Pseudo-review: first release by ewels · Pull Request #88 · nf-core/datasync

ewels · 2026-09-07T15:12:54Z

Warning

Not intended to be merged.
This PR is just to give a meaningful whole-pipeline diff for a first-release code view.

Because master is on a very old version of the template, much of the diff in #82 is from template updates.

This PR is to a branch that comes from template v4.0.3, which I believe is the latest version of the template that has been merged into dev. As a result, the diff should be a minimal version of "what's new in the pipeline versus the boilerplate template".

It's not intended for this PR to be merged. Once used for review, it can be closed and the branch discarded, then #8 merged and first release.

…datasync into implement_rclone

Implement rclone

Generate MultiQC Report with `comparechecksum` tables and input samplesheet

Implement review suggestions

Add local test profile

github-actions · 2026-09-07T15:14:08Z

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

Posted for pipeline commit d25e58a

+| ✅ 205 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   5 tests had warnings |!

Details

❗ 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: 1.0.0
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.

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
multiqc_config - multiqc_config

❔ 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-datasync_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-datasync_logo_light.png
files_exist - File found: docs/images/nf-core-datasync_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-datasync_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/WorkflowDatasync.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 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.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/datasync/
nf_test_content - 'tests/edge.nf.test' contains outdir parameter
nf_test_content - 'tests/edge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/edge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/edge.nf.test' contains outdir parameter
nf_test_content - 'tests/edge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/edge.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/edge.nf.test' contains outdir parameter
nf_test_content - 'tests/main_full.nf.test' contains outdir parameter
nf_test_content - 'tests/main_full.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_full.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/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/pr-comment.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-datasync_logo_light.png matches the template
files_unchanged - docs/images/nf-core-datasync_logo_light.png matches the template
files_unchanged - docs/images/nf-core-datasync_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_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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.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: awstest.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
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 - RCLONE_CHECKSUM found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_FILTER_LIST found in conf/modules.config and Nextflow scripts.
modules_config - RCLONE_COPY found in conf/modules.config and Nextflow scripts.
modules_config - RCLONE_CHECK 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: 4.1.0
rocrate_readme_sync - RO-Crate description matches the README.md.
container_configs - conf/containers_conda_lock_files_amd64.config is up to date
container_configs - conf/containers_conda_lock_files_arm64.config is up to date
container_configs - conf/containers_docker_amd64.config is up to date
container_configs - conf/containers_docker_arm64.config is up to date
container_configs - conf/containers_singularity_https_amd64.config is up to date
container_configs - conf/containers_singularity_https_arm64.config is up to date
container_configs - conf/containers_singularity_oras_amd64.config is up to date
container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

nf-core/tools version 4.1.0
Run at 2026-09-09 15:44:17

ewels

Great stuff! Quick pass on the pipeline as an overview (not too much on the actual dataflow code and modules, on the assumption that it's already well tested there).

Looks great: some minor comments, but hopefully all quite quick to resolve.

ewels · 2026-09-07T15:20:20Z

@@ -0,0 +1,52 @@
+/* Keep the internal row identifier available to MultiQC without displaying it. */


This, in contrast, makes me nervous 😆

I think I get at what you're doing with most of this, though some of the CSS makes me wonder if you're papering over rendering issues that should be solved at MultiQC level. Please make issues if that's the case (can always cut this out of the pipeline in the future, doesn't need to be a blocker).

If it's okay, we will leave this as-is now and create a new issue to tackle this once the release is done

delfiterradas · 2026-09-08T15:23:35Z

Hi @ewels,
Thank you for taking the time to review the code, we really appreciate your suggestions!
I am currently working on implementing the changes in #89. The suggestions marked as resolved have already been addressed and I will continue implementing the rest
I can let you know when it is done. Thanks again!

Change default branch

Implement review suggestions

delfiterradas · 2026-09-09T14:09:02Z

Hi @ewels, I have merged the branch with the changes you suggested :)

When you have the time, would you mind taking a look at it again?

I think the only suggestion I didn't include for the time being is the MultiQC one (I have opened an issue to address that after the release), but please let me know if there is anything I have missed.

Thank you!

Add memory definition to avoid failing on seqera platform

zxBIB and others added 30 commits July 6, 2026 00:49

include http handling

43be5b3

make rclone config an optional input

c982567

include rclone in nf test

d52ff84

include rclone dry run in nf test config

36c1d2f

add output path to input samplesheet + make rclone conf optional input

9aaa7df

Merge branch 'implement_rclone' of https://github.com/antoniasaracco/…

d0079ba

…datasync into implement_rclone

include rclone --dry-run as a parameter

aafb97b

ignore rclone log file

5897bc2

include rclone --dry-run as a parameter

a4516c8

update tests snapshots

e5a0157

update samplesheet format

6a5d7af

Add input samplesheet to report and add description

eecb805

Add citation text

8a7632a

move rclone to local folder

d45029e

run commit fix

f70feec

update nextflow version

5513e64

Merge branch 'nf-core:implement_rclone' into implement_rclone

70f8209

move rclone to local folder

3a98fc6

run fix lint

80b09ca

fix

03a79a3

Update CHANGELOG with new features and fixes

db581e8

Merge pull request #38 from antoniasaracco/implement_rclone

dad2dc2

Implement rclone

Merge remote-tracking branch 'upstream/dev' into report

4968204

Do not expert plots for multiqc and update snapshots

7da1d5a

Ignore linting for multiqc_config file

b550108

Remove notes from report

018e1af

Update multiqc module

c889174

Update citations

a7d6b58

Update CHANGELOG

27c8a9e

Merge pull request #41 from delfiterradas/report

9fee02b

Generate MultiQC Report with `comparechecksum` tables and input samplesheet

delfiterradas and others added 9 commits September 3, 2026 12:46

Update rclone modules

9178433

Run prek

29f8ee9

Update CHANGELOG

46d4636

Merge pull request #84 from delfiterradas/review_dev

23f779f

Implement review suggestions

Add local test profile

412a67d

Fix linting

4cf6105

Update CHANGELOG.md

d68d8bf

Addexplanation for real data test profile

23161e1

Merge pull request #87 from delfiterradas/review_dev

366487c

Add local test profile

ewels commented Sep 7, 2026

View reviewed changes

Implement review suggestions

5cd483d

delfiterradas and others added 8 commits September 8, 2026 15:38

Template update for nf-core/tools version 4.1.0

e4372d9

Merge branch 'TEMPLATE' into dev

5619860

Change default branch and update rclone checksum

a3bfda8

Fix linting

5117470

Skip linting for PULL_REQUEST_TEMPLATE.md

ba00df5

Merge pull request #90 from delfiterradas/dev

0bdf8b9

Change default branch

Update changelog for first release

bcfdc6a

Merge remote-tracking branch 'upstream/dev' into review_dev

69ad859

delfiterradas mentioned this pull request Sep 8, 2026

Improve rendering issues in MULTIQC #91

Open

delfiterradas and others added 2 commits September 8, 2026 20:53

Add nf-metro plot

4cbf146

Fix linting

c43ec12

delfiterradas mentioned this pull request Sep 9, 2026

Implement review suggestions 2 #89

Merged

11 tasks

delfiterradas added 2 commits September 9, 2026 10:51

Clean up CHANGELOG by removing empty sections

89905cb

Merge pull request #89 from delfiterradas/review_dev

d2afa32

Implement review suggestions

delfiterradas and others added 2 commits September 9, 2026 17:30

Add memory definition to avoid failing on seqera platform

d6056fc

Merge pull request #92 from delfiterradas/review_dev

d25e58a

Add memory definition to avoid failing on seqera platform

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Pseudo-review: first release - #88

Pseudo-review: first release#88
ewels wants to merge 368 commits into
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		@@ -0,0 +1,52 @@
		/* Keep the internal row identifier available to MultiQC without displaying it. */

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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