diff --git a/.github/workflows/conventional-prs.yml b/.github/workflows/conventional-prs.yml index c777f4b2de4..9e21169b769 100644 --- a/.github/workflows/conventional-prs.yml +++ b/.github/workflows/conventional-prs.yml @@ -1,4 +1,4 @@ -name: PR +name: Lint PR Title on: pull_request_target: types: @@ -9,8 +9,10 @@ on: jobs: title-format: - runs-on: ubuntu-latest + runs-on: [self-hosted, Linux, v1.0.2] steps: - - uses: amannn/action-semantic-pull-request@v3.4.0 + - uses: amannn/action-semantic-pull-request@v3.6.0 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + validateSingleCommit: true diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a95ccd98303..3b55dac8f4e 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -10,7 +10,7 @@ on: jobs: docs: - runs-on: ubuntu-latest + runs-on: [self-hosted, Linux, python-3.10] steps: - uses: actions/checkout@v1 @@ -27,21 +27,26 @@ jobs: make html testing: - runs-on: ubuntu-latest + runs-on: [self-hosted, Linux, python-3.10] steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 with: submodules: recursive fetch-depth: 0 - - - name: Setup mamba + # This is a hybrid of things, might need some tweaking + - name: create environment with mamba uses: conda-incubator/setup-miniconda@v2 + env: + CONDA: "/usr/bin/conda" with: + mamba-version: "*" + # ?miniforge-variant: Mambaforge + # ?miniforge-version: latest + channels: conda-forge, bioconda + auto-activate-base: true activate-environment: snakemake - channels: "conda-forge, bioconda" - miniforge-variant: Mambaforge - miniforge-version: latest - + use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly! + auto-update-conda: true - name: Setup Snakemake environment shell: bash -el {0} run: | diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 126e299a6ec..1296c20ce80 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -2,11 +2,10 @@ name: Code quality on: pull_request: - branches_ignore: [] jobs: formatting: - runs-on: ubuntu-latest + runs-on: [self-hosted, Linux, python-3.10] steps: - uses: actions/checkout@v3 @@ -37,7 +36,7 @@ jobs: # snakefmt --check $(git diff origin/master --name-only | grep Snakefile) linting: - runs-on: ubuntu-latest + runs-on: [self-hosted, Linux, python-3.10] steps: - uses: actions/checkout@v1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 5439d1e5ff5..bfcbb117fae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,135 @@ # Changelog +## [1.26.0](https://www.github.com/sansterbioanalytics/snakemake-wrappers/compare/v1.25.0...v1.26.0) (2023-04-17) + + +### Features + +* add logs to refgenie rules ([fce4bb0](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/fce4bb092c8e703d548c98138dd0d11d5467ad41)) +* added vsearch wrapper ([#1149](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1149)) ([79342b7](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/79342b73df13b135e09dd61da5d185f84c20f6a1)) +* also define overhang on params.extra ([#1173](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1173)) ([7e63821](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/7e6382183ea02e086360dba5946a8725a3cdc98d)) +* automate inference of index name ([#1169](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1169)) ([0d2c92a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0d2c92a5be480dd60cdb1c422282b9812aa01e2f)) +* Enhance deeptools compute matrix ([#1236](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1236)) ([a44bef5](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a44bef54526ea07da64305147aa8cfa9f74497a9)) +* Lofreq indelqual wrapper ([#1166](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1166)) ([e2215f2](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/e2215f2e3cc18ed0ee165a440c3bb1752babab59)) +* update datavzrd 2.18.1 ([#1171](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1171)) ([00b9b1c](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/00b9b1cfac184303f70716749977e0343a09e8d0)) + + +### Bug Fixes + +* allow for arbitrary filename prefixes in the optitype wrapper ([#500](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/500)) ([0bf7175](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0bf71755787c9c207f578d74007948ec7f89dfa8)) +* Allow for large assets in refgenie ([1c99871](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1c9987155288f55e10d00eed6534b9ff6519d715)) +* force string in reference_prefix ([fe7b05a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/fe7b05a189fed7fdc79a761df07b0d12482acdc0)) +* formatting refgenie ([ee3bad5](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/ee3bad5b0a925ff98b393e0da5f997cce6429070)) +* handle refgenconf write lock error ([4d3758c](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/4d3758c0048e0cecdd4ea96c588698f7857641e3)) +* read-only conf acces for concurrent rules dl ([d0dcc61](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/d0dcc615a8bc9f5e45c304b85c4cb942665abe95)) +* remove input string from rsem wrapper ([73e3a02](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/73e3a0242e0d443e84b2aa72491ccd6cf5f25000)) +* reorder to prioritize bioconda ([8eb7a1d](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/8eb7a1df6992f726b4d143f564b6054d07327ecb)) +* switch to Path in order to resolve basename more robustly ([0d10e6a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0d10e6ad6f4f72907e12e25af92ab59f3e85dd01)) + + +### Performance Improvements + +* autobump bio/bazam ([#1187](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1187)) ([df7d90e](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/df7d90e18cb33d3bd57c8720ab00971a26ee952a)) +* autobump bio/bbtools/bbduk ([#1269](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1269)) ([86c7a0a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/86c7a0ac481bbb643a1d5460cc6668e134dc74e4)) +* autobump bio/bcftools/call ([#1181](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1181)) ([7fbc611](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/7fbc61182b3f9163c946306ec01ffd3575988970)) +* autobump bio/bcftools/concat ([#1183](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1183)) ([93d7103](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/93d71037234a1162036225065ac2ec329f1d1c34)) +* autobump bio/bcftools/merge ([#1266](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1266)) ([b0a2c88](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/b0a2c88ac6239b55ac6638d35f80946c839220cd)) +* autobump bio/bcftools/norm ([#1192](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1192)) ([9e06c59](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/9e06c59da15866ea0f6c4793e053cb5169815fcd)) +* autobump bio/bcftools/norm ([#1212](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1212)) ([3667c6b](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/3667c6b1d3f824f4153212c18b9abbcca19a31e7)) +* autobump bio/bcftools/sort ([#1257](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1257)) ([dd478d2](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/dd478d216b6865a8828728a51354ad09ab286967)) +* autobump bio/bcftools/stats ([#1197](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1197)) ([c844da5](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/c844da5a713c588f3aaacd0d17494312c0901b43)) +* autobump bio/bellerophon ([#1199](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1199)) ([a2fe593](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a2fe593f4e4f98dd3a135617129c817669f83b71)) +* autobump bio/bismark/bismark_methylation_extractor ([#1220](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1220)) ([05964de](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/05964de5e1e9c738654bd18c8f07cecf2626711b)) +* autobump bio/bismark/bismark2bedGraph ([#1258](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1258)) ([3eb60c2](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/3eb60c226ed74464e3b31b16c22cc5d99cf465e5)) +* autobump bio/bismark/bismark2summary ([#1235](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1235)) ([74a9de2](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/74a9de2c0896bc4ced38561bfa978bd99bd01e02)) +* autobump bio/bowtie2/align ([#1206](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1206)) ([d3544b0](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/d3544b024545620f4f17ca390d1466cebf5bca21)) +* autobump bio/busco ([#1255](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1255)) ([402aaaa](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/402aaaaf2cbbc47314db353905292a6e572ceb61)) +* autobump bio/bwa-mem2/mem ([#1202](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1202)) ([90e1d60](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/90e1d60c7f9f9c518814196f2e9d94b9a7fb6496)) +* autobump bio/bwa-meme/index ([#1180](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1180)) ([1f0378c](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1f0378cdb6ed256362cf753fdba82d6f71677307)) +* autobump bio/bwa-meme/mem ([#1163](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1163)) ([5236667](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/52366674dbfaac0796041db97397e10b216bdf1a)) +* autobump bio/bwa-meme/mem ([#1231](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1231)) ([1ad2b8d](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1ad2b8deb38664ebd2c92d67ce77fc095b6a4a18)) +* autobump bio/bwa-memx/index ([#1207](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1207)) ([59be498](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/59be498ccf3c3eb267c27db84ddbb4ad78157d29)) +* autobump bio/bwa-memx/mem ([#1268](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1268)) ([a2fe8b9](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a2fe8b975f3ac9e61cdcea172e506292b6a69a97)) +* autobump bio/bwa/sampe ([#1225](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1225)) ([d759781](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/d759781ec230084724d3dad2005aee196c135889)) +* autobump bio/cutadapt/pe ([#1219](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1219)) ([44f346e](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/44f346e2094a5d1c69d4bad14c98dfe3fb641b57)) +* autobump bio/cutadapt/se ([#1253](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1253)) ([95c8278](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/95c8278409f14990147d501a019cbe875ad4b28b)) +* autobump bio/delly ([#1267](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1267)) ([75a0d1a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/75a0d1a0a2b03622f76f814258719c396691e5c7)) +* autobump bio/diamond/blastp ([#1161](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1161)) ([1f89877](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1f898770af5b3c41135ede213508885bb214ab5f)) +* autobump bio/diamond/blastx ([#1221](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1221)) ([480fc20](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/480fc206378e088a1c7a46e71523a63bb7fe048a)) +* autobump bio/diamond/makedb ([#1223](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1223)) ([49d1484](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/49d14842fa6be1be1ed439b1107b3b4a952f6e45)) +* autobump bio/fgbio/collectduplexseqmetrics ([#1201](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1201)) ([04e4ec7](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/04e4ec73d53f15993ad55563c9477fb2885ff0f8)) +* autobump bio/gatk/applybqsrspark ([#1194](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1194)) ([65f53d8](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/65f53d89cee7a2b7903891fd33b40a33fd328c2f)) +* autobump bio/gatk/applybqsrspark ([#1250](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1250)) ([56efdd1](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/56efdd137d91a8bcbeebcfdb1591a5f7ccba2c32)) +* autobump bio/gatk/baserecalibrator ([#1249](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1249)) ([788ed8f](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/788ed8f9d5c9fbdceece90cf2f53ca02dfa0bc14)) +* autobump bio/gatk/baserecalibratorspark ([#1185](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1185)) ([f5a5f47](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/f5a5f47382b2a7d9fce892d5564b8ef73dae9b0e)) +* autobump bio/gatk/combinegvcfs ([#1261](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1261)) ([bd3066a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/bd3066a4b8444e00ed6fefa6d6aab8483d73f5fe)) +* autobump bio/gatk/estimatelibrarycomplexity ([#1252](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1252)) ([12f5440](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/12f54404f391cdd250471bde20442e131ce62e5b)) +* autobump bio/gatk/filtermutectcalls ([#1155](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1155)) ([0071533](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/00715334b70c8b0e2ae1e52b47351320fe8157af)) +* autobump bio/gatk/filtermutectcalls ([#1195](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1195)) ([7f05ddf](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/7f05ddf98bf36db83fb4846188f0b512cd08b68f)) +* autobump bio/gatk/genomicsdbimport ([#1215](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1215)) ([300dbe8](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/300dbe83c2ed9e573318a8b30fd22293541695ab)) +* autobump bio/gatk/genotypegvcfs ([#1179](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1179)) ([85758b7](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/85758b7f4d36fb40b9e9826200cba5cf5e95b29b)) +* autobump bio/gatk/haplotypecaller ([#1256](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1256)) ([5caa178](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/5caa178fbcbc1dca8444f6a238c868d096b3785a)) +* autobump bio/gatk/learnreadorientationmodel ([#1158](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1158)) ([97cd747](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/97cd7470196fa28fa229361b81cc10466f87b495)) +* autobump bio/gatk/leftalignandtrimvariants ([#1205](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1205)) ([377f253](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/377f2533992ff68f563faed1a37059aeadf041bb)) +* autobump bio/gatk/markduplicatesspark ([#1224](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1224)) ([0893b4e](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0893b4ec8d1cfecfc2a80c77e6170bbe2bbc981e)) +* autobump bio/gatk/mutect ([#1262](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1262)) ([a01e719](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a01e7190abb6f08f8fbcd54d886d36b752171165)) +* autobump bio/gatk/splitintervals ([#1188](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1188)) ([2d610dd](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/2d610dd129d1b179ff550932416a0dcec6991cb9)) +* autobump bio/gatk/variantannotator ([#1160](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1160)) ([f7001e2](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/f7001e2c2a6ce9e3fef0fe700bb1a37c56d86c22)) +* autobump bio/gatk3/printreads ([#1174](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1174)) ([22f8e69](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/22f8e696259744d09af4d07053bbe1124f5ca0e5)) +* autobump bio/gatk3/printreads ([#1217](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1217)) ([5d05b88](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/5d05b8828266a4a33dbeb80900faf6f2df971c7d)) +* autobump bio/gdc-api/bam-slicing ([#1159](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1159)) ([96a1a42](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/96a1a42b672bdf9fca9a8e8ef5d140cc02d93753)) +* autobump bio/homer/makeTagDirectory ([#1246](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1246)) ([44847e2](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/44847e2ef5f63c51f03a2370a0d6768dc49fed46)) +* autobump bio/last/lastal ([#1165](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1165)) ([ca0d13f](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/ca0d13fad8396327826d41d394861809305c87d5)) +* autobump bio/last/lastdb ([#1254](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1254)) ([2f11b1e](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/2f11b1e181be6435687bf28ac00c4183ea2868d9)) +* autobump bio/lofreq/call ([#1156](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1156)) ([c750bbf](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/c750bbf2b0fd45abd3d0ba8b926a6cf404b38c0d)) +* autobump bio/mashmap ([#1244](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1244)) ([fad0092](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/fad0092b61dba723b7d653894950121553f5b126)) +* autobump bio/microphaser/filter ([#1164](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1164)) ([8932d38](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/8932d3882426094d0de56fc32c8e9b81a72c37e5)) +* autobump bio/minimap2/aligner ([#1177](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1177)) ([07f4e02](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/07f4e0238bd7c9207aa6c56744dcfe9c5090f7b5)) +* autobump bio/open-cravat/module ([#1232](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1232)) ([be62998](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/be629987465b94a9f616c3754af8349d33dd875a)) +* autobump bio/paladin/align ([#1234](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1234)) ([df3c213](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/df3c213a390bd4a9fdebb809ecf31debef74b8f7)) +* autobump bio/picard/collectalignmentsummarymetrics ([#1175](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1175)) ([856224a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/856224a4db42aa3ea9937c39745a1c7dfab7ff20)) +* autobump bio/picard/collectgcbiasmetrics ([#1247](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1247)) ([202ab81](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/202ab81a08990a4d9c2b6915130430928c3414e0)) +* autobump bio/picard/collecthsmetrics ([#1198](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1198)) ([874fc3f](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/874fc3f6ab40df13dcc3be0a8f68510c2da555f2)) +* autobump bio/picard/collectinsertsizemetrics ([#1190](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1190)) ([543540a](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/543540aca4afc447f8e22eae8ec01a7a4f143839)) +* autobump bio/picard/collecttargetedpcrmetrics ([#1203](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1203)) ([7e55cfc](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/7e55cfc9f208bc95ea50fae9e5d52ccb6cd43998)) +* autobump bio/picard/markduplicates ([#1233](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1233)) ([1708e12](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1708e127dbd80e5f96bc8224bbcbad7b14daa111)) +* autobump bio/picard/mergesamfiles ([#1176](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1176)) ([554f501](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/554f501f1c04cf90335b39e38d9919af1aa62d20)) +* autobump bio/picard/samtofastq ([#1218](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1218)) ([da9e010](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/da9e0101e9e9be9aa124dc454c43e5196746523e)) +* autobump bio/picard/sortsam ([#1248](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1248)) ([4cf9fdd](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/4cf9fdd2a49cc733f9917ff4c7f2257c770f9bd1)) +* autobump bio/pretext/map ([#1227](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1227)) ([fafa6ee](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/fafa6eeff201564f274ade75a3c1d31b21b575df)) +* autobump bio/qualimap/bamqc ([#1251](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1251)) ([4dc2495](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/4dc249559d4f59e9aec43c2b3757ca0a8fc61adb)) +* autobump bio/rbt/csvreport ([#1243](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1243)) ([25acb2f](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/25acb2f0c99dda2d36da474706dce1f18796022c)) +* autobump bio/reference/ensembl-variation ([#1265](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1265)) ([ede45c7](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/ede45c783b659b54758b4eee9570c8bd76d0a8da)) +* autobump bio/samtools/faidx ([#1182](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1182)) ([c223f0c](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/c223f0c429a41bdf3d10652c5a2286fc6034d4eb)) +* autobump bio/samtools/fixmate ([#1264](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1264)) ([f42a717](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/f42a717fa58bb3a1b9b442caa4d32b8778830568)) +* autobump bio/samtools/flagstat ([#1184](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1184)) ([4f5349c](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/4f5349cf64c1129ddb81b79cb29e9993f34af193)) +* autobump bio/samtools/idxstats ([#1193](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1193)) ([f930f9e](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/f930f9e15ae64f07415fa6a0ba808b7e3ba12765)) +* autobump bio/samtools/idxstats ([#1259](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1259)) ([c6b3b40](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/c6b3b4088f4dea4645e1c95203cacaa400eacd4c)) +* autobump bio/samtools/index ([#1214](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1214)) ([a1ca2a1](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a1ca2a110b8de164a14aaa9d9964e8681ba95d6b)) +* autobump bio/samtools/stats ([#1222](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1222)) ([0eb7652](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0eb76529d289920319bd5368294a2c51fbc8834e)) +* autobump bio/seqkit/rmdup ([#1162](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1162)) ([88f74d4](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/88f74d4bc502b3299b40eb127f8eefa7e0554fcf)) +* autobump bio/seqkit/stats ([#1213](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1213)) ([523b69b](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/523b69b193b3e9d5b56964785626f4b07949f7b9)) +* autobump bio/snpeff/annotate ([#1189](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1189)) ([d873ee8](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/d873ee83265f6f34903a6e8d69f574422cb4f6da)) +* autobump bio/snpsift/annotate ([#1204](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1204)) ([8c069ff](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/8c069ff88aadba45c394f55a558a2b70cd3d4735)) +* autobump bio/snpsift/genesets ([#1245](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1245)) ([a2649a7](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a2649a7e563758599af1834c2871ac19b8c0aa3f)) +* autobump bio/snpsift/gwascat ([#1191](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1191)) ([0c3c051](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0c3c0519db9a75c78750a26b407bd9d0ebb88741)) +* autobump bio/snpsift/gwascat ([#1211](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1211)) ([53d82b9](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/53d82b92e41bf2eab92bd2eb6c92d10f94e4a09a)) +* autobump bio/snpsift/varType ([#1196](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1196)) ([75bd430](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/75bd430edf46275f075a6b344642dece836532fe)) +* autobump bio/snpsift/varType ([#1196](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1196)) ([eaee058](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/eaee0581606c601eda849d0cbfe255839ae91d46)) +* autobump bio/strling/call ([#1216](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1216)) ([fa539be](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/fa539be3e05ac73058c7dc450719363117014d28)) +* autobump bio/strling/index ([#1228](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1228)) ([6cc0059](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/6cc00599fa9dd88d8559501f08fdd691a1b6668c)) +* autobump bio/umis/bamtag ([#1260](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1260)) ([1334743](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1334743834a811551f799d7e18038a5a546b9dbb)) +* autobump bio/varscan/mpileup2indel ([#1186](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1186)) ([72816c8](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/72816c80df421f1dad58f63559e1671c4b00a5af)) +* autobump bio/varscan/mpileup2snp ([#1230](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1230)) ([0266507](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/0266507d87ed97c4a67bef33cf39362fe32ec174)) +* autobump bio/varscan/somatic ([#1178](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1178)) ([1882608](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/18826087b21fb1f5279cfa8eea349fda58bcd50a)) +* autobump bio/vembrane/filter ([#1229](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1229)) ([1a30d43](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/1a30d43738fccdf0b9bfdc3477adbd4cbb3a8c38)) +* autobump bio/vep/plugins ([#1200](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1200)) ([a7909be](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a7909be8b31e68c2f933d77b0befaf8bfe005d80)) +* autobump bio/vg/construct ([#1226](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1226)) ([4b2745f](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/4b2745f6ed8d987b355db06af29c62ffa0ad54f4)) +* autobump bio/vg/prune ([#1263](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1263)) ([8a36dec](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/8a36deccdf7750b41625f152843d02e5ef0bd257)) +* bump Salmon to v1.10.1 ([61758c3](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/61758c3eab60df898e7164d677d794db27ef6337)) +* bump Salmon to v1.10.1 ([#1168](https://www.github.com/sansterbioanalytics/snakemake-wrappers/issues/1168)) ([a718777](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a718777f285f175c5f6c67170b6d6440d504184b)) +* reorganize inputs and add back input_string ([a3b02b8](https://www.github.com/sansterbioanalytics/snakemake-wrappers/commit/a3b02b8d6169041d506744fe9d50d2474ec1eb58)) + ## [1.25.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.24.0...v1.25.0) (2023-03-23) diff --git a/bio/refgenie/test/Snakefile b/bio/refgenie/test/Snakefile index 095658c7fae..c18c98a7eab 100644 --- a/bio/refgenie/test/Snakefile +++ b/bio/refgenie/test/Snakefile @@ -1,11 +1,25 @@ rule obtain_asset: output: # the name refers to the refgenie seek key (see attributes on http://refgenomes.databio.org) - fai="refs/genome.fasta" + fai="refs/genome.fasta", # Multiple outputs/seek keys are possible here. params: genome="human_alu", asset="fasta", - tag="default" + tag="default", + log: + "logs/refgenie/obtain_large_asset.log", + wrapper: + "master/bio/refgenie" + +rule obtain_large_asset: + output: + star_index=directory("refs/star_index/hg38/star_index"), + params: + genome="hg38", + asset="star_index", + tag="default", + log: + "logs/refgenie/obtain_large_asset.log", wrapper: "master/bio/refgenie" diff --git a/bio/refgenie/wrapper.py b/bio/refgenie/wrapper.py index cdb36644397..2268875acac 100644 --- a/bio/refgenie/wrapper.py +++ b/bio/refgenie/wrapper.py @@ -5,6 +5,7 @@ import os import refgenconf +from refgenconf.exceptions import RefgenconfError genome = snakemake.params.genome asset = snakemake.params.asset @@ -12,10 +13,19 @@ conf_path = os.environ["REFGENIE"] -rgc = refgenconf.RefGenConf(conf_path, writable=True) - +# BUG If there are multiple concurrent refgenie commands, this will fail due to +# unable to acquire lock of the config file. +try: + rgc = refgenconf.RefGenConf(conf_path, writable=True) +except RefgenconfError: + # If read lock timeout, attempt to skip the read lock + rgc = refgenconf.RefGenConf( + conf_path, writable=True, skip_read_lock=True, genome_exact=False + ) # pull asset if necessary -gat, archive_data, server_url = rgc.pull(genome, asset, tag, force=False) +gat, archive_data, server_url = rgc.pull( + genome, asset, tag, force=False, force_large=True +) for seek_key, out in snakemake.output.items(): path = rgc.seek(genome, asset, tag_name=tag, seek_key=seek_key, strict_exists=True) diff --git a/bio/rsem/calculate-expression/wrapper.py b/bio/rsem/calculate-expression/wrapper.py index 6fe671d5c54..0ea7f7689c0 100644 --- a/bio/rsem/calculate-expression/wrapper.py +++ b/bio/rsem/calculate-expression/wrapper.py @@ -5,7 +5,7 @@ import os - +from pathlib import Path from snakemake.shell import shell bam = snakemake.input.get("bam", "") @@ -60,15 +60,22 @@ "output.isoforms_results file name malformed " "(rsem will append .isoforms.results suffix)" ) - -reference_prefix = os.path.splitext(snakemake.input.reference[0])[0] + +# BUG input_string is 'r' given the input but is should be the reference base path? +# subprocess.CalledProcessError: Command 'set -euo pipefail; rsem-calculate-expression --num-threads 24 --estimate-rspd --calc-ci --strandedness reverse --time --paired-end --alignments results/star/D-1/Aligned.toTranscriptome.out.bam r results/rsem/D-1/D-1 > logs/rsem/calculate_expression/D-1.log 2>&1' returned non-zero exit status 255. +reference_path = Path(snakemake.input.reference[0]) +reference_prefix = str(reference_path.parents[0]/reference_path.stem) extra = snakemake.params.get("extra", "") threads = snakemake.threads log = snakemake.log_fmt_shell(stdout=True, stderr=True) shell( - "rsem-calculate-expression --num-threads {snakemake.threads} {extra} " - "{paired_end_string} {input_bam} {input_string} " - "{reference_prefix} {output_prefix} " + "rsem-calculate-expression --num-threads {snakemake.threads} " + "{extra} " + "{paired_end_string} " + "{input_bam} " + "{input_string} " + "{reference_prefix} " + "{output_prefix} " "{log}" )