Fixes related to polishing for release by KateSakharova · Pull Request #92 · nf-core/seqsubmit

KateSakharova · 2026-07-27T18:44:18Z

Basically that PR reflects all comments that James left in #72

Documentation fixes Update and restructure docs for v1.0 release #83
modules, tools, schemas polishing, tests Changes after review #86
changed parsing schema, changed some types in schema, docs Change schema meta #88
Align docs in usage and schemas Fix/unify schema and docs #93
Template merge Important! Template update for nf-core/tools v4.0.3 #90
many minor fixes and updates here and there

…sion

…istics and coverage calculation

…update metadata schema

Update and restructure docs for v1.0 release

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Change schema meta

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Many different changes after review. Round 2

github-actions · 2026-07-27T18:45:19Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-07-27T18:46:33Z

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

Posted for pipeline commit 670bdc6

+| ✅ 251 tests passed       |+
#| ❔   9 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: .github/workflows/linting_comment.yml
nextflow_config - Config variable ignored: params.input
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png
container_configs - container_configs

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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/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/pr-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-seqsubmit_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/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-seqsubmit_logo_light.png
files_exist - File found: docs/images/nf-core-seqsubmit_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: .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-seqsubmit_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/WorkflowSeqsubmit.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: 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.rrna_limit= 80.0
nextflow_config - Config default value correct: params.trna_limit= 18.0
nextflow_config - Config default value correct: params.checkm2_db_download_id= 14897628
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/
nextflow_config - Config default value correct: params.upload_tpa= false
nextflow_config - Config default value correct: params.test_upload= true
nextflow_config - Config default value correct: params.is_private= false
nextflow_config - Config default value correct: params.webincli_mode= submit
nf_test_content - 'tests/reads_paired_end.nf.test' contains outdir parameter
nf_test_content - 'tests/reads_paired_end.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/reads_paired_end.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_one_contig.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_rna_presence.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_rna_presence.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_rna_presence.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/mag_no_study_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_taxonomy.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_taxonomy.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_taxonomy.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_one_contig.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_one_contig.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/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/workflows/branch.yml matches the template
files_unchanged - .github/workflows/pr-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 - 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: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
pipeline_if_empty_null - No ifEmpty(null) strings 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_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: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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 - FALINT found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_ADDNAMES_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_PREPARE found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FASTA_FOR_CATPACK found in conf/modules.config and Nextflow scripts.
modules_config - BARRNAP found in conf/modules.config and Nextflow scripts.
modules_config - TRNASCANSE found in conf/modules.config and Nextflow scripts.
modules_config - COUNT_RNA found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_DATABASEDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_CONTIG found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ASSEMBLY_METADATA_CSV found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_METADATA found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_UPLOAD found in conf/modules.config and Nextflow scripts.
modules_config - ENA_WEBIN_CLI_WRAPPER found in conf/modules.config and Nextflow scripts.
modules_config - REGISTERSTUDY 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: 4.0.3
rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

nf-core/tools version 4.0.3
Run at 2026-07-30 14:30:25

Fix/unify schema and docs

Important! Template update for nf-core/tools v4.0.3

jfy133 · 2026-07-30T14:05:42Z

+
+Some processes in this pipeline are resource intensive — in particular coverage calculation (CoverM), quality assessment (CheckM2), and taxonomic classification of MAGs/bins (BAT). For real-world data, these steps should be run on an HPC cluster or another compute environment with sufficient CPU, memory, and job scheduling capacity, rather than on a single local machine.
+
+Depending on the resources available on your machine or cluster, you will likely need to adapt the Nextflow configuration to limit the maximum number of concurrently running jobs and other resource settings (e.g. `max_cpus`, `max_memory`, `max_time`, or `executor.queueSize` in a custom config), so that the pipeline does not try to claim more resources than are actually available. See the [nf-core configuration documentation](https://nf-co.re/docs/usage/getting_started/configuration) for guidance on writing a custom config for your infrastructure.


These max_ values do not exist, instead you need to use the nextflow native resourcesLimits directive

jfy133 · 2026-07-30T14:08:27Z

-                    "description": "Flag to control the type of assembly study (third party assembly or not)",
-                    "default": false,
-                    "help": "Use this flag if the study is a third party assembly (TPA). Default: false"
+                    "description": "Mark the assemblies as a Third PArty (TPA)",


I thought TPA stood for 'third party annotation'

We took it from ENA https://www.ebi.ac.uk/ena/browser/about/policies (I also thought A is for assembly)

Updated resource settings reference for Nextflow configuration.

ochkalova and others added 30 commits July 8, 2026 14:05

polish contributions.md

340f3b2

add limitations block

9692ab3

refactor limitations block

4452cb8

add scalability section to README.md

6bda9c7

refactor contributing guidelines

9074e16

start changing

fe61978

fix

3e9998f

update CONTRIBUTING.md to clarify testing requirements for ENA submis…

44c38d9

…sion

add some links

67d436a

update README.md to reference Methods documentation for metadata stat…

b0343f4

…istics and coverage calculation

refactor methods documentation to clarify RNA presence detection and …

f7f99b3

…update metadata schema

add SVG pipeline metromap

36567f4

update README.md Limitations to include issue tracking

c57e865

update README.md to add a Table of Contents

f759e9c

Move Data privacy section to usage.md

a7f6dd6

use one format for tables with column descriptions in usage.md

81e64bd

more fixes

c11bab2

slim Samplesheet descriptions in README to minimum

6aea0f8

Add Table of Contents to usage.md

9394073

move Submission Study section up in usage.md

cd8d99a

Expand Requirements to include required pre-submissions

ae6b462

Apply James' suggesstions in usage.md

bea141a

restructure usage.md

59c7746

polish usage.md structure and wording

b61853e

update pipeline metromap

6d38ce3

restructure README

2db92bd

Add section for Third Party Assemblies (TPA) in usage.md

018d328

Merge pull request #83 from nf-core/doc/limitations-scalability

38b208d

Update and restructure docs for v1.0 release

Merge branch '1.0.0' into fix/docs-review

5a35079

many fixes

36700b4

KateSakharova and others added 12 commits July 22, 2026 12:58

update genome_uploader and fix regexp in multiqc

54acdc9

test multiqc config old version from 1.0.0 branch

648ca9e

change co-assembly and rna_presence to boolean

edd594a

Template update for nf-core/tools version 4.0.3

d3d61ad

change limits for coverage, completeness and contamination

d0e42be

Apply suggestion from @ochkalova

774f69c

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Update subworkflows/local/genome_evaluation/main.nf

99970b6

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Update conf/test_assembly_complete_metadata.config

1a322b6

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Merge pull request #88 from nf-core/fix/meta_objects

fb2db68

Change schema meta

remove nr from main workflow and add to taxonomy subwf

2a0364c

Update docs and schemas for better descriptions

8af5f50

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Merge pull request #86 from nf-core/fix/docs-review

645df17

Many different changes after review. Round 2

KateSakharova changed the title ~~1.0.0~~ Fixes related to polishing for release Jul 27, 2026

KateSakharova and others added 7 commits July 30, 2026 14:19

aligned docs and schemas

b4a5d48

docs polishing

68a9c22

Merge pull request #93 from nf-core/fix/unify-schema-and-docs

4f98fff

Fix/unify schema and docs

Merge branch '1.0.0' into nf-core-template-merge-4.0.3

3a74926

remove files_unchanged

19067fb

revert files_unchanged

decd115

Merge pull request #90 from nf-core/nf-core-template-merge-4.0.3

5673e5b

Important! Template update for nf-core/tools v4.0.3

KateSakharova marked this pull request as ready for review July 30, 2026 13:49

Merge branch 'dev' into 1.0.0

fb3c3f1

KateSakharova requested a review from jfy133 July 30, 2026 13:59

jfy133 approved these changes Jul 30, 2026

View reviewed changes

jfy133 mentioned this pull request Jul 30, 2026

Initial release #72

Merged

Revise resource settings guidance in usage documentation

670bdc6

Updated resource settings reference for Nextflow configuration.

KateSakharova merged commit 361e07b into dev Jul 30, 2026
3 checks passed

KateSakharova deleted the 1.0.0 branch July 31, 2026 13:42

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Fixes related to polishing for release - #92

Fixes related to polishing for release#92
KateSakharova merged 55 commits into
devfrom
1.0.0

KateSakharova commented Jul 27, 2026 •

edited

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github-actions Bot commented Jul 27, 2026 •

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github-actions Bot commented Jul 27, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

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jfy133 Jul 30, 2026

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KateSakharova Jul 30, 2026 •

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		Some processes in this pipeline are resource intensive — in particular coverage calculation (CoverM), quality assessment (CheckM2), and taxonomic classification of MAGs/bins (BAT). For real-world data, these steps should be run on an HPC cluster or another compute environment with sufficient CPU, memory, and job scheduling capacity, rather than on a single local machine.

		Depending on the resources available on your machine or cluster, you will likely need to adapt the Nextflow configuration to limit the maximum number of concurrently running jobs and other resource settings (e.g. `max_cpus`, `max_memory`, `max_time`, or `executor.queueSize` in a custom config), so that the pipeline does not try to claim more resources than are actually available. See the [nf-core configuration documentation](https://nf-co.re/docs/usage/getting_started/configuration) for guidance on writing a custom config for your infrastructure.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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KateSakharova commented Jul 27, 2026 •

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

KateSakharova Jul 30, 2026 •

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