Fix review comments #163

erikrikarddaniel · 2025-10-21T09:39:06Z

PR checklist

This contains a mix of various fixes after review comments.

…ew-comments-2

github-actions · 2025-10-21T09:41:18Z

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

Posted for pipeline commit 9538fdd

+| ✅ 239 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: If you use nf-core/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/magmap/magmap/subworkflows/local/fastqc_trimgalore/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
_
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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-magmap_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-magmap_logo_light.png
files_exist - File found: docs/images/nf-core-magmap_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: nf-test.config
files_exist - File found: tests/default.nf.test
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: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.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-magmap_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/WorkflowMagmap.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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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.remote_genome_sources= https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt,https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
nextflow_config - Config default value correct: params.genome_store_dir= magmap_genomes
nextflow_config - Config default value correct: params.prokka_store_dir= magmap_prokka
nextflow_config - Config default value correct: params.bbmap_minid= 0.9
nextflow_config - Config default value correct: params.bbmap_ambiguous= best
nextflow_config - Config default value correct: params.features= CDS,rRNA,tRNA,tmRNA
nextflow_config - Config default value correct: params.skip_sourmash= true
nextflow_config - Config default value correct: params.sourmash_ksize= 21
nextflow_config - Config default value correct: params.sourmash_save_unassigned= true
nextflow_config - Config default value correct: params.sourmash_save_matches_sig= true
nextflow_config - Config default value correct: params.sourmash_save_prefetch= true
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/
nf_test_content - 'tests/test_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/test_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_sourmash.nf.test' contains outdir parameter
nf_test_content - 'tests/test_sourmash.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_sourmash.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_duplicates.nf.test' contains outdir parameter
nf_test_content - 'tests/test_duplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_duplicates.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_sourmash_mix.nf.test' contains outdir parameter
nf_test_content - 'tests/test_sourmash_mix.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_sourmash_mix.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_single.nf.test' contains outdir parameter
nf_test_content - 'tests/test_single.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_single.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
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-magmap_logo_light.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_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
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_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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
modules_config - CAT_MANY found in conf/modules.config and Nextflow scripts.
modules_config - GENOMES2ORFS found in conf/modules.config and Nextflow scripts.
modules_config - BAM_SORT_STATS_SAMTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - WGET_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
modules_config - PROKKAGFF2TSV found in conf/modules.config and Nextflow scripts.
modules_config - SAMPLE_SKETCH found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_SKETCH found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SOURMASH_GATHER found in conf/modules.config and Nextflow scripts.
modules_config - SOURMASH_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - TIDYVERSE_JOINMETADATA found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_STATS found in conf/modules.config and Nextflow scripts.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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: 3.4.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.4.1
Run at 2025-10-21 10:18:38

danilodileo

It's a pity to not have any tool for estimating the community composition. We should really encourage the users to run taxprofileror even metatdenovoin order to have a full picture of the community. Maybe we should have it somewhere in the documentation?

LGTM

erikrikarddaniel · 2025-10-21T10:03:21Z

It's a pity to not have any tool for estimating the community composition. We should really encourage the users to run taxprofileror even metatdenovoin order to have a full picture of the community. Maybe we should have it somewhere in the documentation?

Yes, we should. I'll add that to this.

LGTM

erikrikarddaniel · 2025-10-21T10:17:18Z

It's a pity to not have any tool for estimating the community composition. We should really encourage the users to run taxprofileror even metatdenovoin order to have a full picture of the community. Maybe we should have it somewhere in the documentation?

Yes, we should. I'll add that to this.

LGTM

erikrikarddaniel added 18 commits October 7, 2025 21:14

Add FastQC and BBDuk to metromap

8a996fa

Add contaminant fasta to metromap

233c53b

'local' -> 'user-provided' in metromap

ce59ab8

Merge branch 'dev' of https://github.com/nf-core/magmap into fix-revi…

0cc6caa

…ew-comments-2

Stub update in cat/many

226fc8d

Move MultiQC in docs/output.md

db53d12

Remove Kraken2

34c6b05

Set bbmap processes to process_high_memory

d5fa2db

An attempt at a better tower.yml

f11a041

png instead of svg for metromap

3839ea3

Move MultiQC part also in README.md

c76c2a3

Aesthetics

02fcdf5

Remove old params things in fastqc_trimgalore swf

75daa5b

Merge branch 'dev' of https://github.com/nf-core/magmap into fix-revi…

2e6a926

…ew-comments-2

Add some citations

0e7aa2d

Update docs/usage.md

bfe387f

Fix missing html tags around files in output.md

6cb28c0

Merge branch 'dev' of https://github.com/nf-core/magmap into fix-revi…

5ba275b

…ew-comments-2

erikrikarddaniel requested a review from danilodileo October 21, 2025 09:39

erikrikarddaniel added 2 commits October 21, 2025 11:42

Prettier

a6a5c13

Sync RO-crate

2095f8c

danilodileo approved these changes Oct 21, 2025

View reviewed changes

Update README.md to point to nf-core/taxprofiler

c645f02

Fix RO-crate

9538fdd

erikrikarddaniel merged commit d5d85ba into nf-core:dev Oct 21, 2025
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Fix review comments #163

Fix review comments #163

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erikrikarddaniel commented Oct 21, 2025 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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erikrikarddaniel commented Oct 21, 2025

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Fix review comments #163

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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erikrikarddaniel commented Oct 21, 2025 •

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