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fix: add error handling to entrez wrapper #2489

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merged 1 commit into from Dec 15, 2023
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johanneskoester
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QC

  • I confirm that:

For all wrappers added by this PR,

  • there is a test case which covers any introduced changes,
  • input: and output: file paths in the resulting rule can be changed arbitrarily,
  • either the wrapper can only use a single core, or the example rule contains a threads: x statement with x being a reasonable default,
  • rule names in the test case are in snake_case and somehow tell what the rule is about or match the tools purpose or name (e.g., map_reads for a step that maps reads),
  • all environment.yaml specifications follow the respective best practices,
  • the environment.yaml pinning has been updated by running snakedeploy pin-conda-envs environment.yaml on a linux machine,
  • wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:),
  • all fields of the example rules in the Snakefiles and their entries are explained via comments (input:/output:/params: etc.),
  • stderr and/or stdout are logged correctly (log:), depending on the wrapped tool,
  • temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to (see here; this also means that using any Python tempfile default behavior works),
  • the meta.yaml contains a link to the documentation of the respective tool or command,
  • Snakefiles pass the linting (snakemake --lint),
  • Snakefiles are formatted with snakefmt,
  • Python wrapper scripts are formatted with black.
  • Conda environments use a minimal amount of channels, in recommended ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as conda-forge should have highest priority and defaults channels are usually not needed because most packages are in conda-forge nowadays).

@johanneskoester johanneskoester merged commit 7d654d5 into master Dec 15, 2023
6 checks passed
@johanneskoester johanneskoester deleted the fix/entrez branch December 15, 2023 13:56
johanneskoester pushed a commit that referenced this pull request Dec 15, 2023
🤖 I have created a release \*beep\* \*boop\*
---
##
[3.3.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v3.2.0...v3.3.0)
(2023-12-15)


### Features

* add wrapper for fetching files from EGA
([#2488](https://www.github.com/snakemake/snakemake-wrappers/issues/2488))
([3d29dcf](https://www.github.com/snakemake/snakemake-wrappers/commit/3d29dcf31a51e466796e48659402680cfd4d9290))


### Bug Fixes

* add error handling to entrez wrapper
([#2489](https://www.github.com/snakemake/snakemake-wrappers/issues/2489))
([7d654d5](https://www.github.com/snakemake/snakemake-wrappers/commit/7d654d5a3553455400454c4f38c8a64762e54594))


### Performance Improvements

* autobump bio/bcftools/call
([#2431](https://www.github.com/snakemake/snakemake-wrappers/issues/2431))
([3fb48df](https://www.github.com/snakemake/snakemake-wrappers/commit/3fb48df8a946a48194e0287d97906a09586275da))
* autobump bio/bcftools/concat
([#2413](https://www.github.com/snakemake/snakemake-wrappers/issues/2413))
([5bf2d39](https://www.github.com/snakemake/snakemake-wrappers/commit/5bf2d39710d1a10139b7d9e5cd54b5e474b0e56c))
* autobump bio/bcftools/filter
([#2428](https://www.github.com/snakemake/snakemake-wrappers/issues/2428))
([6819cb8](https://www.github.com/snakemake/snakemake-wrappers/commit/6819cb8b71e5d4be04018deb1418664454aee76f))
* autobump bio/bcftools/index
([#2418](https://www.github.com/snakemake/snakemake-wrappers/issues/2418))
([53259a7](https://www.github.com/snakemake/snakemake-wrappers/commit/53259a700164f91540155c424b7d8b4778300da5))
* autobump bio/bcftools/merge
([#2432](https://www.github.com/snakemake/snakemake-wrappers/issues/2432))
([778ea14](https://www.github.com/snakemake/snakemake-wrappers/commit/778ea14f174b4ecc809caacde9012e1cd10d22f4))
* autobump bio/bcftools/mpileup
([#2437](https://www.github.com/snakemake/snakemake-wrappers/issues/2437))
([304d0b8](https://www.github.com/snakemake/snakemake-wrappers/commit/304d0b8605665eb31805c9d1e85c4b1ef77d0939))
* autobump bio/bcftools/norm
([#2442](https://www.github.com/snakemake/snakemake-wrappers/issues/2442))
([17a025a](https://www.github.com/snakemake/snakemake-wrappers/commit/17a025ad934d6abe56fff43c310f9098b7f4bf00))
* autobump bio/bcftools/reheader
([#2427](https://www.github.com/snakemake/snakemake-wrappers/issues/2427))
([d737204](https://www.github.com/snakemake/snakemake-wrappers/commit/d73720445433d3ff12f7c8e8ac2be736979d0736))
* autobump bio/bcftools/sort
([#2421](https://www.github.com/snakemake/snakemake-wrappers/issues/2421))
([a6e4426](https://www.github.com/snakemake/snakemake-wrappers/commit/a6e44263b0cbf189c5f44ff9044c0775587801e3))
* autobump bio/bcftools/stats
([#2441](https://www.github.com/snakemake/snakemake-wrappers/issues/2441))
([8c6f632](https://www.github.com/snakemake/snakemake-wrappers/commit/8c6f63282630326e051da8e15e8b0eca4761eb05))
* autobump bio/bcftools/view
([#2423](https://www.github.com/snakemake/snakemake-wrappers/issues/2423))
([ba73c90](https://www.github.com/snakemake/snakemake-wrappers/commit/ba73c9018a294803101bd92c66bac63b2b42da10))
* autobump bio/bellerophon
([#2439](https://www.github.com/snakemake/snakemake-wrappers/issues/2439))
([439488e](https://www.github.com/snakemake/snakemake-wrappers/commit/439488eac380b2d528240fcaee5457ff362780ba))
* autobump bio/benchmark/chm-eval-sample
([#2440](https://www.github.com/snakemake/snakemake-wrappers/issues/2440))
([fd6981a](https://www.github.com/snakemake/snakemake-wrappers/commit/fd6981ae6f9734f0dd3ac62fd15370f844f81956))
* autobump bio/bgzip
([#2429](https://www.github.com/snakemake/snakemake-wrappers/issues/2429))
([8f3b527](https://www.github.com/snakemake/snakemake-wrappers/commit/8f3b5278fcb985a9b68862fd321cbbf60af1af43))
* autobump bio/bismark/bam2nuc
([#2416](https://www.github.com/snakemake/snakemake-wrappers/issues/2416))
([32f9515](https://www.github.com/snakemake/snakemake-wrappers/commit/32f9515e315b1a4e694e92eb57151ac8387649af))
* autobump bio/bismark/bismark
([#2443](https://www.github.com/snakemake/snakemake-wrappers/issues/2443))
([2c156a9](https://www.github.com/snakemake/snakemake-wrappers/commit/2c156a9011d9694c08be5ab5368dcbf1748a7442))
* autobump bio/bismark/bismark_genome_preparation
([#2434](https://www.github.com/snakemake/snakemake-wrappers/issues/2434))
([4a1b858](https://www.github.com/snakemake/snakemake-wrappers/commit/4a1b85846f4ee85bf0f6efb0c8f7746f0eed39de))
* autobump bio/bismark/bismark_methylation_extractor
([#2415](https://www.github.com/snakemake/snakemake-wrappers/issues/2415))
([ae1848d](https://www.github.com/snakemake/snakemake-wrappers/commit/ae1848db14173cb06d8047688f3b3fdc8b2c0669))
* autobump bio/bismark/bismark2bedGraph
([#2435](https://www.github.com/snakemake/snakemake-wrappers/issues/2435))
([ddbc964](https://www.github.com/snakemake/snakemake-wrappers/commit/ddbc964b016746be56e2682fa3be20ad895560b7))
* autobump bio/bismark/bismark2report
([#2422](https://www.github.com/snakemake/snakemake-wrappers/issues/2422))
([b3b1f78](https://www.github.com/snakemake/snakemake-wrappers/commit/b3b1f78c0da8fc71a5b5748665b615fab2bf1c47))
* autobump bio/bismark/bismark2summary
([#2420](https://www.github.com/snakemake/snakemake-wrappers/issues/2420))
([31a87bf](https://www.github.com/snakemake/snakemake-wrappers/commit/31a87bf24443051bde41283473b5eb3e803ea64f))
* autobump bio/bismark/deduplicate_bismark
([#2426](https://www.github.com/snakemake/snakemake-wrappers/issues/2426))
([490e276](https://www.github.com/snakemake/snakemake-wrappers/commit/490e27668ee4ebf2e1d1c6e10a481d5f853a6c41))
* autobump bio/bowtie2/align
([#2414](https://www.github.com/snakemake/snakemake-wrappers/issues/2414))
([8fe3716](https://www.github.com/snakemake/snakemake-wrappers/commit/8fe37169b72216ed862add0f992d72e5a9d2f53e))
* autobump bio/bwa-mem2/mem
([#2430](https://www.github.com/snakemake/snakemake-wrappers/issues/2430))
([8ae7338](https://www.github.com/snakemake/snakemake-wrappers/commit/8ae7338165b7b7fad677486208c23b7caeefe73f))
* autobump bio/bwa-meme/mem
([#2433](https://www.github.com/snakemake/snakemake-wrappers/issues/2433))
([2389bba](https://www.github.com/snakemake/snakemake-wrappers/commit/2389bba482f497e2b61b6be14ea2ab6d81772918))
* autobump bio/bwa-memx/mem
([#2424](https://www.github.com/snakemake/snakemake-wrappers/issues/2424))
([ad72b7b](https://www.github.com/snakemake/snakemake-wrappers/commit/ad72b7b8048c53498df0951cf1deaf8e34c7f7cd))
* autobump bio/bwa/mem
([#2417](https://www.github.com/snakemake/snakemake-wrappers/issues/2417))
([bb679e9](https://www.github.com/snakemake/snakemake-wrappers/commit/bb679e9a13a275e314fba628bfdd1703a87a4205))
* autobump bio/bwa/sampe
([#2438](https://www.github.com/snakemake/snakemake-wrappers/issues/2438))
([ddefb15](https://www.github.com/snakemake/snakemake-wrappers/commit/ddefb155e42e6a7867abd88b8f0b1d0773c3a943))
* autobump bio/bwa/samse
([#2436](https://www.github.com/snakemake/snakemake-wrappers/issues/2436))
([a845fa4](https://www.github.com/snakemake/snakemake-wrappers/commit/a845fa4b50966965a04b4c27895c740e4916ef45))
* autobump bio/bwa/samxe
([#2425](https://www.github.com/snakemake/snakemake-wrappers/issues/2425))
([973ac6f](https://www.github.com/snakemake/snakemake-wrappers/commit/973ac6f531ac2a8735a3a344f548f5d3140054e1))
* autobump bio/cnvkit/export
([#2444](https://www.github.com/snakemake/snakemake-wrappers/issues/2444))
([36a3d1e](https://www.github.com/snakemake/snakemake-wrappers/commit/36a3d1ef1782963483087a1cbdf7af3d49e360de))
* autobump bio/fgbio/annotatebamwithumis
([#2446](https://www.github.com/snakemake/snakemake-wrappers/issues/2446))
([e896272](https://www.github.com/snakemake/snakemake-wrappers/commit/e89627231ac00d4a4f0a545bfc8dd3418611310f))
* autobump bio/fgbio/collectduplexseqmetrics
([#2448](https://www.github.com/snakemake/snakemake-wrappers/issues/2448))
([2abdd7f](https://www.github.com/snakemake/snakemake-wrappers/commit/2abdd7f64d4e1ba0aa2429fe88e7e5d463a6c340))
* autobump bio/fgbio/filterconsensusreads
([#2447](https://www.github.com/snakemake/snakemake-wrappers/issues/2447))
([96ad8bc](https://www.github.com/snakemake/snakemake-wrappers/commit/96ad8bc0343989e928ca1d19114735854e088c7d))
* autobump bio/fgbio/groupreadsbyumi
([#2445](https://www.github.com/snakemake/snakemake-wrappers/issues/2445))
([d8bc1d7](https://www.github.com/snakemake/snakemake-wrappers/commit/d8bc1d73c6e165c0b5bf58ddae7611db55e39ff9))
* autobump bio/fgbio/setmateinformation
([#2449](https://www.github.com/snakemake/snakemake-wrappers/issues/2449))
([866cedc](https://www.github.com/snakemake/snakemake-wrappers/commit/866cedca8690a14f198fc962db9c38ed89a1a27d))
* autobump bio/gatk/applybqsr
([#2450](https://www.github.com/snakemake/snakemake-wrappers/issues/2450))
([63c744a](https://www.github.com/snakemake/snakemake-wrappers/commit/63c744a9791ed0b476637a89bff613b80216b2d5))
* autobump bio/hisat2/align
([#2452](https://www.github.com/snakemake/snakemake-wrappers/issues/2452))
([3549c8e](https://www.github.com/snakemake/snakemake-wrappers/commit/3549c8e89904d762e3abcf9d2a09efb423cfba06))
* autobump bio/hisat2/index
([#2453](https://www.github.com/snakemake/snakemake-wrappers/issues/2453))
([017190a](https://www.github.com/snakemake/snakemake-wrappers/commit/017190ad66419df64941a8928adc2cc8b2cd64d5))
* autobump bio/homer/makeTagDirectory
([#2451](https://www.github.com/snakemake/snakemake-wrappers/issues/2451))
([22d8f8d](https://www.github.com/snakemake/snakemake-wrappers/commit/22d8f8dc5f5a803e60894e397dd6baa783266048))
* autobump bio/lofreq/call
([#2454](https://www.github.com/snakemake/snakemake-wrappers/issues/2454))
([08bac48](https://www.github.com/snakemake/snakemake-wrappers/commit/08bac487ac8fdac031f1e36c2d33433aeaba1c30))
* autobump bio/lofreq/indelqual
([#2455](https://www.github.com/snakemake/snakemake-wrappers/issues/2455))
([2637859](https://www.github.com/snakemake/snakemake-wrappers/commit/26378599f8b02a8c0d37cfe2557abda2dd12e4e0))
* autobump bio/mosdepth
([#2456](https://www.github.com/snakemake/snakemake-wrappers/issues/2456))
([3caefb0](https://www.github.com/snakemake/snakemake-wrappers/commit/3caefb0fa0cb3953687c06458b900dccea1fe2da))
* autobump bio/paladin/align
([#2457](https://www.github.com/snakemake/snakemake-wrappers/issues/2457))
([32fb56f](https://www.github.com/snakemake/snakemake-wrappers/commit/32fb56f4284d079a88c8f087be8f35349ccc9b3d))
* autobump bio/paladin/index
([#2461](https://www.github.com/snakemake/snakemake-wrappers/issues/2461))
([e3bc12a](https://www.github.com/snakemake/snakemake-wrappers/commit/e3bc12a3d9a6e245efe8fa1af24198f06ded1696))
* autobump bio/paladin/prepare
([#2459](https://www.github.com/snakemake/snakemake-wrappers/issues/2459))
([bb0f509](https://www.github.com/snakemake/snakemake-wrappers/commit/bb0f509113021d131c211165135f04713c334371))
* autobump bio/picard/markduplicates
([#2460](https://www.github.com/snakemake/snakemake-wrappers/issues/2460))
([778f1fd](https://www.github.com/snakemake/snakemake-wrappers/commit/778f1fdf5e3479ac97fddb031b431047fd984729))
* autobump bio/pretext/map
([#2458](https://www.github.com/snakemake/snakemake-wrappers/issues/2458))
([8535686](https://www.github.com/snakemake/snakemake-wrappers/commit/8535686db2eb1920a747dcaddcff4824aa34807f))
* autobump bio/reference/ensembl-variation
([#2462](https://www.github.com/snakemake/snakemake-wrappers/issues/2462))
([26c321a](https://www.github.com/snakemake/snakemake-wrappers/commit/26c321a7e62e37eba26f3f75cb0833a8f7415cdf))
* autobump bio/samtools/calmd
([#2463](https://www.github.com/snakemake/snakemake-wrappers/issues/2463))
([d1c7b4a](https://www.github.com/snakemake/snakemake-wrappers/commit/d1c7b4a8a48757443110d43e3982ddb0ec39eb0a))
* autobump bio/samtools/depth
([#2477](https://www.github.com/snakemake/snakemake-wrappers/issues/2477))
([da2a62b](https://www.github.com/snakemake/snakemake-wrappers/commit/da2a62b805b096ec61c54aeef84ed0b67d1953ed))
* autobump bio/samtools/faidx
([#2470](https://www.github.com/snakemake/snakemake-wrappers/issues/2470))
([7298ed1](https://www.github.com/snakemake/snakemake-wrappers/commit/7298ed1f515f915f17104354ed2f121c42b3150d))
* autobump bio/samtools/fastx
([#2474](https://www.github.com/snakemake/snakemake-wrappers/issues/2474))
([ddbfa88](https://www.github.com/snakemake/snakemake-wrappers/commit/ddbfa884296d5f97ef7ab5cec7bf05bb00863ed6))
* autobump bio/samtools/fixmate
([#2481](https://www.github.com/snakemake/snakemake-wrappers/issues/2481))
([71ecb0d](https://www.github.com/snakemake/snakemake-wrappers/commit/71ecb0dff6d027bee70232df03f71c4ebfc92fd3))
* autobump bio/samtools/flagstat
([#2471](https://www.github.com/snakemake/snakemake-wrappers/issues/2471))
([93c93e3](https://www.github.com/snakemake/snakemake-wrappers/commit/93c93e31fdbb67dafa009f67577f0224878f3020))
* autobump bio/samtools/idxstats
([#2480](https://www.github.com/snakemake/snakemake-wrappers/issues/2480))
([304c854](https://www.github.com/snakemake/snakemake-wrappers/commit/304c854a0a96caf417d50395a3635fc1e4db0cb3))
* autobump bio/samtools/index
([#2473](https://www.github.com/snakemake/snakemake-wrappers/issues/2473))
([eed7721](https://www.github.com/snakemake/snakemake-wrappers/commit/eed772107289a59438d06bd51fdbae43bb08c6db))
* autobump bio/samtools/merge
([#2479](https://www.github.com/snakemake/snakemake-wrappers/issues/2479))
([d6995ca](https://www.github.com/snakemake/snakemake-wrappers/commit/d6995ca4ba9987d96f5cc601b0a7dea09cc2f86a))
* autobump bio/samtools/mpileup
([#2475](https://www.github.com/snakemake/snakemake-wrappers/issues/2475))
([c3707b0](https://www.github.com/snakemake/snakemake-wrappers/commit/c3707b04154b72196fc52c3872141c84dff9c9a9))
* autobump bio/samtools/sort
([#2468](https://www.github.com/snakemake/snakemake-wrappers/issues/2468))
([f04208c](https://www.github.com/snakemake/snakemake-wrappers/commit/f04208c7ca7957755a17e6cc101821d69df80946))
* autobump bio/samtools/stats
([#2466](https://www.github.com/snakemake/snakemake-wrappers/issues/2466))
([82c5af8](https://www.github.com/snakemake/snakemake-wrappers/commit/82c5af8b774d69ee625d5decb5974f617f4c5a03))
* autobump bio/samtools/view
([#2469](https://www.github.com/snakemake/snakemake-wrappers/issues/2469))
([5ecc368](https://www.github.com/snakemake/snakemake-wrappers/commit/5ecc368c8f2fe29ecc8efbf8fff20eae0ec67d5f))
* autobump bio/snpeff/annotate
([#2472](https://www.github.com/snakemake/snakemake-wrappers/issues/2472))
([41cbb4d](https://www.github.com/snakemake/snakemake-wrappers/commit/41cbb4d5ca2d765bfdcc70ba9cf2fa22259ed308))
* autobump bio/snpeff/download
([#2478](https://www.github.com/snakemake/snakemake-wrappers/issues/2478))
([e8d0586](https://www.github.com/snakemake/snakemake-wrappers/commit/e8d0586f043152e85101fed0a0e2fcbf238aec74))
* autobump bio/snpsift/annotate
([#2464](https://www.github.com/snakemake/snakemake-wrappers/issues/2464))
([7123087](https://www.github.com/snakemake/snakemake-wrappers/commit/712308755a24985f808679ba4ff116ba6d51ff5e))
* autobump bio/snpsift/dbnsfp
([#2467](https://www.github.com/snakemake/snakemake-wrappers/issues/2467))
([4071e38](https://www.github.com/snakemake/snakemake-wrappers/commit/4071e38375713220e456d22be8d55fb0a07e01a2))
* autobump bio/snpsift/genesets
([#2476](https://www.github.com/snakemake/snakemake-wrappers/issues/2476))
([8db87de](https://www.github.com/snakemake/snakemake-wrappers/commit/8db87defb87e7729e672bfda0b579cdab351b544))
* autobump bio/snpsift/gwascat
([#2465](https://www.github.com/snakemake/snakemake-wrappers/issues/2465))
([74a030f](https://www.github.com/snakemake/snakemake-wrappers/commit/74a030fe1ca68f81136203722ee875a95802fb17))
* autobump bio/tabix/query
([#2483](https://www.github.com/snakemake/snakemake-wrappers/issues/2483))
([1e15361](https://www.github.com/snakemake/snakemake-wrappers/commit/1e15361f6d9173d40a3de81379dc7c7ad386679c))
* autobump bio/tximport
([#2482](https://www.github.com/snakemake/snakemake-wrappers/issues/2482))
([e97353f](https://www.github.com/snakemake/snakemake-wrappers/commit/e97353fac526b730b054a4b756fb59a6d0a6512a))
* autobump bio/umis/bamtag
([#2484](https://www.github.com/snakemake/snakemake-wrappers/issues/2484))
([d0501aa](https://www.github.com/snakemake/snakemake-wrappers/commit/d0501aa052218dbca8b28124bff34c20f7db6d39))
* autobump bio/vembrane/filter
([#2486](https://www.github.com/snakemake/snakemake-wrappers/issues/2486))
([b0b3cc9](https://www.github.com/snakemake/snakemake-wrappers/commit/b0b3cc9565e9723375a187c2536cabf4a30a87a2))
* autobump bio/vembrane/table
([#2485](https://www.github.com/snakemake/snakemake-wrappers/issues/2485))
([a34fd66](https://www.github.com/snakemake/snakemake-wrappers/commit/a34fd66f3dcb6ae701ba756bcb8381ec83d7ecfa))
* autobump bio/vep/annotate
([#2487](https://www.github.com/snakemake/snakemake-wrappers/issues/2487))
([530fe3f](https://www.github.com/snakemake/snakemake-wrappers/commit/530fe3f635634410ee57c2d2ffbe1e5737645a17))
---


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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