v1.2.3 - Bouncy Basenji Patch PR #583

sofstam · 2025-03-11T10:09:40Z

PR checklist

…ofiler into bump_version_1.3.0

Post release bump version

Fix is a template change, see nf-core/tools#3416 If your pipeline is affected by this error I think it should be fine to manually apply this patch.

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

Important! Template update for nf-core/tools v3.1.2

Important! Template update for nf-core/tools v3.2.0

Better docs for taxpasta related flags

Sort the input channel to ensure batches of input will remain constant across runs.

@Midnighter

As suggested by @Midnighter, using toSortedList in place of collect improves clarity. Also: [ suggested by @Midnighter ] Remove closure argument to flatMap. The operator with closure argument performed the default behavior of the operator without closure.

Changelog for for #573

A samplesheet with both integer and non-numeric ( string ) values of sample caused type-mismatch error when compared. Generate prefix string from meta and compare on prefix.

Remove links to multiqc plots

Minor typo fixes

Sort input to krakenuniq to enable retrieval of cached batch runs. #570

Changelog post-3.1.2 and 3.2.0 template updates

jfy133 · 2025-03-11T10:22:39Z

Forgot version bump I think @sofstam 😬

sofstam · 2025-03-11T10:24:55Z

I realized it a bit late but I am updating the PR :)

github-actions · 2025-03-11T10:27:43Z

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

Posted for pipeline commit 26d0721

+| ✅ 280 tests passed       |+
!| ❗  18 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
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
local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ 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 manifest.version does not contain dev for release: 1.2.3
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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.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: 3.2.0
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.2.0
Run at 2025-03-12 16:33:54

erikrikarddaniel

LGTM.

sofstam · 2025-03-11T12:03:20Z

#584

Prelease bump version

fix code blocks

…stqs in docs.

Switch from using save_analysis_ready_reads to save_analysis_ready_fa…

jfy133 · 2025-03-13T08:11:08Z

I can force merge because the conda overlapping errors are not related to the pipeline (an Nextflow issue)

sofstam and others added 30 commits January 15, 2025 10:50

Post-release bump version

26e610c

Update CHANGELOG.md

4f49fde

Prettier

2dea5b1

Merge branch 'bump_version_1.3.0' of https://github.com/nf-core/taxpr…

575ef87

…ofiler into bump_version_1.3.0

[automated] Fix code linting

7f5a785

Merge pull request #568 from nf-core/bump_version_1.3.0

071bcfb

Post release bump version

Template update for nf-core/tools version 3.1.2

64dcb04

Merge branch 'dev' into nf-core-template-merge-3.1.2

898866f

Update nextflow.config

ac960d4

Fix is a template change, see nf-core/tools#3416 If your pipeline is affected by this error I think it should be fine to manually apply this patch.

Update nextflow.config

a33a73f

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

Update zenodo

f2226be

Update nextflow.config

3d54880

Update README.md

8b62db7

Apply suggestions from code review

b8a42de

Merge pull request #569 from nf-core/nf-core-template-merge-3.1.2

34c5079

Important! Template update for nf-core/tools v3.1.2

Template update for nf-core/tools version 3.2.0

622585a

Merge branch 'dev' into nf-core-template-merge-3.2.0

b524cb0

Merge pull request #571 from nf-core/nf-core-template-merge-3.2.0

f11fd27

Important! Template update for nf-core/tools v3.2.0

Improve docs for taxpasta related flags

22380d6

Merge pull request #573 from nf-core/better-docs

7415c81

Better docs for taxpasta related flags

Update CHANGELOG.md

ec1ac99

Include batch index in task label.

c802f6f

Fix: Use db_name in process tag.

84b4b9c

Sort input channel to krakenuniq to enable task caching.

e981c70

Sort the input channel to ensure batches of input will remain constant across runs.

Update CHANGELOG.md

9c697c5

Update CHANGELOG.md

7500711

Merge pull request #575 from nf-core/changelog-for-docschagnes

c3a6b58

Changelog for for #573

Merge branch 'dev' into master

184d1f8

Changed sort comparator to avoid type mismatch error.

cb510bd

A samplesheet with both integer and non-numeric ( string ) values of sample caused type-mismatch error when compared. Generate prefix string from meta and compare on prefix.

jfy133 and others added 10 commits February 27, 2025 12:46

Merge pull request #579 from nf-core/remove-links-multiqc-plot

593aba1

Remove links to multiqc plots

analysis_read_reads -> analysis_ready_reads

e61d649

space after full stop

e3e680a

not can -> nor can

595ae3d

added me to README.md

f4f4b33

Merge pull request #580 from AlexHoratio/minor_typos_fix

220f2c7

Minor typo fixes

Merge pull request #576 from muniheart/master

3c82ed6

Sort input to krakenuniq to enable retrieval of cached batch runs. #570

Add missing template updates

07cbf7f

add missing typo fixes

919dbfd

Merge pull request #582 from nf-core/changelog-post3.20t-tools

5db1dc1

Changelog post-3.1.2 and 3.2.0 template updates

erikrikarddaniel approved these changes Mar 11, 2025

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Prelease bump version

14744d4

nf-core-bot and others added 11 commits March 11, 2025 12:06

[automated] Fix code linting

acee020

Merge pull request #584 from sofstam/prelease-bump

29b09ae

Prelease bump version

fix code blocks

5f947d6

Update CHANGELOG.md

077626b

[automated] Fix code linting

dc83cb9

Merge pull request #585 from nf-core/fix-code-blocks

48d4070

fix code blocks

Switch from using save_analysis_ready_reads to save_analysis_ready_fa…

32749b6

…stqs in docs.

Update CHANGELOG.md

f417da2

Merge branch 'dev' into fix_docs_saves

c2b9c18

Update README.md

5fbcfec

Merge pull request #586 from epstein6/fix_docs_saves

26d0721

Switch from using save_analysis_ready_reads to save_analysis_ready_fa…

LilyAnderssonLee approved these changes Mar 12, 2025

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jfy133 merged commit 970bdc2 into master Mar 13, 2025
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v1.2.3 - Bouncy Basenji Patch PR #583

v1.2.3 - Bouncy Basenji Patch PR #583

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v1.2.3 - Bouncy Basenji Patch PR #583

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sofstam commented Mar 11, 2025

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