Deploy dev branch to crazy-corgi #560

LilyAnderssonLee · 2024-12-19T10:27:41Z

PR checklist

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Important! Template update for nf-core/tools v3.0.2

Add darkmode version of metromap

The KrakenUniq module has a breaking change requiring a further input.

In the rare case that there are two samples with the same identifier and run accession, one being single-end and the other paired-end, this change makes the prefix and thus the KrakenUniq output filenames unique.

Add darkmode diagram

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Important! Template update for nf-core/tools v3.1.0

github-actions · 2024-12-19T10:30:15Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 6a9da1a

+| ✅ 277 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
nextflow_config - Config manifest.version should end in dev: 1.2.2
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-taxprofiler_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-taxprofiler_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowTaxprofiler.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.preprocessing_qc_tool= fastqc
nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
nextflow_config - Config default value correct: params.longread_adapterremoval_tool= porechop_abi
nextflow_config - Config default value correct: params.longread_filter_tool= nanoq
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minquality= 7
nextflow_config - Config default value correct: params.shortread_redundancyestimation_mode= kmer
nextflow_config - Config default value correct: params.diamond_output_format= tsv
nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
nextflow_config - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
nextflow_config - Config default value correct: params.malt_mode= BlastN
nextflow_config - Config default value correct: params.ganon_report_type= reads
nextflow_config - Config default value correct: params.ganon_report_rank= default
nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
nextflow_config - Config default value correct: params.ganon_report_mincount= 0
nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - BRACKEN_BRACKEN found in conf/base.config and Nextflow scripts.
base_config - CENTRIFUGE_KREPORT found in conf/base.config and Nextflow scripts.
base_config - KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE found in conf/base.config and Nextflow scripts.
base_config - MEGAN_RMA2INFO_TSV found in conf/base.config and Nextflow scripts.
base_config - MEGAN_RMA2INFO_KRONA found in conf/base.config and Nextflow scripts.
base_config - FALCO found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FALCO found in conf/modules.config and Nextflow scripts.
modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_NONPAREIL found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_CURVE found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_SET found in conf/modules.config and Nextflow scripts.
modules_config - NONPAREIL_NONPAREILCURVESR found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - PORECHOP_PORECHOP found in conf/modules.config and Nextflow scripts.
modules_config - PORECHOP_ABI found in conf/modules.config and Nextflow scripts.
modules_config - FILTLONG found in conf/modules.config and Nextflow scripts.
modules_config - NANOQ found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_RUNS found in conf/modules.config and Nextflow scripts.
modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO_TSV found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_STANDARD_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - BRACKEN_BRACKEN found in conf/modules.config and Nextflow scripts.
modules_config - BRACKEN_COMBINEBRACKENOUTPUTS found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_COMBINEKREPORTS_KRAKEN found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_KREPORT2KRONA found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_CLEANUP found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_KTIMPORTTEXT found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO_KRONA found in conf/modules.config and Nextflow scripts.
modules_config - KRONA_KTIMPORTTAXONOMY found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_MERGEMETAPHLANTABLES found in conf/modules.config and Nextflow scripts.
modules_config - CENTRIFUGE_CENTRIFUGE found in conf/modules.config and Nextflow scripts.
modules_config - CENTRIFUGE_KREPORT found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU2TABLE_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU2TABLE_COMBINED found in conf/modules.config and Nextflow scripts.
modules_config - KAIJU_KAIJU2KRONA found in conf/modules.config and Nextflow scripts.
modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
modules_config - MOTUS_PROFILE found in conf/modules.config and Nextflow scripts.
modules_config - MOTUS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - KMCP_SEARCH found in conf/modules.config and Nextflow scripts.
modules_config - KMCP_PROFILE found in conf/modules.config and Nextflow scripts.
modules_config - GANON_CLASSIFY found in conf/modules.config and Nextflow scripts.
modules_config - GANON_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - GANON_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.1.0

Run details

nf-core/tools version 3.1.0
Run at 2024-12-20 11:17:48

jfy133 · 2024-12-19T11:39:03Z

I didn't look ;) Assume it's OK

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Fix centrifuge on conda via version bump

Bump the version before the patch release v.1.2.2

nf-core-bot and others added 30 commits October 8, 2024 12:32

Template update for nf-core/tools version 3.0.0

79d1535

Template update for nf-core/tools version 3.0.1

56e023f

Template update for nf-core/tools version 3.0.2

69969cf

resolve the conflicts

226abd9

remove max_cpu from test.config

ff4d28f

update schema wit new release

f3ef6aa

add exists:true to the sechma to check the file path

5e90741

change db_path format back to the original value path in schema_database

a9af810

update the type of run_accession into string and integer

9e20ff1

Update CITATIONS.md

88c9f46

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update conf/modules.config

2900ae2

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

address comments from James

b0c1154

Update nextflow.config

340b0af

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Add Lili as co-author

05b743f

Fix CI to run each test separately

fb38fb7

Update main.nf

353188d

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update .nf-core.yml

f7c6176

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

[automated] Fix code linting

dbabb5d

Fix mOTUs if/else statemetn

fe84cc3

update configs and database schema

00067f5

Merge pull request #545 from nf-core/nf-core-template-merge-3.0.2

e34437b

Important! Template update for nf-core/tools v3.0.2

Add darkmode version of metromap

8262e0a

Merge pull request #548 from nf-core/darkmode-diagram

93aa499

Add darkmode version of metromap

Fix darkmode diagram

6c6cd8c

refactor: prepare the additional prefixes input

2e6f37d

The KrakenUniq module has a breaking change requiring a further input.

chore: update krakenuniq/preloadedkrakenuniq

a1a8289

fix: create always unique prefix

c0311a1

fix: make prefix unique across PE and SE

30fc22a

In the rare case that there are two samples with the same identifier and run accession, one being single-end and the other paired-end, this change makes the prefix and thus the KrakenUniq output filenames unique.

Update CHANGELOG.md

163d600

Merge pull request #549 from nf-core/darkmode-diagram

b2cac44

Add darkmode diagram

LilyAnderssonLee and others added 17 commits December 17, 2024 08:44

remove genomes definition from schema

cd526a1

update nextflow_schema.json

35bf598

Update nextflow.config: remove emails

14cc312

update nextflow.config

b280ccb

Update nextflow.config

4d14b16

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

7b59380

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

1e377c0

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update docs/usage.md

50ca9c6

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

1a9062a

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

1b8dce3

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

2b50c34

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

be0e916

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

d5fcd74

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

a5fc4e4

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

4f81446

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Update nextflow.config

6caf426

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Merge pull request #558 from nf-core/nf-core-template-merge-3.1.0

e41ed10

Important! Template update for nf-core/tools v3.1.0

LilyAnderssonLee requested a review from jfy133 December 19, 2024 11:00

jfy133 approved these changes Dec 19, 2024

View reviewed changes

jfy133 and others added 9 commits December 19, 2024 13:09

Update centrifuge to fix CONDA bug

4946d78

Merge branch 'dev' into fix-centrifuge-conda

bb61c8f

Update CHANGELOG.md

ec47fd0

Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>

Merge pull request #561 from nf-core/fix-centrifuge-conda

2564db7

Fix centrifuge on conda via version bump

Bump the version before the patch release v.1.2.2

9b0e463

correct the format

a81eed0

reformat the multiqc_config.yml

728aafc

update CHANGELOG.md

8b4ec22

Merge pull request #562 from nf-core/pre-release_vbump

6a9da1a

Bump the version before the patch release v.1.2.2

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Deploy dev branch to crazy-corgi #560

Deploy dev branch to crazy-corgi #560

LilyAnderssonLee commented Dec 19, 2024

github-actions bot commented Dec 19, 2024 •

edited

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❗ Test warnings:

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jfy133 commented Dec 19, 2024

Deploy dev branch to crazy-corgi #560

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Deploy dev branch to crazy-corgi #560

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LilyAnderssonLee commented Dec 19, 2024

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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jfy133 commented Dec 19, 2024

github-actions bot commented Dec 19, 2024 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️