diff --git a/bio/trimmomatic/pe/environment.linux-64.pin.txt b/bio/trimmomatic/pe/environment.linux-64.pin.txt new file mode 100644 index 00000000000..5ff002257d3 --- /dev/null +++ b/bio/trimmomatic/pe/environment.linux-64.pin.txt @@ -0,0 +1,78 @@ +# 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/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda#720523eb0d6a9b0f6120c16b2aa4e7de +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_2.conda#048b02e3962f066da18efe3a21b77672 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.13-5_cp313.conda#381bbd2a92c863f640a55b6ff3c35161 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda#dbcace4706afdfb7eb891f7b37d07c04 +https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29 +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/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/alsa-lib-1.2.13-hb9d3cd8_0.conda#ae1370588aa6a5157c34c73e9bbb36a0 +https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.23-h4ddbbb0_0.conda#8dfae1d2e74767e9ce36d5fa0d8605db +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/liblzma-5.6.3-hb9d3cd8_1.conda#2ecf2f1c7e4e21fcfe6423a51a992d84 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328 +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_2.conda#04b34b9a40cdc48cfdab261ab176ff74 +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-h7b32b05_1.conda#4ce6875f75469b2757a65e10a5d05e31 +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/libedit-3.1.20240808-pl5321h7949ede_0.conda#8247f80f3dc464d9322e85007e307fe8 +https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 +https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e +https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8 +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-1.6.45-h943b412_0.conda#85cbdaacad93808395ac295b5667d25b +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.48.0-hee588c1_1.conda#3fa05c528d8a1e2a67bbf1e36f22d3bc +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/libxcb-1.17.0-h8a09558_0.conda#92ed62436b625154323d40d5f2f11dd7 +https://conda.anaconda.org/conda-forge/linux-64/pigz-2.8-h2797004_0.conda#1832561770273ca7cf52b989dd83e6c3 +https://conda.anaconda.org/conda-forge/linux-64/pixman-0.44.2-h29eaf8c_0.conda#5e2a7acfa2c24188af39e7944e1b3604 +https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4 +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/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb +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/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f +https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.44-hba22ea6_2.conda#df359c09c41cd186fffb93a2d87aa6f5 +https://conda.anaconda.org/conda-forge/linux-64/python-3.13.1-ha99a958_105_cp313.conda#34945787453ee52a8f8271c1d19af1e8 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.5-he73a12e_0.conda#4c3e9fab69804ec6077697922d70c6e2 +https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.10-h4f16b4b_1.conda#125f34a17d7b4bea418a83904ea82ea6 +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45 +https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda#8f5b0b297b59e1ac160ad4beec99dbee +https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-h4637d8d_4.conda#d4529f4dff3057982a7617c7ac58fde3 +https://conda.anaconda.org/conda-forge/linux-64/libglib-2.82.2-h2ff4ddf_1.conda#37d1af619d999ee8f1f73cf5a06f4e2f +https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.7.0-hd9ff511_3.conda#0ea6510969e1296cc19966fad481f6de +https://conda.anaconda.org/conda-forge/noarch/pip-24.3.1-pyh145f28c_2.conda#76601b0ccfe1fe13a21a5f8813cb38de +https://conda.anaconda.org/bioconda/noarch/snakemake-wrapper-utils-0.6.2-pyhdfd78af_0.tar.bz2#fd8759bbd04116eace828c4fab906096 +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/cairo-1.18.2-h3394656_1.conda#b34c2833a1f56db610aeb27f206d800d +https://conda.anaconda.org/conda-forge/linux-64/lcms2-2.16-hb7c19ff_0.conda#51bb7010fc86f70eee639b4bb7a894f5 +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/harfbuzz-10.2.0-h4bba637_0.conda#9e38e86167e8b1ea0094747d12944ce4 +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-23.0.2-h68779a4_0.conda#a32abf2adc6e8dfabee20ac39c72ec7a +https://conda.anaconda.org/bioconda/noarch/trimmomatic-0.39-hdfd78af_2.tar.bz2#42a827a3e09b4207a89f0d22f77163d3 diff --git a/bio/trimmomatic/pe/environment.yaml b/bio/trimmomatic/pe/environment.yaml index b590aaab5d9..93ccdea9a09 100644 --- a/bio/trimmomatic/pe/environment.yaml +++ b/bio/trimmomatic/pe/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 =0.6.2 diff --git a/bio/trimmomatic/pe/meta.yaml b/bio/trimmomatic/pe/meta.yaml index d9b1a49527f..61425dd101b 100644 --- a/bio/trimmomatic/pe/meta.yaml +++ b/bio/trimmomatic/pe/meta.yaml @@ -1,5 +1,17 @@ name: "trimmomatic pe" -description: Trim paired-end reads with `trimmomatic `_ . (De)compress with pigz. +description: Trim paired-end reads with Trimmomatic (de)compress with pigz. +url: http://www.usadellab.org/cms/?page=trimmomatic authors: - Johannes Köster - Jorge Langa +input: + - fastq(gz) files +output: + - trimmed R1 fastq file + - trimmed R2 fastq file + - unpaired R1 fastq file + - unpaired R2 fastq file + - failed reads (optional) +params: + - trimmer: trimming steps + - extra: additional program arguments \ No newline at end of file diff --git a/bio/trimmomatic/pe/test/Snakefile_fq_fq b/bio/trimmomatic/pe/test/Snakefile_fq_fq index e27f80f2ce4..7187df302d1 100644 --- a/bio/trimmomatic/pe/test/Snakefile_fq_fq +++ b/bio/trimmomatic/pe/test/Snakefile_fq_fq @@ -17,10 +17,6 @@ rule trimmomatic_pe: 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/pe/test/Snakefile_fq_gz b/bio/trimmomatic/pe/test/Snakefile_fq_gz index be06e639bf9..e00ff106da0 100644 --- a/bio/trimmomatic/pe/test/Snakefile_fq_gz +++ b/bio/trimmomatic/pe/test/Snakefile_fq_gz @@ -18,10 +18,6 @@ rule trimmomatic_pe_fq_gz: 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: diff --git a/bio/trimmomatic/pe/test/Snakefile_gz_fq b/bio/trimmomatic/pe/test/Snakefile_gz_fq index 3981dfd5fb7..c94a68887c1 100644 --- a/bio/trimmomatic/pe/test/Snakefile_gz_fq +++ b/bio/trimmomatic/pe/test/Snakefile_gz_fq @@ -17,10 +17,6 @@ rule trimmomatic_pe_gz_fq: 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/pe/test/Snakefile_gz_gz b/bio/trimmomatic/pe/test/Snakefile_gz_gz index 53c897499c4..a62a3ecd274 100644 --- a/bio/trimmomatic/pe/test/Snakefile_gz_gz +++ b/bio/trimmomatic/pe/test/Snakefile_gz_gz @@ -18,10 +18,6 @@ rule trimmomatic_pe: 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: