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chore: release 3.11.0 (snakemake#2925)
🤖 I have created a release \*beep\* \*boop\* --- ## [3.11.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.10.2...v3.11.0) (2024-05-31) ### Features * add samtools markdup wrapper ([snakemake#2926](https://www.github.com/snakemake/snakemake-wrappers/issues/2926)) ([3c86bae](https://www.github.com/snakemake/snakemake-wrappers/commit/3c86baef4586b596c6c3375336828257e8bb815f)) * Add support for regions file and arbitrary FAI/GZI paths ([snakemake#2936](https://www.github.com/snakemake/snakemake-wrappers/issues/2936)) ([445b35f](https://www.github.com/snakemake/snakemake-wrappers/commit/445b35f314f035d8248ca84cb16b273b0e65847c)) * add wrapper to samtools collate ([snakemake#2929](https://www.github.com/snakemake/snakemake-wrappers/issues/2929)) ([0c7ae27](https://www.github.com/snakemake/snakemake-wrappers/commit/0c7ae27622e45167b9cc1aaf1be238b0d25429b9)) * All ngsderive subcommands ([snakemake#2732](https://www.github.com/snakemake/snakemake-wrappers/issues/2732)) ([847ab1d](https://www.github.com/snakemake/snakemake-wrappers/commit/847ab1d918c09908bcdb40fa3413b6dbc88d4803)) * auto infer run mode ([snakemake#2937](https://www.github.com/snakemake/snakemake-wrappers/issues/2937)) ([08bd3cd](https://www.github.com/snakemake/snakemake-wrappers/commit/08bd3cd79243c4c0636f88d229667e58595611bd)) * Goleft indexcov ([snakemake#2734](https://www.github.com/snakemake/snakemake-wrappers/issues/2734)) ([ebef6f8](https://www.github.com/snakemake/snakemake-wrappers/commit/ebef6f8259e89d9a06b2264a5d0a34da23d2e84e)) ### Bug Fixes * bamcoverage without effective genome size ([snakemake#2941](https://www.github.com/snakemake/snakemake-wrappers/issues/2941)) ([b6ad55f](https://www.github.com/snakemake/snakemake-wrappers/commit/b6ad55f4d2c702ecc904d6b40b4b35b2463c895a)) * issue [snakemake#366](https://www.github.com/snakemake/snakemake-wrappers/issues/366) and [snakemake#2649](https://www.github.com/snakemake/snakemake-wrappers/issues/2649) ([snakemake#2928](https://www.github.com/snakemake/snakemake-wrappers/issues/2928)) ([e10ab57](https://www.github.com/snakemake/snakemake-wrappers/commit/e10ab571a63b36ce1295e50b6f6b7e4742e0beae)) * remove NA string replacement, fixed upstream ([snakemake#2940](https://www.github.com/snakemake/snakemake-wrappers/issues/2940)) ([8f4d223](https://www.github.com/snakemake/snakemake-wrappers/commit/8f4d223ec6c1e1e2715708d0532399ede4ed2727)) ### Performance Improvements * autobump bio/bismark/bam2nuc ([snakemake#2943](https://www.github.com/snakemake/snakemake-wrappers/issues/2943)) ([9228479](https://www.github.com/snakemake/snakemake-wrappers/commit/9228479896c2410ae6a58849bf59e5f01bc5e712)) * autobump bio/bismark/bismark ([snakemake#2948](https://www.github.com/snakemake/snakemake-wrappers/issues/2948)) ([d9abb20](https://www.github.com/snakemake/snakemake-wrappers/commit/d9abb20e0e002d9ec16507d86211b0555a2546ba)) * autobump bio/bismark/bismark_genome_preparation ([snakemake#2945](https://www.github.com/snakemake/snakemake-wrappers/issues/2945)) ([899ae0d](https://www.github.com/snakemake/snakemake-wrappers/commit/899ae0d96d04fa56a7ba5989d9dea18be0d3ebc6)) * autobump bio/bismark/bismark_methylation_extractor ([snakemake#2944](https://www.github.com/snakemake/snakemake-wrappers/issues/2944)) ([1b232d2](https://www.github.com/snakemake/snakemake-wrappers/commit/1b232d24816a40f75568bec224eff4e164b3f953)) * autobump bio/bismark/bismark2bedGraph ([snakemake#2947](https://www.github.com/snakemake/snakemake-wrappers/issues/2947)) ([ab29098](https://www.github.com/snakemake/snakemake-wrappers/commit/ab29098757c3eef17884f198234ec456e19414f9)) * autobump bio/bismark/bismark2report ([snakemake#2951](https://www.github.com/snakemake/snakemake-wrappers/issues/2951)) ([13dd155](https://www.github.com/snakemake/snakemake-wrappers/commit/13dd155a20025b8aaaa80ce3747e6822562bb6b1)) * autobump bio/bismark/bismark2summary ([snakemake#2946](https://www.github.com/snakemake/snakemake-wrappers/issues/2946)) ([bfb3d30](https://www.github.com/snakemake/snakemake-wrappers/commit/bfb3d305daa519faee4ad4ea7dbd313941f4c128)) * autobump bio/bismark/deduplicate_bismark ([snakemake#2950](https://www.github.com/snakemake/snakemake-wrappers/issues/2950)) ([bcf3c06](https://www.github.com/snakemake/snakemake-wrappers/commit/bcf3c06887443dae9749254f0e8d34e30f880b7e)) * autobump bio/bowtie2/align ([snakemake#2949](https://www.github.com/snakemake/snakemake-wrappers/issues/2949)) ([6b0593f](https://www.github.com/snakemake/snakemake-wrappers/commit/6b0593facfcae0b9c92cb1f31423426752c0230d)) * autobump bio/bowtie2/build ([snakemake#2942](https://www.github.com/snakemake/snakemake-wrappers/issues/2942)) ([5b3ca20](https://www.github.com/snakemake/snakemake-wrappers/commit/5b3ca20635bd0e427a548e68cd8a40fdb0047f10)) * autobump bio/bwa-mem2/mem-samblaster ([snakemake#2962](https://www.github.com/snakemake/snakemake-wrappers/issues/2962)) ([ff613f3](https://www.github.com/snakemake/snakemake-wrappers/commit/ff613f37f857f23d19e4dc0cace22b02113a7e07)) * autobump bio/bwa/mem-samblaster ([snakemake#2961](https://www.github.com/snakemake/snakemake-wrappers/issues/2961)) ([83754dd](https://www.github.com/snakemake/snakemake-wrappers/commit/83754dd9f158ea978faa1ed33668a6dda648cdb7)) * autobump bio/fastq_screen ([snakemake#2952](https://www.github.com/snakemake/snakemake-wrappers/issues/2952)) ([e45fcac](https://www.github.com/snakemake/snakemake-wrappers/commit/e45fcac221ef45f345a516bff905a53c864e7355)) * autobump bio/freebayes ([snakemake#2963](https://www.github.com/snakemake/snakemake-wrappers/issues/2963)) ([7a0d553](https://www.github.com/snakemake/snakemake-wrappers/commit/7a0d553e09921cebc77b54d314c211b91099f7bd)) * autobump bio/gatk/applybqsr ([snakemake#2938](https://www.github.com/snakemake/snakemake-wrappers/issues/2938)) ([498c67f](https://www.github.com/snakemake/snakemake-wrappers/commit/498c67fb12691b0021a7b234dfc279957b46708c)) * autobump bio/gatk3/realignertargetcreator ([snakemake#2931](https://www.github.com/snakemake/snakemake-wrappers/issues/2931)) ([2d2835c](https://www.github.com/snakemake/snakemake-wrappers/commit/2d2835c51f974f7f45420f832b8084520d2d3ec0)) * autobump bio/gdc-api/bam-slicing ([snakemake#2954](https://www.github.com/snakemake/snakemake-wrappers/issues/2954)) ([32d25c1](https://www.github.com/snakemake/snakemake-wrappers/commit/32d25c1560b4c581694c49dc6d3a596e5ca581ab)) * autobump bio/goleft/indexcov ([snakemake#2930](https://www.github.com/snakemake/snakemake-wrappers/issues/2930)) ([5ccbdb0](https://www.github.com/snakemake/snakemake-wrappers/commit/5ccbdb078a835ad0c2fd3e9e63677103fe216eeb)) * autobump bio/gseapy/gsea ([snakemake#2953](https://www.github.com/snakemake/snakemake-wrappers/issues/2953)) ([dda3d16](https://www.github.com/snakemake/snakemake-wrappers/commit/dda3d16c9b49145bd58d287db1021c41d5a24710)) * autobump bio/hifiasm ([snakemake#2932](https://www.github.com/snakemake/snakemake-wrappers/issues/2932)) ([3722de7](https://www.github.com/snakemake/snakemake-wrappers/commit/3722de7000d0b74a3c56bfdb27aad6cf318562ee)) * autobump bio/multiqc ([snakemake#2955](https://www.github.com/snakemake/snakemake-wrappers/issues/2955)) ([91ad107](https://www.github.com/snakemake/snakemake-wrappers/commit/91ad1079fa03b07f8ebb9ebf21fe92d21c8a3c13)) * autobump bio/ngsderive ([snakemake#2964](https://www.github.com/snakemake/snakemake-wrappers/issues/2964)) ([df82b38](https://www.github.com/snakemake/snakemake-wrappers/commit/df82b381a49b7810087f73b7c83db4fff6d57b66)) * autobump bio/open-cravat/module ([snakemake#2966](https://www.github.com/snakemake/snakemake-wrappers/issues/2966)) ([f1ffa3e](https://www.github.com/snakemake/snakemake-wrappers/commit/f1ffa3eee366cba828314cc9a368ba69f17d98c2)) * autobump bio/open-cravat/run ([snakemake#2965](https://www.github.com/snakemake/snakemake-wrappers/issues/2965)) ([9b371ca](https://www.github.com/snakemake/snakemake-wrappers/commit/9b371ca6014a38cf23e78598638e4c709a5e82af)) * autobump bio/ptrimmer ([snakemake#2933](https://www.github.com/snakemake/snakemake-wrappers/issues/2933)) ([cd37e0b](https://www.github.com/snakemake/snakemake-wrappers/commit/cd37e0bb19e341ad40560828f3c052ef69529088)) * autobump bio/rasusa ([snakemake#2967](https://www.github.com/snakemake/snakemake-wrappers/issues/2967)) ([9f25643](https://www.github.com/snakemake/snakemake-wrappers/commit/9f2564323429bea84dfb0b01a5b9f53b37fa397c)) * autobump bio/rbt/csvreport ([snakemake#2956](https://www.github.com/snakemake/snakemake-wrappers/issues/2956)) ([b2a469d](https://www.github.com/snakemake/snakemake-wrappers/commit/b2a469dc907c8f3761399affd29ca53f012cc3ee)) * autobump bio/sambamba/flagstat ([snakemake#2973](https://www.github.com/snakemake/snakemake-wrappers/issues/2973)) ([4575792](https://www.github.com/snakemake/snakemake-wrappers/commit/4575792deb144dd80401d46bc2fb72175976305a)) * autobump bio/sambamba/index ([snakemake#2971](https://www.github.com/snakemake/snakemake-wrappers/issues/2971)) ([18359ac](https://www.github.com/snakemake/snakemake-wrappers/commit/18359ac437bb9f1065c703b3bf2da1d3da9548be)) * autobump bio/sambamba/markdup ([snakemake#2968](https://www.github.com/snakemake/snakemake-wrappers/issues/2968)) ([191542d](https://www.github.com/snakemake/snakemake-wrappers/commit/191542d475853f6f19495e136e105970928a9fd8)) * autobump bio/sambamba/merge ([snakemake#2975](https://www.github.com/snakemake/snakemake-wrappers/issues/2975)) ([adf9a28](https://www.github.com/snakemake/snakemake-wrappers/commit/adf9a28b64f87aec3fa8286f356f44b6bb77561e)) * autobump bio/sambamba/slice ([snakemake#2972](https://www.github.com/snakemake/snakemake-wrappers/issues/2972)) ([88ac3f6](https://www.github.com/snakemake/snakemake-wrappers/commit/88ac3f6dfae93606f74ae8c88b6f8b9e2d059a02)) * autobump bio/sambamba/sort ([snakemake#2976](https://www.github.com/snakemake/snakemake-wrappers/issues/2976)) ([990e841](https://www.github.com/snakemake/snakemake-wrappers/commit/990e8416b730267a65ba5a97b71537655bbfe6db)) * autobump bio/sambamba/view ([snakemake#2970](https://www.github.com/snakemake/snakemake-wrappers/issues/2970)) ([613e55d](https://www.github.com/snakemake/snakemake-wrappers/commit/613e55d915215348651e878fe37f6533e6d77363)) * autobump bio/seqkit ([snakemake#2969](https://www.github.com/snakemake/snakemake-wrappers/issues/2969)) ([e25b840](https://www.github.com/snakemake/snakemake-wrappers/commit/e25b8409af3cc9e591b5106f1ebb00289f628207)) * autobump bio/sra-tools/fasterq-dump ([snakemake#2974](https://www.github.com/snakemake/snakemake-wrappers/issues/2974)) ([d8b4b5f](https://www.github.com/snakemake/snakemake-wrappers/commit/d8b4b5fab114c66bf712ee271b00f831a5ed558d)) * autobump bio/unicycler ([snakemake#2957](https://www.github.com/snakemake/snakemake-wrappers/issues/2957)) ([185ce7e](https://www.github.com/snakemake/snakemake-wrappers/commit/185ce7e4bd6adbdf840effa665f62e358865c8b8)) * autobump bio/vep/annotate ([snakemake#2958](https://www.github.com/snakemake/snakemake-wrappers/issues/2958)) ([728658d](https://www.github.com/snakemake/snakemake-wrappers/commit/728658d5fae40ea784f7b8d3c567c4f7240ef7c7)) * autobump bio/vep/cache ([snakemake#2959](https://www.github.com/snakemake/snakemake-wrappers/issues/2959)) ([f4e5b66](https://www.github.com/snakemake/snakemake-wrappers/commit/f4e5b66f8765d09d51d4a640d2d775d781c3018f)) * autobump bio/whatshap/haplotag ([snakemake#2934](https://www.github.com/snakemake/snakemake-wrappers/issues/2934)) ([f0b638a](https://www.github.com/snakemake/snakemake-wrappers/commit/f0b638a55280c0727ccef5aab24e03b3d565f290)) * Update Datavzrd to 2.36.12 ([snakemake#2924](https://www.github.com/snakemake/snakemake-wrappers/issues/2924)) ([beb9d22](https://www.github.com/snakemake/snakemake-wrappers/commit/beb9d2231c5d59ba74f23f56bbfc5e004aa72331)) * Use samtools collate in fastq separate wrapper ([snakemake#2960](https://www.github.com/snakemake/snakemake-wrappers/issues/2960)) ([9c8cf81](https://www.github.com/snakemake/snakemake-wrappers/commit/9c8cf81c1894fc019ffbf0f906eb88e0960c3e7d)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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