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fix: empty emu combined output #2899
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fgvieira
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Apr 22, 2024
johanneskoester
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Apr 23, 2024
🤖 I have created a release \*beep\* \*boop\* --- ## [3.9.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.8.0...v3.9.0) (2024-04-22) ### Features * Add wrapper for defining columns in TTree in ROOT ([#2898](https://www.github.com/snakemake/snakemake-wrappers/issues/2898)) ([48730cd](https://www.github.com/snakemake/snakemake-wrappers/commit/48730cddcfb8035a927ee65912c0bda0f88f5ae5)) * Emu support ([#2792](https://www.github.com/snakemake/snakemake-wrappers/issues/2792)) ([149ef14](https://www.github.com/snakemake/snakemake-wrappers/commit/149ef14dca9d836d297c95cd4e010c360375f51d)) ### Bug Fixes * deeptools bamcoverage fix ([#2719](https://www.github.com/snakemake/snakemake-wrappers/issues/2719)) ([206425b](https://www.github.com/snakemake/snakemake-wrappers/commit/206425b0de89ce97fadd7f4a5af89f4c401470cb)) * empty emu combined output ([#2899](https://www.github.com/snakemake/snakemake-wrappers/issues/2899)) ([7b10806](https://www.github.com/snakemake/snakemake-wrappers/commit/7b10806933d735251039fc3e89193e82bb86d936)) ### Performance Improvements * autobump bio/bcftools/call ([#2828](https://www.github.com/snakemake/snakemake-wrappers/issues/2828)) ([cd25cc8](https://www.github.com/snakemake/snakemake-wrappers/commit/cd25cc85f238ebfcdcc01b7c550744e2ecee1e6c)) * autobump bio/bcftools/concat ([#2832](https://www.github.com/snakemake/snakemake-wrappers/issues/2832)) ([785cd77](https://www.github.com/snakemake/snakemake-wrappers/commit/785cd779e9fc4824b232919f33a76e231000713c)) * autobump bio/bcftools/filter ([#2821](https://www.github.com/snakemake/snakemake-wrappers/issues/2821)) ([c4c2315](https://www.github.com/snakemake/snakemake-wrappers/commit/c4c2315fd955fd101d6aee88807d4f5d23409629)) * autobump bio/bcftools/index ([#2829](https://www.github.com/snakemake/snakemake-wrappers/issues/2829)) ([3ea7efb](https://www.github.com/snakemake/snakemake-wrappers/commit/3ea7efbd36bf216a0a9f8af5ed325fe5587ceca3)) * autobump bio/bcftools/merge ([#2827](https://www.github.com/snakemake/snakemake-wrappers/issues/2827)) ([b1aee95](https://www.github.com/snakemake/snakemake-wrappers/commit/b1aee9585c4952b3f24ced6e216c1b9ec5765b82)) * autobump bio/bcftools/mpileup ([#2817](https://www.github.com/snakemake/snakemake-wrappers/issues/2817)) ([9b9c0ea](https://www.github.com/snakemake/snakemake-wrappers/commit/9b9c0ea91bc0ad00fa1d65b1737d3ed8f7ef44fd)) * autobump bio/bcftools/norm ([#2819](https://www.github.com/snakemake/snakemake-wrappers/issues/2819)) ([7126185](https://www.github.com/snakemake/snakemake-wrappers/commit/712618518f313737db725edf53bd19847478ad1a)) * autobump bio/bcftools/reheader ([#2822](https://www.github.com/snakemake/snakemake-wrappers/issues/2822)) ([a77fa02](https://www.github.com/snakemake/snakemake-wrappers/commit/a77fa020ea307926ccde2659d2146c6a9c413d8e)) * autobump bio/bcftools/sort ([#2825](https://www.github.com/snakemake/snakemake-wrappers/issues/2825)) ([7c9bb6d](https://www.github.com/snakemake/snakemake-wrappers/commit/7c9bb6d76a326ab8bfb91c38da4520cb4dfa79b0)) * autobump bio/bcftools/stats ([#2813](https://www.github.com/snakemake/snakemake-wrappers/issues/2813)) ([78e1ed6](https://www.github.com/snakemake/snakemake-wrappers/commit/78e1ed6cb3e9a5682eb05943c01afdc24769012d)) * autobump bio/bcftools/view ([#2837](https://www.github.com/snakemake/snakemake-wrappers/issues/2837)) ([ba4cb3b](https://www.github.com/snakemake/snakemake-wrappers/commit/ba4cb3b8f437916f6c49714c803e6ad9bb07604a)) * autobump bio/bellerophon ([#2834](https://www.github.com/snakemake/snakemake-wrappers/issues/2834)) ([f9c272e](https://www.github.com/snakemake/snakemake-wrappers/commit/f9c272eeb9c0760ef02985ec903a8422733fc8aa)) * autobump bio/benchmark/chm-eval-sample ([#2830](https://www.github.com/snakemake/snakemake-wrappers/issues/2830)) ([9911338](https://www.github.com/snakemake/snakemake-wrappers/commit/9911338baf4d0bcaf0db039195293675c4e0aaac)) * autobump bio/bgzip ([#2839](https://www.github.com/snakemake/snakemake-wrappers/issues/2839)) ([8b1d2d7](https://www.github.com/snakemake/snakemake-wrappers/commit/8b1d2d73c0b509ca71666974245c6b019028d168)) * autobump bio/bismark/bam2nuc ([#2815](https://www.github.com/snakemake/snakemake-wrappers/issues/2815)) ([1462242](https://www.github.com/snakemake/snakemake-wrappers/commit/146224245966bffff9211b808847102e5e481611)) * autobump bio/bismark/bismark ([#2812](https://www.github.com/snakemake/snakemake-wrappers/issues/2812)) ([62ee915](https://www.github.com/snakemake/snakemake-wrappers/commit/62ee9153a45f0ff18e3a6d5464a5ec3309202b0d)) * autobump bio/bismark/bismark_genome_preparation ([#2820](https://www.github.com/snakemake/snakemake-wrappers/issues/2820)) ([108387c](https://www.github.com/snakemake/snakemake-wrappers/commit/108387c294ad2019df29ff91efa1be80619c25b8)) * autobump bio/bismark/bismark_methylation_extractor ([#2814](https://www.github.com/snakemake/snakemake-wrappers/issues/2814)) ([47a2c50](https://www.github.com/snakemake/snakemake-wrappers/commit/47a2c507a7516082ef3d0eab6332d62255cf8980)) * autobump bio/bismark/bismark2bedGraph ([#2831](https://www.github.com/snakemake/snakemake-wrappers/issues/2831)) ([556aadd](https://www.github.com/snakemake/snakemake-wrappers/commit/556aaddc88dc4a0ab8cb5f6daf213e238d86d617)) * autobump bio/bismark/bismark2report ([#2808](https://www.github.com/snakemake/snakemake-wrappers/issues/2808)) ([b788b96](https://www.github.com/snakemake/snakemake-wrappers/commit/b788b963c4964ad862576362639107d3e269b54a)) * autobump bio/bismark/bismark2summary ([#2809](https://www.github.com/snakemake/snakemake-wrappers/issues/2809)) ([ff32047](https://www.github.com/snakemake/snakemake-wrappers/commit/ff320479233c211c11ae2c99a5f7ba583fc538d6)) * autobump bio/bismark/deduplicate_bismark ([#2841](https://www.github.com/snakemake/snakemake-wrappers/issues/2841)) ([d897740](https://www.github.com/snakemake/snakemake-wrappers/commit/d897740f94c32755233351e6d8880499baa450e9)) * autobump bio/bowtie2/align ([#2810](https://www.github.com/snakemake/snakemake-wrappers/issues/2810)) ([f9b273e](https://www.github.com/snakemake/snakemake-wrappers/commit/f9b273ec3d87d317a4c4ad15e6f9c253660c16af)) * autobump bio/bwa-mem2/mem ([#2824](https://www.github.com/snakemake/snakemake-wrappers/issues/2824)) ([a4451ea](https://www.github.com/snakemake/snakemake-wrappers/commit/a4451eae221446e7be759de3409e43ff1857acb3)) * autobump bio/bwa-meme/mem ([#2836](https://www.github.com/snakemake/snakemake-wrappers/issues/2836)) ([7f2a24b](https://www.github.com/snakemake/snakemake-wrappers/commit/7f2a24babbaf0dc6b894b3b412bac4587b8e9127)) * autobump bio/bwa-memx/index ([#2816](https://www.github.com/snakemake/snakemake-wrappers/issues/2816)) ([d218b2b](https://www.github.com/snakemake/snakemake-wrappers/commit/d218b2b4b8569869c4ad0f416e98c28f28f38b9c)) * autobump bio/bwa-memx/mem ([#2826](https://www.github.com/snakemake/snakemake-wrappers/issues/2826)) ([e7baf43](https://www.github.com/snakemake/snakemake-wrappers/commit/e7baf43d02a4e7c8606c2730d584a02508e07244)) * autobump bio/bwa/aln ([#2833](https://www.github.com/snakemake/snakemake-wrappers/issues/2833)) ([b41d0b4](https://www.github.com/snakemake/snakemake-wrappers/commit/b41d0b411e8a3eb5426afde949409d245549d80f)) * autobump bio/bwa/index ([#2838](https://www.github.com/snakemake/snakemake-wrappers/issues/2838)) ([946d5c3](https://www.github.com/snakemake/snakemake-wrappers/commit/946d5c3ebfe32d9c3cf15a6891c2a8f075a2e108)) * autobump bio/bwa/mem ([#2818](https://www.github.com/snakemake/snakemake-wrappers/issues/2818)) ([2d49db7](https://www.github.com/snakemake/snakemake-wrappers/commit/2d49db7de49030835c6a98c78a10e39557606515)) * autobump bio/bwa/mem-samblaster ([#2840](https://www.github.com/snakemake/snakemake-wrappers/issues/2840)) ([0fc7d78](https://www.github.com/snakemake/snakemake-wrappers/commit/0fc7d787ae8467112d8dbaf59ba1e1acf3fe0a1f)) * autobump bio/bwa/sampe ([#2811](https://www.github.com/snakemake/snakemake-wrappers/issues/2811)) ([a6367ba](https://www.github.com/snakemake/snakemake-wrappers/commit/a6367ba49220e1cd2a6b6e260613104d7a7427b2)) * autobump bio/bwa/samse ([#2823](https://www.github.com/snakemake/snakemake-wrappers/issues/2823)) ([6d2b199](https://www.github.com/snakemake/snakemake-wrappers/commit/6d2b19929db4b786afb18111ccb370932a09b226)) * autobump bio/bwa/samxe ([#2835](https://www.github.com/snakemake/snakemake-wrappers/issues/2835)) ([a375c11](https://www.github.com/snakemake/snakemake-wrappers/commit/a375c11180ab2c24c246cd88569e0ecaa067830b)) * autobump bio/cnvkit/antitarget ([#2848](https://www.github.com/snakemake/snakemake-wrappers/issues/2848)) ([91354dc](https://www.github.com/snakemake/snakemake-wrappers/commit/91354dcf037dae7dba3ca5ebb4db270e4c38525e)) * autobump bio/cnvkit/batch ([#2849](https://www.github.com/snakemake/snakemake-wrappers/issues/2849)) ([9fae85d](https://www.github.com/snakemake/snakemake-wrappers/commit/9fae85d27cad290e08c4bb186aed6bda0881ef71)) * autobump bio/cnvkit/call ([#2844](https://www.github.com/snakemake/snakemake-wrappers/issues/2844)) ([5437973](https://www.github.com/snakemake/snakemake-wrappers/commit/54379737d0474daaf982ed98eddad39aaae5446e)) * autobump bio/cnvkit/diagram ([#2846](https://www.github.com/snakemake/snakemake-wrappers/issues/2846)) ([bcfcbed](https://www.github.com/snakemake/snakemake-wrappers/commit/bcfcbed4cfb7134ad676bd0c704d17a75b6d201d)) * autobump bio/cnvkit/export ([#2843](https://www.github.com/snakemake/snakemake-wrappers/issues/2843)) ([c499d71](https://www.github.com/snakemake/snakemake-wrappers/commit/c499d719efb0947bd59134c1bc3f5eb8f76b8fed)) * autobump bio/cnvkit/target ([#2847](https://www.github.com/snakemake/snakemake-wrappers/issues/2847)) ([a41c0a0](https://www.github.com/snakemake/snakemake-wrappers/commit/a41c0a094c367343980265c6155a65fd833dbcf7)) * autobump bio/cutadapt/pe ([#2845](https://www.github.com/snakemake/snakemake-wrappers/issues/2845)) ([77a7990](https://www.github.com/snakemake/snakemake-wrappers/commit/77a79909f8e8e3dbc61e62fe9d6fab6998464219)) * autobump bio/cutadapt/se ([#2842](https://www.github.com/snakemake/snakemake-wrappers/issues/2842)) ([d258f5b](https://www.github.com/snakemake/snakemake-wrappers/commit/d258f5bdcb1ed8b8b3ae0550e864238394384225)) * autobump bio/deeptools/bamcoverage ([#2851](https://www.github.com/snakemake/snakemake-wrappers/issues/2851)) ([35d5649](https://www.github.com/snakemake/snakemake-wrappers/commit/35d5649d2a9bc18bcc321a8338a15c9406d31630)) * autobump bio/delly ([#2850](https://www.github.com/snakemake/snakemake-wrappers/issues/2850)) ([3fa1540](https://www.github.com/snakemake/snakemake-wrappers/commit/3fa154029b46cb4d8ad871a745edcb3e4c420881)) * autobump bio/emu/abundance ([#2853](https://www.github.com/snakemake/snakemake-wrappers/issues/2853)) ([fc3d8b6](https://www.github.com/snakemake/snakemake-wrappers/commit/fc3d8b62712c683938d1c5a7be2c804f78a04958)) * autobump bio/emu/collapse-taxonomy ([#2855](https://www.github.com/snakemake/snakemake-wrappers/issues/2855)) ([2ec61a4](https://www.github.com/snakemake/snakemake-wrappers/commit/2ec61a4f5d4a91d8e27d1125d7c9afa60caf8396)) * autobump bio/emu/combine-outputs ([#2854](https://www.github.com/snakemake/snakemake-wrappers/issues/2854)) ([ce414e9](https://www.github.com/snakemake/snakemake-wrappers/commit/ce414e9ea040fda1b5ceac1afa6f814538b1ff7f)) * autobump bio/encode_fastq_downloader ([#2852](https://www.github.com/snakemake/snakemake-wrappers/issues/2852)) ([b71c6d6](https://www.github.com/snakemake/snakemake-wrappers/commit/b71c6d6e380d8a0839a55c1d6c0ac02221bad4ba)) * autobump bio/freebayes ([#2856](https://www.github.com/snakemake/snakemake-wrappers/issues/2856)) ([6f33607](https://www.github.com/snakemake/snakemake-wrappers/commit/6f33607e04c7e80e2bf4dd693cb72900058f0c6a)) * autobump bio/gatk3/printreads ([#2857](https://www.github.com/snakemake/snakemake-wrappers/issues/2857)) ([e42c565](https://www.github.com/snakemake/snakemake-wrappers/commit/e42c565cfc0fe296ef0be29f0a0e192d36707c3a)) * autobump bio/hisat2/align ([#2858](https://www.github.com/snakemake/snakemake-wrappers/issues/2858)) ([b354fc1](https://www.github.com/snakemake/snakemake-wrappers/commit/b354fc1da877c92dd757e804fe07bb1996514ca4)) * autobump bio/hisat2/index ([#2860](https://www.github.com/snakemake/snakemake-wrappers/issues/2860)) ([5d6bdd1](https://www.github.com/snakemake/snakemake-wrappers/commit/5d6bdd137d0d0f4a3ba2ef27d3c2bd76a58e5f51)) * autobump bio/homer/makeTagDirectory ([#2859](https://www.github.com/snakemake/snakemake-wrappers/issues/2859)) ([b3b9dfd](https://www.github.com/snakemake/snakemake-wrappers/commit/b3b9dfdc8513a9523205c3d84bf71178b52d88d9)) * autobump bio/lofreq/call ([#2861](https://www.github.com/snakemake/snakemake-wrappers/issues/2861)) ([3f66fd1](https://www.github.com/snakemake/snakemake-wrappers/commit/3f66fd18ecb0099ed0f535f677c282ed4e10285a)) * autobump bio/lofreq/indelqual ([#2862](https://www.github.com/snakemake/snakemake-wrappers/issues/2862)) ([736bc9c](https://www.github.com/snakemake/snakemake-wrappers/commit/736bc9cd3af8465df355cbe80806788ea6cf641c)) * autobump bio/minimap2/aligner ([#2863](https://www.github.com/snakemake/snakemake-wrappers/issues/2863)) ([0fdbb99](https://www.github.com/snakemake/snakemake-wrappers/commit/0fdbb99f2588780f34a5c789cfcac8483830584d)) * autobump bio/paladin/align ([#2865](https://www.github.com/snakemake/snakemake-wrappers/issues/2865)) ([50b5c90](https://www.github.com/snakemake/snakemake-wrappers/commit/50b5c9024636f55c0a087853b12cadb6d2ea37d7)) * autobump bio/paladin/index ([#2867](https://www.github.com/snakemake/snakemake-wrappers/issues/2867)) ([9d31d8d](https://www.github.com/snakemake/snakemake-wrappers/commit/9d31d8d3ca7c5643d0b5dd6e407f092e75fdc47c)) * autobump bio/paladin/prepare ([#2866](https://www.github.com/snakemake/snakemake-wrappers/issues/2866)) ([e327ba7](https://www.github.com/snakemake/snakemake-wrappers/commit/e327ba7c3551dca0a2592d840974876d72fb6766)) * autobump bio/picard/markduplicates ([#2864](https://www.github.com/snakemake/snakemake-wrappers/issues/2864)) ([f5ddedc](https://www.github.com/snakemake/snakemake-wrappers/commit/f5ddedccc9a04ce610666ed4e099f07791996509)) * autobump bio/pretext/map ([#2868](https://www.github.com/snakemake/snakemake-wrappers/issues/2868)) ([68ba090](https://www.github.com/snakemake/snakemake-wrappers/commit/68ba0909728a349208b55ac9f818197a35d21995)) * autobump bio/rbt/collapse_reads_to_fragments-bam ([#2870](https://www.github.com/snakemake/snakemake-wrappers/issues/2870)) ([8b36d24](https://www.github.com/snakemake/snakemake-wrappers/commit/8b36d24b7bb6c5f228329dfca6b422b4ab58141b)) * autobump bio/reference/ensembl-variation ([#2869](https://www.github.com/snakemake/snakemake-wrappers/issues/2869)) ([c8df691](https://www.github.com/snakemake/snakemake-wrappers/commit/c8df691a9a210052101e0274cf6612b82292518e)) * autobump bio/samtools/calmd ([#2885](https://www.github.com/snakemake/snakemake-wrappers/issues/2885)) ([031bdfa](https://www.github.com/snakemake/snakemake-wrappers/commit/031bdfa9320abdb04d763b3a51e493bb7b2fdc50)) * autobump bio/samtools/depth ([#2875](https://www.github.com/snakemake/snakemake-wrappers/issues/2875)) ([16a53d6](https://www.github.com/snakemake/snakemake-wrappers/commit/16a53d6fe09439cc17d262b36218c35aabb2aa85)) * autobump bio/samtools/faidx ([#2874](https://www.github.com/snakemake/snakemake-wrappers/issues/2874)) ([6a1b758](https://www.github.com/snakemake/snakemake-wrappers/commit/6a1b758344904c1293215f0a568417ae3f213c34)) * autobump bio/samtools/fastx ([#2884](https://www.github.com/snakemake/snakemake-wrappers/issues/2884)) ([60b6495](https://www.github.com/snakemake/snakemake-wrappers/commit/60b6495e145fc098dab87495eeb1bc82513aedce)) * autobump bio/samtools/fixmate ([#2872](https://www.github.com/snakemake/snakemake-wrappers/issues/2872)) ([6a14082](https://www.github.com/snakemake/snakemake-wrappers/commit/6a14082b7335343f6b920eb148e380f6097ec401)) * autobump bio/samtools/flagstat ([#2880](https://www.github.com/snakemake/snakemake-wrappers/issues/2880)) ([b5b67be](https://www.github.com/snakemake/snakemake-wrappers/commit/b5b67be7ca6cac5433395e6a08d7c40cfd4d5501)) * autobump bio/samtools/idxstats ([#2876](https://www.github.com/snakemake/snakemake-wrappers/issues/2876)) ([1f5f13e](https://www.github.com/snakemake/snakemake-wrappers/commit/1f5f13e2cc31b3a8f548df38c2077ef5971cd19c)) * autobump bio/samtools/index ([#2890](https://www.github.com/snakemake/snakemake-wrappers/issues/2890)) ([f3f5be3](https://www.github.com/snakemake/snakemake-wrappers/commit/f3f5be30759d3a5e3a1fa4a464f423efb5b5a1c0)) * autobump bio/samtools/merge ([#2883](https://www.github.com/snakemake/snakemake-wrappers/issues/2883)) ([162ab43](https://www.github.com/snakemake/snakemake-wrappers/commit/162ab43c5b4eda63ea5d85c071e698156f3f22c4)) * autobump bio/samtools/mpileup ([#2877](https://www.github.com/snakemake/snakemake-wrappers/issues/2877)) ([376b565](https://www.github.com/snakemake/snakemake-wrappers/commit/376b5651e9829480e96c30d228cff2cfb6d71918)) * autobump bio/samtools/sort ([#2886](https://www.github.com/snakemake/snakemake-wrappers/issues/2886)) ([da3cc4c](https://www.github.com/snakemake/snakemake-wrappers/commit/da3cc4c8f259f7e2a59e0118840415f35fde4b20)) * autobump bio/samtools/stats ([#2888](https://www.github.com/snakemake/snakemake-wrappers/issues/2888)) ([5a11e6a](https://www.github.com/snakemake/snakemake-wrappers/commit/5a11e6a752a8fcdf03d4331ac773b399b98c265d)) * autobump bio/samtools/view ([#2878](https://www.github.com/snakemake/snakemake-wrappers/issues/2878)) ([d54caec](https://www.github.com/snakemake/snakemake-wrappers/commit/d54caecdb626b42c0e8c7e8eba7308a80fddf1a9)) * autobump bio/snpeff/annotate ([#2871](https://www.github.com/snakemake/snakemake-wrappers/issues/2871)) ([3732019](https://www.github.com/snakemake/snakemake-wrappers/commit/37320198fe14ccca7db2f90eee7b3f67051e0d52)) * autobump bio/snpeff/download ([#2889](https://www.github.com/snakemake/snakemake-wrappers/issues/2889)) ([6700901](https://www.github.com/snakemake/snakemake-wrappers/commit/6700901b9ce60732fbbf87b843b4145bf73fac36)) * autobump bio/snpsift/annotate ([#2879](https://www.github.com/snakemake/snakemake-wrappers/issues/2879)) ([8b5882d](https://www.github.com/snakemake/snakemake-wrappers/commit/8b5882d8e6ee00f54516de38ee62fbf3b65e22af)) * autobump bio/snpsift/dbnsfp ([#2881](https://www.github.com/snakemake/snakemake-wrappers/issues/2881)) ([af992da](https://www.github.com/snakemake/snakemake-wrappers/commit/af992daef072949309d833ea3edf995aa42a98fb)) * autobump bio/snpsift/genesets ([#2882](https://www.github.com/snakemake/snakemake-wrappers/issues/2882)) ([c58973e](https://www.github.com/snakemake/snakemake-wrappers/commit/c58973e90dc46fb3d92acb249d776c1b053164ed)) * autobump bio/snpsift/gwascat ([#2873](https://www.github.com/snakemake/snakemake-wrappers/issues/2873)) ([bd82454](https://www.github.com/snakemake/snakemake-wrappers/commit/bd82454a3ee003736478461a61f6aca48609909e)) * autobump bio/spades/metaspades ([#2887](https://www.github.com/snakemake/snakemake-wrappers/issues/2887)) ([a678d26](https://www.github.com/snakemake/snakemake-wrappers/commit/a678d26f4e40c1df1c8524bb63085b088b5b9274)) * autobump bio/tabix/index ([#2892](https://www.github.com/snakemake/snakemake-wrappers/issues/2892)) ([91122a4](https://www.github.com/snakemake/snakemake-wrappers/commit/91122a4fba60bd6658d30208207b392d190cf031)) * autobump bio/tabix/query ([#2891](https://www.github.com/snakemake/snakemake-wrappers/issues/2891)) ([67caa45](https://www.github.com/snakemake/snakemake-wrappers/commit/67caa4567fba4e2221a2209792929d05ad4f0a6d)) * autobump bio/umis/bamtag ([#2894](https://www.github.com/snakemake/snakemake-wrappers/issues/2894)) ([50d9fba](https://www.github.com/snakemake/snakemake-wrappers/commit/50d9fba291bba5e26b655b1e9c699ba793cce1b5)) * autobump bio/unicycler ([#2893](https://www.github.com/snakemake/snakemake-wrappers/issues/2893)) ([591095b](https://www.github.com/snakemake/snakemake-wrappers/commit/591095ba04afbfb3051a86d6d144d5a343da5920)) * autobump bio/vep/annotate ([#2896](https://www.github.com/snakemake/snakemake-wrappers/issues/2896)) ([85acb44](https://www.github.com/snakemake/snakemake-wrappers/commit/85acb44c4b787e554fab3aedd864f6db49a333e0)) * autobump bio/vep/cache ([#2897](https://www.github.com/snakemake/snakemake-wrappers/issues/2897)) ([529d832](https://www.github.com/snakemake/snakemake-wrappers/commit/529d832e8613bb5686fea9b3a5c25f83f4eb204d)) * autobump bio/vep/plugins ([#2895](https://www.github.com/snakemake/snakemake-wrappers/issues/2895)) ([e2045c6](https://www.github.com/snakemake/snakemake-wrappers/commit/e2045c6b91eaf5f50b31dcbac37f0e19668e2510)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). 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I just noticed a bug for some input in the wrapper I made a few weeks ago :( It didn't fail, but produced empty files. I have fixed it now and and modify the test to consider more flexible filenames. I don't know how to assert in the test whether the output file is not empty. And I'm not sure that's something we should do in the wrapper, as it is technically a valid output. So far, I have checked manually it now works as expected.
QC
For all wrappers added by this PR,
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,environment.yaml
pinning has been updated by runningsnakedeploy pin-conda-envs environment.yaml
on a linux machine,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,