diff --git a/bio/trimmomatic/se/environment.linux-64.pin.txt b/bio/trimmomatic/se/environment.linux-64.pin.txt new file mode 100644 index 00000000000..5c9bfe16a03 --- /dev/null +++ b/bio/trimmomatic/se/environment.linux-64.pin.txt @@ -0,0 +1,80 @@ +# This file may be used to create an environment using: +# $ conda create --name --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-2025.4.26-hbd8a1cb_0.conda#95db94f75ba080a22eb623590993167b +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb +https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda#49023d73832ef61042f6a237cb2687e7 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda#01f8d123c96816249efd255a31ad7712 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_2.conda#fbe7d535ff9d3a168c148e07358cd5b1 +https://conda.anaconda.org/conda-forge/noarch/python_abi-3.13-7_cp313.conda#e84b44e6300f1703cb25d29120c5b1d8 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda#4222072737ccff51314b5ece9c7d6f5a +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-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_2.conda#ea8ac52380885ed41c1baa8f1d6d2b93 +https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda#76df83c2a9035c54df5d04ff81bcc02d +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda#64f0c503da58ec25ebd359e4d990afa8 +https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.0-h5888daf_0.conda#db0bfbe7dd197b68ad5f30333bae6ce0 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda#ede4673863426c0883c0063d853bbd85 +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_2.conda#ddca86c7040dd0e73b2b69bd7833d225 +https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h4ce23a2_1.conda#e796ff8ddc598affdf7c173d6145f087 +https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.1.0-hb9d3cd8_0.conda#9fa334557db9f63da6c9285fd2a48638 +https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_1.conda#a76fd702c93cd2dfd89eff30a5fd45a8 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_2.conda#1cb1c67961f6dd257eae9e9691b341aa +https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.5.0-h851e524_0.conda#63f790534398730f59e1b899c3644d4a +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-3.5.0-h7b32b05_1.conda#de356753cfdbffcde5bb1e86e3aa6cd0 +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-1.1.2-hb9d3cd8_0.conda#fb901ff28063514abb6046c9ec2c4a45 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.12-hb9d3cd8_0.conda#f6ebe2cb3f82ba6c057dde5d9debe4f7 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.5-hb9d3cd8_0.conda#8035c64cb77ed555e3f150b7b3972480 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda#62ee74e96c5ebb0af99386de58cf9553 +https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.2-hd590300_0.conda#3bf7b9fd5a7136126e0234db4b87c8b6 +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/lerc-4.0.0-h0aef613_1.conda#9344155d33912347b37f0ae6c410a835 +https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b +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-1.6.47-h943b412_0.conda#55199e2ae2c3651f6f9b2a447b47bdc9 +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.49.2-hee588c1_0.conda#93048463501053a00739215ea3f36324 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_2.conda#9d2072af184b5caa29492bf2344597bb +https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b +https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7 +https://conda.anaconda.org/conda-forge/linux-64/pigz-2.8-hadc24fc_1.conda#b7f0995c7c10a80015668a62f2b608e7 +https://conda.anaconda.org/conda-forge/linux-64/pixman-0.46.0-h29eaf8c_0.conda#d2f1c87d4416d1e7344cf92b1aaee1c4 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda#283b96675859b20a825f8fa30f311446 +https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9 +https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c +https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda#8b189310083baabfb622af68fd9d3ae3 +https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368 +https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.13.3-h48d6fc4_1.conda#3c255be50a506c50765a93a6644f32fe +https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.0-hf01ce69_5.conda#e79a094918988bb1807462cd42c83962 +https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.45-hc749103_0.conda#b90bece58b4c2bf25969b70f3be42d25 +https://conda.anaconda.org/conda-forge/linux-64/python-3.13.3-hf636f53_101_cp313.conda#10622e12d649154af0bd76bcf33a7c5c +https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.6-he73a12e_0.conda#1c74ff8c35dcadf952a16f752ca5aa49 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.12-h4f16b4b_0.conda#db038ce880f100acc74dba10302b5630 +https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.17-h717163a_0.conda#000e85703f0fd9594c81710dd5066471 +https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3 +https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.13.3-ha770c72_1.conda#51f5be229d83ecd401fb369ab96ae669 +https://conda.anaconda.org/conda-forge/linux-64/libglib-2.84.2-h3618099_0.conda#072ab14a02164b7c0c089055368ff776 +https://conda.anaconda.org/conda-forge/noarch/pip-25.1.1-pyh145f28c_0.conda#01384ff1639c6330a0924791413b8714 +https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.7.2-pyhdfd78af_0.tar.bz2#3226d9f73c63e14968e89a5422a1f4d7 +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-0.9.12-hb9d3cd8_0.conda#96d57aba173e878a2089d5638016dc5e +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/freetype-2.13.3-ha770c72_1.conda#9ccd736d31e0c6e41f54e704e5312811 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxi-1.8.2-hb9d3cd8_0.conda#17dcc85db3c7886650b8908b183d6876 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrandr-1.5.4-hb9d3cd8_0.conda#2de7f99d6581a4a7adbff607b5c278ca +https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda#8f5b0b297b59e1ac160ad4beec99dbee +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/cairo-1.18.4-h3394656_0.conda#09262e66b19567aff4f592fb53b28760 +https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-11.2.1-h3beb420_0.conda#0e6e192d4b3d95708ad192d957cf3163 +https://conda.anaconda.org/conda-forge/linux-64/openjdk-23.0.2-h53dfc1b_2.conda#47eea31e0c3f960459237823e5e21a32 +https://conda.anaconda.org/bioconda/noarch/trimmomatic-0.39-hdfd78af_2.tar.bz2#42a827a3e09b4207a89f0d22f77163d3 diff --git a/bio/trimmomatic/se/environment.yaml b/bio/trimmomatic/se/environment.yaml index b590aaab5d9..bec95e1dbfd 100644 --- a/bio/trimmomatic/se/environment.yaml +++ b/bio/trimmomatic/se/environment.yaml @@ -3,6 +3,6 @@ channels: - bioconda - nodefaults dependencies: - - trimmomatic ==0.36 - - pigz ==2.3.4 - - snakemake-wrapper-utils ==0.1.3 + - trimmomatic =0.39 + - pigz =2.8 + - snakemake-wrapper-utils =0.7.2 diff --git a/bio/trimmomatic/se/meta.yaml b/bio/trimmomatic/se/meta.yaml index dca915fc54c..b04a179080e 100644 --- a/bio/trimmomatic/se/meta.yaml +++ b/bio/trimmomatic/se/meta.yaml @@ -1,5 +1,14 @@ name: "trimmomatic se" -description: Trim single-end reads with `trimmomatic `_. (De)compress with pigz. +description: Trim single-end reads with Trimmomatic and (de)compress with pigz. +url: http://www.usadellab.org/cms/?page=trimmomatic authors: - Johannes Köster - Jorge Langa +input: + - fastq(gz) file(s) +output: + - trimmed fastq file(s) + - failed reads (optional) +params: + - trimmer: trimming steps + - extra: additional program arguments diff --git a/bio/trimmomatic/se/test/Snakefile_fq_fq b/bio/trimmomatic/se/test/Snakefile_fq_fq index 1a9f5fe67cd..a0e5b7bda94 100644 --- a/bio/trimmomatic/se/test/Snakefile_fq_fq +++ b/bio/trimmomatic/se/test/Snakefile_fq_fq @@ -12,10 +12,6 @@ rule trimmomatic: extra="", threads: 32 - # optional specification of memory usage of the JVM that snakemake will respect with global - # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources) - # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`: - # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties resources: mem_mb=1024 wrapper: diff --git a/bio/trimmomatic/se/test/Snakefile_fq_gz b/bio/trimmomatic/se/test/Snakefile_fq_gz index 1cd54c29d76..015af1099a4 100644 --- a/bio/trimmomatic/se/test/Snakefile_fq_gz +++ b/bio/trimmomatic/se/test/Snakefile_fq_gz @@ -14,10 +14,6 @@ rule trimmomatic: extra="" threads: 32 - # optional specification of memory usage of the JVM that snakemake will respect with global - # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources) - # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`: - # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties resources: mem_mb=1024 wrapper: diff --git a/bio/trimmomatic/se/test/Snakefile_gz_fq b/bio/trimmomatic/se/test/Snakefile_gz_fq index b5762c0264f..eb57ed0b1be 100644 --- a/bio/trimmomatic/se/test/Snakefile_gz_fq +++ b/bio/trimmomatic/se/test/Snakefile_gz_fq @@ -12,10 +12,6 @@ rule trimmomatic: extra="" threads: 32 - # optional specification of memory usage of the JVM that snakemake will respect with global - # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources) - # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`: - # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties resources: mem_mb=1024 wrapper: diff --git a/bio/trimmomatic/se/test/Snakefile_gz_gz b/bio/trimmomatic/se/test/Snakefile_gz_gz index bea06e3f50e..b78cdae9a7a 100644 --- a/bio/trimmomatic/se/test/Snakefile_gz_gz +++ b/bio/trimmomatic/se/test/Snakefile_gz_gz @@ -14,10 +14,6 @@ rule trimmomatic: compression_level="-9" threads: 32 - # optional specification of memory usage of the JVM that snakemake will respect with global - # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources) - # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`: - # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties resources: mem_mb=1024 wrapper: