+https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda#1a580f7796c7bf6393fddb8bbbde58dc
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
+https://conda.anaconda.org/bioconda/linux-64/bedtools-2.31.1-h13024bc_3.tar.bz2#99c4e90e82db906439e00beafb343d16
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hcf80075_0.conda#eecce068c7e4eddeb169591baac20ac4
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-h4852527_7.conda#f627678cf829bd70bccf141a19c3ad3e
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.67.0-had1ee68_0.conda#b499ce4b026493a13774bcf0f4c33849
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.14.1-h332b0f4_0.conda#45f6713cb00f124af300342512219182
+https://conda.anaconda.org/bioconda/linux-64/htslib-1.22.1-h566b1c6_0.tar.bz2#646b491ab86e0ab7173d35eb3a5f3241
+https://conda.anaconda.org/bioconda/linux-64/samtools-1.22.1-h96c455f_0.tar.bz2#7088984cee084e606b2826b1fc3b5906

workflow/envs/bedtools.linux-64.pin.txt

@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bedtools =2.29
-  - samtools =1.12
+  - bedtools =2.31.1
+  - samtools =1.22.1