Add functionality to parse run dir metadata by kedhammar · Pull Request #106 · nf-core/seqinspector

kedhammar · 2025-03-25T14:45:26Z

PR checklist

github-actions · 2025-03-25T15:49:13Z

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

Posted for pipeline commit fabdac5

+| ✅ 194 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  30 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in README.md: TODO nf-core:
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
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: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in ro-crate-metadata.json: "description": "
\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">\n <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">\n \n
\n\n\n \n\n\n\n\n\n\n\n\n \n\n## Introduction\n\nnf-core/seqinspector is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/seqinspector \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #seqinspector channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/seqinspector for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in meta.yml: #Add a description of the module and list keywords
pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.

❔ Tests ignored:

nextflow_config - Config default ignored: params.fastq_screen_references
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: ro-crate-metadata.json
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nextflow_config - Found nf-schema plugin
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nextflow_config - Config variable found: validation.help.enabled
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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/
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nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.sample_size= 0
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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
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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
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
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actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
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actions_schema_validation - Workflow validation passed: nf-test.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 - SEQTK_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SEQFU_STATS found in conf/modules.config and Nextflow scripts.
modules_config - RUNDIRPARSER found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_PER_TAG 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

Run details

nf-core/tools version 3.2.0
Run at 2025-03-26 16:33:53

…n the multiqc report generation, make function take output name as cmd parameter

… the outfile accordingly, for proper downstream grouping

kedhammar · 2025-03-26T09:23:02Z

Ties into nf-core/test-datasets#1559

…s for test consistency

…illumina mqc file

maxulysse · 2025-12-12T09:24:43Z

What can I do?

Did I mention you again when I meant to tag @matthdsm

matthdsm · 2025-12-12T09:38:07Z

So I think there's a huge overlap between this module and what we're trying to achieve with MultiQC_SAV.
Would you guys be open to contribute your code there and amend the report to your needs?
The plugin used to work great, but needs some love right now.

matrulda · 2025-12-12T10:09:33Z

So I think there's a huge overlap between this module and what we're trying to achieve with MultiQC_SAV. Would you guys be open to contribute your code there and amend the report to your needs? The plugin used to work great, but needs some love right now.

Oh interesting, I have to check it out! If we can avoid a local module that is definitely interesting. Unfortunately I have been swamped with other work duties so have had no time to work with this PR.

maxulysse · 2025-12-12T10:33:18Z

Unfortunately I have been swamped with other work duties so have had no time to work with this PR.

I'm on it 🚀

maxulysse · 2025-12-12T12:36:08Z

@matrulda

@maxulysse If you have time later this week, would you mind having a look at modules/local/rundirparser/tests/main.nf.test and give some advice?

I fully rewrote the tests, and they're now working.
while I was at it, I added topics for the versions.

Now trying to figure out what's the problem with the rest of the tests

FriederikeHanssen · 2025-12-12T14:05:10Z

 */

+// Enable use of module binaries for e.g. module specific Python scripts
+nextflow.enable.moduleBinaries = true


why are you using module binaries? Just wondering since we have typically been using templates in nf-core

I just followed along what was already done to be honest.

ok will approve as i assume there will be clean up before v1

Module binaries require wave to run on cloud if I remember correctly

matthdsm · 2025-12-18T11:31:30Z

FYI, a new version of MultiQC_SAV was just released
https://pypi.org/project/multiqc-sav/

kedhammar added 10 commits March 24, 2025 16:55

wip, need container with pyyaml

be3ec58

fix conda env and functional containers

80caa98

spacing

7144a47

channel magic to refactor meta on rundir-level

aec2ad3

update process versioning and stubs

9b0f0e7

remove todo:s, make process agnostic to mqc file extensions

915965b

generate _mqc.txt dummy file with table from rundir keys

5546c10

clean up formatting and underscore unused variables

c87f476

use module binary instead of supplying script as process input

4d3a70f

add all multiqc files to channel, not just first

137629a

kedhammar added the enhancement New feature or request label Mar 25, 2025

kedhammar assigned matrulda and kedhammar Mar 25, 2025

kedhammar added 2 commits March 25, 2025 14:54

Merge remote-tracking branch 'upstream/dev' into run-dirs

7d6dd42

extend suffix to differentiate from other _mqc files

82d285a

kedhammar added 2 commits March 26, 2025 08:49

give mqc outputs the same name so they will be merged automatically i…

70cacab

…n the multiqc report generation, make function take output name as cmd parameter

actually, let the script differentiate between seq platforms and name…

f0999e8

… the outfile accordingly, for proper downstream grouping

editorconfig

e38676d

matrulda mentioned this pull request Mar 26, 2025

Add option for rundir input types #11

Closed

11 tasks

kedhammar and others added 4 commits March 26, 2025 13:16

fix quotes and make rundirparser publish results with individual name…

7873d53

…s for test consistency

clean up meta object names

d45ee52

docs and formatting

9c66ff8

Add parse_illumina.py

fabdac5

maxulysse added this to the 1.0.0 milestone Nov 6, 2025

FranBonath mentioned this pull request Nov 7, 2025

Display sequencing metadata from the run_dir #4

Closed

matrulda added 3 commits November 24, 2025 10:37

Merge branch 'dev' into run-dirs

48b4cee

Update rundirparser test and add nextflow config for it

3cb2c6b

Rundirparser: Add tar support, remove dummy script, update format of …

0b22867

…illumina mqc file

maxulysse added 6 commits December 12, 2025 11:39

Merge branch 'dev' into run-dirs

8d400b9

update snapshots

dde9b4d

update module

a1c5207

code polish + topics

07e1f7f

code polish

8bec73e

fix tests

5397e93

no need for view()

d902891

maxulysse marked this pull request as ready for review December 12, 2025 12:45

maxulysse added 3 commits December 12, 2025 13:53

simplify config

28dc3d0

dir_meta -> meta

bae6f35

Delete modules/local/rundirparser/meta.yml

ec40b9f

maxulysse reviewed Dec 12, 2025

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Comment thread tests/NovaSeq6000.main.nf.test.config Outdated

maxulysse added 3 commits December 12, 2025 13:58

Update tests/NovaSeq6000.main.nf.test.config

e9d0c00

sort modules import

7207ccf

sort import

68a674c

maxulysse approved these changes Dec 12, 2025

View reviewed changes

maxulysse added 2 commits December 12, 2025 14:07

Trigger Build

780d28a

update snapshots

c3bda22

maxulysse self-requested a review December 12, 2025 13:23

FriederikeHanssen reviewed Dec 12, 2025

View reviewed changes

FriederikeHanssen approved these changes Dec 12, 2025

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maxulysse merged commit 88aa3c8 into nf-core:dev Dec 12, 2025
23 checks passed

maxulysse mentioned this pull request Dec 12, 2025

Minor tests refactoring and code polish #164

Merged

11 tasks

maxulysse added a commit that referenced this pull request Jan 13, 2026

Merge pull request #106 from kedhammar/run-dirs

5c68a10

Conversation

kedhammar commented Mar 25, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">\n <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">\n \n

❔ Tests ignored:

✅ Tests passed:

Run details

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kedhammar commented Mar 26, 2025

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maxulysse commented Dec 12, 2025

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matthdsm commented Dec 12, 2025

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matrulda commented Dec 12, 2025

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maxulysse commented Dec 12, 2025

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maxulysse commented Dec 12, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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github-actions Bot commented Mar 25, 2025 •

edited

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

maxulysse commented Dec 12, 2025 •

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