Get renovate to work with conda envs #22
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edmundmiller
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* ci(renovate): Change schedule to monthly and pinDigests https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#default-renovate-config * ci(renovate): Add security PRs immediately https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#custom-renovate-config * ci(renovate): Just use best-practices https://docs.renovatebot.com/presets-config/#configbest-practices * ci(renovate): Set PR hourly limit to 3 * ci(renovate): Add conda support Ulthran/ShotgunUnifrac#22 * ci(renovate): Add pre-commit * ci(renovate): Request modules instead of maintainers * ci(renovate): Don't scan the meta.ymls
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* ci(renovate): Change schedule to monthly and pinDigests https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#default-renovate-config * ci(renovate): Add security PRs immediately https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#custom-renovate-config * ci(renovate): Just use best-practices https://docs.renovatebot.com/presets-config/#configbest-practices * ci(renovate): Set PR hourly limit to 3 * ci(renovate): Add conda support Ulthran/ShotgunUnifrac#22 * ci(renovate): Add pre-commit * ci(renovate): Request modules instead of maintainers * ci(renovate): Don't scan the meta.ymls
mirpedrol
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* ci(renovate): Change schedule to monthly and pinDigests https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#default-renovate-config * ci(renovate): Add security PRs immediately https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#custom-renovate-config * ci(renovate): Just use best-practices https://docs.renovatebot.com/presets-config/#configbest-practices * ci(renovate): Set PR hourly limit to 3 * ci(renovate): Add conda support Ulthran/ShotgunUnifrac#22 * ci(renovate): Add pre-commit * ci(renovate): Request modules instead of maintainers * ci(renovate): Don't scan the meta.ymls
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* Add template module with nf-core with some modifications * checkqc: Removed TODOs, added tests (need improvement), copy files when staging * Use nf-tests for checkQC * Change logic of mitohifi/mitohifi api (#4193) * Code refactoring for mitohifi input * Fix md5sum * Fix md5sum for versions * Bring back md5sum value * Update md5sum again * Remove md5sum * Bring back versions.yml * It looks like $HOME needs be writable in the container. Trying mounting it * Add test for reads * Update modules/nf-core/mitohifi/mitohifi/main.nf Refactor the mitohifi command line Co-authored-by: Solenne Correard <54953390+scorreard@users.noreply.github.com> * Fix md5sums --------- Co-authored-by: Ksenia Krasheninnikova <kk16@sanger.ac.uk> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Solenne Correard <54953390+scorreard@users.noreply.github.com> * Sentieon/tnfilter (#4208) * Adding module sentieon/tnfilter * WIP: CI-tests for sentieon/tnfilter. (test-data just local for now.) * Skipping conda-based test of sentieon/tnfilter * Remove avail_mem stuff. * Fix description of output vcf * Using test-data from nf-core test-datasets repo * add tests for sentieon/tnfilter * pycoqc: add nf-test (#4238) * nf-test for pycoqc. snapshots for versions and json['All reads'] * tags.yml * test naming conventions. Fix indentation. Add test for html output --------- Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update seqkit/fx2tab to version 2.5.1 (#4240) * FEAT: update bclconvert to 4.2.4 (#4253) * update bclconvert to 4.2.4 * regenerate snapshot * Add conda to renovate (#4216) * ci(renovate): Change schedule to monthly and pinDigests https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#default-renovate-config * ci(renovate): Add security PRs immediately https://emmer.dev/blog/keep-docker-base-images-updated-with-renovate/#custom-renovate-config * ci(renovate): Just use best-practices https://docs.renovatebot.com/presets-config/#configbest-practices * ci(renovate): Set PR hourly limit to 3 * ci(renovate): Add conda support Ulthran/ShotgunUnifrac#22 * ci(renovate): Add pre-commit * ci(renovate): Request modules instead of maintainers * ci(renovate): Don't scan the meta.ymls * chore(deps): update pre-commit hook python-jsonschema/check-jsonschema to v0.27.0 (#4256) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * chore(deps): update pre-commit hook pre-commit/mirrors-prettier to v3 (#4257) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix conda declaration (#4252) * new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * fix all modules conda declaration * chore(config): migrate renovate config (#4255) chore(config): migrate config .github/renovate.json5 Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * chore(deps): update docker.io/continuumio/miniconda3 docker tag to v22 (#4220) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix linting test not being run for modules with only nf-test tests (#4231) * new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * try to fix linting with nf-test * small change to trigger tests * fix if statement * also test pytest * remove nf-test exclude from linting * try for a conda fix * revert last commit * Update .github/workflows/test.yml Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * temporarily reactivate pytest for vardictjava * run fastp test * revert test triggers --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Nf-test rtgtools/rocplot (#4200) * new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * nf-test rtgtools rocplot * remove pytest tag * update according to comments * Update modules/nf-core/rtgtools/rocplot/tests/main.nf.test Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se> * Update modules/nf-core/rtgtools/rocplot/tests/main.nf.test * update conda declaration --------- Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se> * samtools/merge - emit crai file when cram file created (#4258) Emit crai file for CRAM file * chore(deps): update biocontainers/chromap docker tag to v0.2.5 (#4214) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Use "error" rather than "exit 1", and removed `quay.io/` (#4248) * We should use "error" rather than "exit 1" * Fixed the syntax * Removed the quay.io prefix since it is the default registry * chore(deps): update biocontainers/goat docker tag to v0.2.5 (#4259) * chore(deps): update biocontainers/goat docker tag to v0.2.5 * Version bump (across all 3 package systems) * Fixed the type of the "taxon" parameter * Updated the test md5 * Added me as a maintainer since GoaT is (partly) in my team --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * change database sufix to nin which is more common in v5 and v4 database (#4245) change ndb to nin Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> * add nf-tests and snapshots for kallisto index & quant (#4250) * add nf-tests and snapshots for kallisto index & quant * rm kallisto tags from pytest_modules.yml * Update modules/nf-core/kallisto/index/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update modules/nf-core/kallisto/quant/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update modules/nf-core/kallisto/quant/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * update kallisto quant * Update modules/nf-core/kallisto/index/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update modules/nf-core/kallisto/quant/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update modules/nf-core/kallisto/quant/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update modules/nf-core/kallisto/quant/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * remove superfluous quote marks * fix linting --------- Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> * Update genomescope (#4267) * Add Kmer coverage to module output * Update test.yml * Update modules/nf-core/genescopefk/meta.yml Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr> * Add bash directive * Fix whitespace --------- Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr> * nf-test interproscan (#4269) * Update busco (#4270) * Move mandatory busco arg to input: * bump busco version * Update test.yml * chore(deps): update biocontainers/bowtie2 docker tag to v2.4.5 (#4212) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * chore(deps): update biocontainers/checkm-genome docker tag to v1.2.2 (#4213) * chore(deps): update biocontainers/checkm-genome docker tag to v1.2.2 * Fix meta.yml and update singularity container --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Mitohifi channel input (#4254) * Main changes * Add check for correct input parameters * Code clean-up * Conda is not supported * Dropping the hyphen, as per @mahesh-panchal suggestion --------- Co-authored-by: Ksenia Krasheninnikova <kk16@sanger.ac.uk> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * chore(deps): Bump checkm-genome conda env (#4279) Follow up to #4213 Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * chore(deps): update biocontainers/htseq docker tag to v2.0.3 (#4266) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix up kallisto (#4271) * Try to fix up kallisto quant for real usage * More kallisto fixes * appease eclint * Fix tests * Add single-end config specifically * try to fix kallisto nf-test * Fix snapshot testing * Tidy up config * Just check the tsv * syntax fix * Revert "syntax fix" This reverts commit 1becc26. * Revert "Just check the tsv" This reverts commit 7a9d272. * Poor nf-test attempt * [skip ci] Apply suggestions from code review Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Last fix-up to tests, re-add paired * Bump indexing to match quant in kallisto * Bump kallisto index snapshot --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * FIX: More coherence in all gatk4spark modules (#4282) * fix gatk4 version * rename and update all gatk4_<module>spark to gatk4spark_<module> * update pytest_modules.yml * fix meta.yml * fix typo * remove now useless exclude statements * fix output path * update multiqc to 1.17 in custom/dumpsoftwareversions (#4295) * update multiqc to 1.17 * update snapshot * update snapshot * Rename utility subworkflows (#4268) * Rename utility subworkflows Changes: - nextflow_pipeline_utils -> utils_nextflow_pipeline - nfcore_pipeline_utils -> utils_nf_core_pipeline - nfvalidation_plugin_utils -> utils_nf_validatation_plugin Names by @drpatelh Not 100% on the names, I think it would be better if it said what they _did_ rather than what they _are_. However, this is usable right now. Better answers here please. * Correct utility subworkflow tags * Fixup comments * config fix * fix linting by faking pytest tests * rename files * update pytest_modules.yml * fix fake pytest tests --------- Co-authored-by: maxulysse <max.u.garcia@gmail.com> * Ucsc/bedgraphtobigwig nftest (#4136) * add nf-test and snapshot for umitools/extract * remove pytest tag and add nf-test tag * add nftest and snapshot for ucsc/bedgraphtobigwig * Update modules/nf-core/ucsc/bedgraphtobigwig/tests/tags.yml Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update modules/nf-core/umitools/extract/tests/main.nf.test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * [automated] Fix linting with Prettier * Feat/fastp nf-test (#4028) * init nf-test fastp * add initial test fastp * init html test fastp * all tests fastp * unequal files reads.fastq.gz * finishing tests (finally) * removing fastp from pytest * fixing tag fastp * adding the s * adding relative path --------- Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * Rasusa nf test (#4081) * Initial main.nf.test * Full nf-test suite for module rasusa * add "modules" tag to nf-test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Remove tags from tests/config/pytest_modules.yml --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Glimpse ligate nftest (#4048) * Restart as new * Delete pytest from config * Update main.nf.test * Glimpse chunk nftest (#4034) * Add nf-test for glimpse_chunk * Delete pytest for glimpse 1 not glimpse 2 * Update main.nf.test * Added fq nf-tests (#4084) * Added fq nf-tests * Removed from pytest suite * Test fix --------- Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> * Feat/gunzip nf tests (#4103) * add nf-test and snapshot for gunzip * add modules/nf-core/gunzip/tests/tags.yml * remove gunzip from tests/config/pytest_modules.yml for switch to nf-test --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * added nf-test files for art/illumina (#4038) * added nf-test files - two tests (single- and paired-end) - including two nextflow.configs for `ext.args` * change tests topass on conda/mamba and singularity/docker - due to gzip the fastq files will have different md5sums with different engines * added art/illumina - should trigger the nf-test CI * extended tag to art/illumina * fixed typos -.- * fixed typo again - missing quote * renamed test.yml to tags.yml * removed art/illumina * added <tool> tag * added nf-tests for -stub-run --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * nf-test for module sourmash/sketch (#4104) * nf-test for module sourmash/sketch * add "sourmash" and "sourmash/sketch" tags Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Renovate migrate (#4114) * chore: Migrate renovate config https://github.com/renovatebot/renovate/blob/main/docs/usage/config-validation.md renovate-config-validator * style: Add renovate to prettier ignore list * Feat/picard_markduplicates nf-test (#4096) * picard nf-test init * created first (failing)test * tests succeeding --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Rename test.yml in getchromsizes (#4118) * Rename test.yml and trigger pytest * Update main.nf * Feat/trimgalore nf-test (#4110) * trimgalore nf-test init * relative paths * Update modules/nf-core/trimgalore/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * nf-test migration (#4113) * nf-test for module fastqscan (#4097) Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Mlst nf test and version bump to 2.23 (#4061) * add nf-test to module mlst * fix ownership for nf-test * add "modules" tag to nf-test Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Add module keywords to meta.yml * Lint meta.yml * Update to mlst version 2.23 * Update snap with new versions.yml after bump to v2.23 * Remove mlst from pytest_modules --------- Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * remove umitools/extract files * Apply suggestions from code review * remove umitools tests * Apply suggestions from code review * Update tests/config/pytest_modules.yml --------- Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: Koen Bossers <61537771+koenbossers@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: KamilMaliszArdigen <32459801+KamilMaliszArdigen@users.noreply.github.com> Co-authored-by: Kevin Ryan <65914327+kevinpryan@users.noreply.github.com> Co-authored-by: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> * Update missed renovate environments (#4296) * chore(deps): Bump htseq conda env * chore(deps): Update bowtie2 conda env * ci(renovate): Assign CodeOwners to PRs * ci(renovate): Move gitAuthor to main config * ci(renovate): Try to add a header to stop the merge * build: Add renovate comments to conda packages (#4298) * Fix conda and renovate (#4299) * ci(renovate): Remove docker hub * ci(renovate): Update environment.yml regex * ci(renovate): Copy regex from anaconda https://github.com/anaconda/renovate-config/blob/176696853379d878a87575ba03b1b12fd29d24ac/default.json#L64-L71 * ci(renovate): Toss in pypi while we're here * chore: Try adding :'s * ci(renovate): Finally figured it out https://github.com/anaconda/renovate-config/blob/176696853379d878a87575ba03b1b12fd29d24ac/docs/conda-environment.md?plain=1#L24 https://github.com/search?q=renovate%3A+datasource%3Dconda&type=code * Add renovate config check (#4297) * ci(renovate): Add pre-commit hook * ci: Add a pre-commit workflow * ci: Validate GitHub Workflows with pre-commit * ci: Run pre-commit on only changed files * add arriba download (#4280) * initial commit * add full module details and run tests * fix linting * fix linting and version number * Update modules/nf-core/arriba/download/meta.yml Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> --------- Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> * add agat/convertspgff2tsv module (#4265) * add agat/convertspgff2tsv module * correct output path * update getting the version * reverse other agat modules as not updated software * correct md5sum * Bug: nf-test bam_sort_stats_samtools (#4190) * adding bam bai * Fix typo * md5sum not text * use correct tag name in tags.yml * add missing tag * add subworkflow tag * copy pasta typo --------- Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * new module gridss GeneratePonBedpe (#4196) * new module gridss GeneratePonBedpe * Update main.nf quay.io removed * Update modules/nf-core/gridss/gridssgenerateponbedpe/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/gridss/gridssgenerateponbedpe/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update main.nf fix input and output names change meta names * Update meta.yml add meta 3 and meta 4 information * Update main.nf --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 3167 new module gridss gridss somatic filter (#4247) * initial commit * new module: gridss_somatic_filter * Update main.nf quay.io removed * Update modules/nf-core/gridss/gridsssomaticfilter/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/gridss/gridsssomaticfilter/meta.yml Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Added a meta map for the reference genome of minimap2 (#4285) * Added a meta map for the reference genome of minimap2 * Added a meta map for the reference genome of minimap2 * Skip the Conda test since it produces a slightly different BAM file * Add ngscheckmate bed file to test_data config (#4308) * Diamond tools: nf-test, container update, stubs added, makedb meta added, gz input support, megan makedb test updated (#4194) * diamond/makedb container, stub, meta, gz updated * diamond/blastp container, stub, prefix, gz updated * diamond/blastx container, stub, gz, megan module test upgraded * nf-test diamond/makedb * nf-test diamond/blastp * nf-test diamond/blastx * diamond blastp and blastx daa md5sums removed * db input fix for blastp and blastx * megan test makedb updated * updated conda version in environment.yml * correct conda paths per tool * nf-tests with new conda envs and zipped tests for diamond tools * diamond tools revision points * db to tuple with meta * blastp daa snapshot added * revert snapshot * revisions + debugging snapshots - conda failing * daa check for existence instead of snapshot due to conda error * blastp added choice for xml or tsv outputs other than the existing csv (#4197) * blastp added choice for xml or tsv outputs other than the existing csv * rerun skipped jobs * nf-tests with new conda env + zipped file tests added for blast modules * meta updated * testing snapshots * updated snapshots to work properly where possible * Apply suggestions from code review Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Remove trailing white space * Apply suggestions from code review Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * Handle Failed QC and add test for it * Update modules/nf-core/checkqc/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/nf-core/checkqc/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update to CheckQC v4.0.1 * Address lint errors and warnings * update main.nf.test to new guidelines * using an env.yaml for conda * add community wave container * update snapshot * remove conda config * add metamap * update test and snapshot * add yml for tracking versions * skip checkqc conda profile * fix linting * Update test.yml disable in nf-test not in pytest * Update .github/workflows/test.yml * add fixme note as requested in slack --------- Co-authored-by: Ksenia <krasheninnikova@gmail.com> Co-authored-by: Ksenia Krasheninnikova <kk16@sanger.ac.uk> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Solenne Correard <54953390+scorreard@users.noreply.github.com> Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Koen Bossers <61537771+koenbossers@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se> Co-authored-by: Guoying Qi <729395+gq1@users.noreply.github.com> Co-authored-by: YSims <yy5@sanger.ac.uk> Co-authored-by: Damon-Lee Pointon <51855558+DLBPointon@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: mashehu <mashehu3@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com> Co-authored-by: Laramie Lindsey <144381129+laramiellindsey@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: KamilMaliszArdigen <32459801+KamilMaliszArdigen@users.noreply.github.com> Co-authored-by: Kevin Ryan <65914327+kevinpryan@users.noreply.github.com> Co-authored-by: MarieLataretu <52002068+MarieLataretu@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io> Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> Co-authored-by: Annick Renevey <47788523+rannick@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> Co-authored-by: Kübra Narcı <kbrnrc@gmail.com> Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be> Co-authored-by: Felipe Marques de Almeida <almeidafmarques@gmail.com> Co-authored-by: atrigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: Felipe Marques de Almeida <felipemarques89@gmail.com>
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What?
Have renovate find conda env files and update the annotated deps
Why?
How?
Conda has been added as a Datasource but not a Manager for RenovateBot, so need to follow this issue:
renovatebot/renovate#2213
Testing?
Screenshots (optional)
Anything Else?