Bulk MultiQC reporting as a pipeline-installed Python module by keiran-rowell-unsw · Pull Request #45 · Australian-Structural-Biology-Computing/proteinfold

keiran-rowell-unsw · 2026-09-09T06:06:53Z

Implements 'bulk' MultiQC reporting as per proteinfold/issues/439.

Recommendation from Phil Ewels when evaluating contribute into MultiQC modules was instead using setup.py in this specific pipeline whereas MultiQC modules typically work with only one CLI tool (MultiQC/MultiQC#3462)

github-actions · 2026-09-09T06:09:26Z

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

Posted for pipeline commit a4a242c

+| ✅ 281 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  15 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
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 nextflow.config: Specify any additional parameters here
local_component_structure - prepare_boltz_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_alphafold2_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_esmfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_colabfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - post_processing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - aria2_uncompress.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_alphafold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_schema_validation - actions_schema_validation
multiqc_config - multiqc_config

✅ 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-proteinfold_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-proteinfold_logo_light.png
files_exist - File found: docs/images/nf-core-proteinfold_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-proteinfold_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/WorkflowProteinfold.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 manifest.version ends in dev: 2.1.0dev
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.mode= alphafold2
nextflow_config - Config default value correct: params.uniref30_prefix= UniRef30_2023_02
nextflow_config - Config default value correct: params.alphafold2_max_template_date= 2038-01-19
nextflow_config - Config default value correct: params.alphafold2_model_preset= monomer_ptm
nextflow_config - Config default value correct: params.alphafold2_params_prefix= alphafold_params_2022-12-06
nextflow_config - Config default value correct: params.colabfold_num_recycles= 3
nextflow_config - Config default value correct: params.colabfold_use_amber= true
nextflow_config - Config default value correct: params.colabfold_use_templates= false
nextflow_config - Config default value correct: params.colabfold_params_prefix= alphafold_params_2022-12-06
nextflow_config - Config default value correct: params.esmfold_num_recycles= 4
nextflow_config - Config default value correct: params.boltz_use_kernels= true
nextflow_config - Config default value correct: params.skip_foldseek= 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.alphafold2_bfd_link= https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
nextflow_config - Config default value correct: params.alphafold2_small_bfd_link= https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz
nextflow_config - Config default value correct: params.alphafold2_params_link= https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar
nextflow_config - Config default value correct: params.alphafold2_mgnify_link= https://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.fa.gz
nextflow_config - Config default value correct: params.alphafold2_pdb70_link= https://wwwuser.gwdguser.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_220313.tar.gz
nextflow_config - Config default value correct: params.alphafold2_pdb_mmcif_link= rsync.rcsb.org::ftp_data/structures/divided/mmCIF/
nextflow_config - Config default value correct: params.alphafold2_pdb_obsolete_link= https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat
nextflow_config - Config default value correct: params.alphafold2_uniref30_link= https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz
nextflow_config - Config default value correct: params.alphafold2_uniref90_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz
nextflow_config - Config default value correct: params.alphafold2_pdb_seqres_link= https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
nextflow_config - Config default value correct: params.alphafold2_uniprot_sprot_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
nextflow_config - Config default value correct: params.alphafold2_uniprot_trembl_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
nextflow_config - Config default value correct: params.alphafold2_bfd_path= null/bfd/*
nextflow_config - Config default value correct: params.alphafold2_small_bfd_path= null/small_bfd/*
nextflow_config - Config default value correct: params.alphafold2_params_path= null/params/alphafold_params_2022-12-06/*
nextflow_config - Config default value correct: params.alphafold2_mgnify_path= null/mgnify/*
nextflow_config - Config default value correct: params.alphafold2_pdb70_path= null/pdb70/**
nextflow_config - Config default value correct: params.alphafold2_pdb_mmcif_path= null/pdb_mmcif/mmcif_files
nextflow_config - Config default value correct: params.alphafold2_pdb_obsolete_path= null/pdb_mmcif/obsolete.dat
nextflow_config - Config default value correct: params.alphafold2_uniref30_path= null/uniref30/*
nextflow_config - Config default value correct: params.alphafold2_uniref90_path= null/uniref90/*
nextflow_config - Config default value correct: params.alphafold2_pdb_seqres_path= null/pdb_seqres/*
nextflow_config - Config default value correct: params.alphafold2_uniprot_path= null/uniprot/*
nextflow_config - Config default value correct: params.alphafold3_small_bfd_link= https://storage.googleapis.com/alphafold-databases/v3.0/bfd-first_non_consensus_sequences.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_mgnify_link= https://storage.googleapis.com/alphafold-databases/v3.0/mgy_clusters_2022_05.fa.zst
nextflow_config - Config default value correct: params.alphafold3_pdb_mmcif_link= https://storage.googleapis.com/alphafold-databases/v3.0/pdb_2022_09_28_mmcif_files.tar.zst
nextflow_config - Config default value correct: params.alphafold3_uniref90_link= https://storage.googleapis.com/alphafold-databases/v3.0/uniref90_2022_05.fa.zst
nextflow_config - Config default value correct: params.alphafold3_pdb_seqres_link= https://storage.googleapis.com/alphafold-databases/v3.0/pdb_seqres_2022_09_28.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_uniprot_link= https://storage.googleapis.com/alphafold-databases/v3.0/uniprot_all_2021_04.fa.zst
nextflow_config - Config default value correct: params.alphafold3_rnacentral_link= https://storage.googleapis.com/alphafold-databases/v3.0/rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_nt_rna_link= https://storage.googleapis.com/alphafold-databases/v3.0/nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_rfam_link= https://storage.googleapis.com/alphafold-databases/v3.0/rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_small_bfd_path= null/small_bfd/*
nextflow_config - Config default value correct: params.alphafold3_mgnify_path= null/mgnify/*
nextflow_config - Config default value correct: params.alphafold3_pdb_mmcif_path= null/pdb_mmcif/mmcif_files
nextflow_config - Config default value correct: params.alphafold3_uniref90_path= null/uniref90/*
nextflow_config - Config default value correct: params.alphafold3_pdb_seqres_path= null/pdb_seqres/*
nextflow_config - Config default value correct: params.alphafold3_uniprot_path= null/uniprot/*
nextflow_config - Config default value correct: params.alphafold3_rnacentral_path= null/rnacentral/*
nextflow_config - Config default value correct: params.alphafold3_nt_rna_path= null/nt_rna/*
nextflow_config - Config default value correct: params.alphafold3_rfam_path= null/rfam/*
nextflow_config - Config default value correct: params.colabfold_db_link= https://opendata.mmseqs.org/colabfold/colabfold_envdb_202108.db.tar.gz
nextflow_config - Config default value correct: params.colabfold_uniref30_link= https://opendata.mmseqs.org/colabfold/uniref30_2302.db.tar.gz
nextflow_config - Config default value correct: params.colabfold_alphafold2_params_link= https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar
nextflow_config - Config default value correct: params.colabfold_envdb_path= null/colabfold_envdb/*
nextflow_config - Config default value correct: params.colabfold_uniref30_path= null/colabfold_uniref30/*
nextflow_config - Config default value correct: params.colabfold_alphafold2_params_path= null/params/alphafold_params_2022-12-06
nextflow_config - Config default value correct: params.esmfold_3B_v1= https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt
nextflow_config - Config default value correct: params.esm2_t36_3B_UR50D= https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt
nextflow_config - Config default value correct: params.esm2_t36_3B_UR50D_contact_regression= https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt
nextflow_config - Config default value correct: params.esmfold_params_path= null/params/*
nextflow_config - Config default value correct: params.boltz_ccd_link= https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl
nextflow_config - Config default value correct: params.boltz_model_link= https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_aff_link= https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_aff.ckpt
nextflow_config - Config default value correct: params.boltz2_conf_link= https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_mols_link= https://huggingface.co/boltz-community/boltz-2/resolve/main/mols.tar
nextflow_config - Config default value correct: params.boltz_ccd_path= null/params/ccd.pkl
nextflow_config - Config default value correct: params.boltz_model_path= null/params/boltz1_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_aff_path= null/params/boltz2_aff.ckpt
nextflow_config - Config default value correct: params.boltz2_conf_path= null/params/boltz2_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_mols_path= null/params/mols/
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/split_fasta.nf.test' contains outdir parameter
nf_test_content - 'tests/split_fasta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/esmfold.nf.test' contains outdir parameter
nf_test_content - 'tests/esmfold.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/esmfold.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_webserver.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_webserver.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold3.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold3.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold3.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold2_download.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold2_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold2_split.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold2_split.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold3_download.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold3_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/boltz.nf.test' contains outdir parameter
nf_test_content - 'tests/boltz.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_download.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_local.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_local.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/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/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.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-proteinfold_logo_light.png matches the template
files_unchanged - docs/images/nf-core-proteinfold_logo_light.png matches the template
files_unchanged - docs/images/nf-core-proteinfold_logo_dark.png matches the template
files_unchanged - docs/README.md 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.
readme - README Zenodo placeholder was replaced with DOI.
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
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 modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - ARIA2 found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_MULTIQC_CONTENTS found in conf/modules.config and Nextflow scripts.
modules_config - GENERATE_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - FOLDSEEK_EASYSEARCH 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 descriptions are in sync with 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 4.0.3
Run at 2026-10-01 01:54:55

…line Implement 'bulk' MultiQC reporting as a pipeline-installed Python module. - Add/setup module packaging for multiqc_proteinfold - won't be upstreamed into MultiQC as per Phil's comments PR#3462 - Install module from pipeline runtime with Docker linting behavior (escaping PWD) - Handle pip target/PYTHONPATH and improve install robustness - Ensure MultiQC YAML packag usable - Apply related lint/format cleanup (e.g. escape PWD) rank typo Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> use logger not print Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> remove unused multiqc modules Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> typos Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> makesure user can specify sample merge rules make nextflow lint happy by using shell substitution not VARS docker container doesn't like shell substitution without escape chars

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> remove SBF logo and custom links

…use in comparison report

Also add setuptools/wheel to the module env (required by --no-build-isolation, conda-forge python >=3.12 no longer bundles setuptools)

jscgh · 2026-09-23T07:33:44Z

Nice simplification moving bulk reporting to a pipeline-local MultiQC plugin.

I've updated the multiqc module to 1.35 (via nf-tools) and added pip/pandas/setuptools/wheel to the module env and rebuilt the containers so the plugin install works (verified end-to-end), and tidied the tests.

jscgh

I'm getting blank sections of reports running the current branch. I've tried to trace the sources and commented on them.

This reverts commit e4502f5.

keiran-rowell-unsw · 2026-09-29T02:04:03Z

I hadn't noticed the agent swapped multiqc:1.34 for a more involved multiqc_pandas_pip_setuptools_wheel.

It makes it more explicit, but happy to revert to simplify the install process.

Sort ranked models, make the embedded config JSON injection-safe, de-duplicate model images and fix rendering for the ipTM/ipSAE/chainwise tables.

… downloads

jscgh

Thanks! I can tell this was a huge body of work. 🚀
I was able to rebuild the plugin into a small module with mqc custom-content files, so we can use the native nf-core/multiqc version. This should help with keeping it up to date and changing things locally in the future.
I also added some tests for reports to make it easier to track drift.

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keiran-rowell-unsw added the enhancement New feature or request label Sep 9, 2026

keiran-rowell-unsw changed the base branch from master to dev September 9, 2026 06:27

keiran-rowell-unsw assigned keiran-rowell-unsw and jscgh and unassigned keiran-rowell-unsw and jscgh Sep 9, 2026

keiran-rowell-unsw requested a review from jscgh September 10, 2026 03:38

jscgh reviewed Sep 16, 2026

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jscgh reviewed Sep 16, 2026

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Comment thread multiqc_proteinfold/multiqc_proteinfold_config.yml Outdated

jscgh reviewed Sep 16, 2026

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Comment thread multiqc_proteinfold/proteinfold.py Outdated

jscgh force-pushed the dev branch from 793fe5c to a414fd1 Compare September 19, 2026 03:56

keiran-rowell-unsw and others added 7 commits September 23, 2026 10:28

Remove facility logo for codebase PR

500b124

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> remove SBF logo and custom links

PYTHONPATH with pip install target

4f47313

docker container doesn't like shell substitution without escape chars

890668a

Fix git rebase messages that had been pulled into the install string

4705b78

Fix git rebase messages that had been pulled into the environment.yml

d15840b

ASBC CI doesn't allow 'dev' in version number

e983709

jscgh force-pushed the multiqc_bulk_report branch from a816184 to 2a402a2 Compare September 23, 2026 00:33

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keiran-rowell-unsw added 6 commits September 23, 2026 11:08

migrate away from old labelling and having plddt_raw etc

e1b4d77

Don't change the _msa.tsv renaming mv commands since I think they're …

78cf423

…use in comparison report

remove duplicate multiqc config block

780043a

mutliqc -> plddt purge for proper multiqc bulk

982a132

migrate away from _raw. Metrics are just themselves

bea8aef

more explicit pattern matching

39564cd

Clean up stale MultiQC and Foldseek wiring

5cb1311

jscgh force-pushed the multiqc_bulk_report branch from 2a402a2 to 5cb1311 Compare September 23, 2026 02:08

jscgh added 3 commits September 23, 2026 13:52

Updated snapshots

2c5f878

Update nf-core multiqc module to v1.35

61b8567

Fix linting for gh actions using old nf-core tools

a67c33f

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keiran-rowell-unsw requested a review from jscgh September 23, 2026 06:40

Fix multiqc plugin install: add pip/pandas to module env

31950f4

Also add setuptools/wheel to the module env (required by --no-build-isolation, conda-forge python >=3.12 no longer bundles setuptools)

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jscgh requested changes Sep 23, 2026

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Comment thread assets/report_template.html

Comment thread multiqc_proteinfold/proteinfold.py Outdated

Comment thread workflows/boltz.nf Outdated

keiran-rowell-unsw added 9 commits September 24, 2026 15:17

try a manifest generated by qwen local agent

873cdb4

use --cl-config to pass through meta.model

e4502f5

function to pass through all mulitqc metrics

fe804be

Revert "use --cl-config to pass through meta.model"

8367be9

This reverts commit e4502f5.

AF2 arity fixed

795286c

lint

c40227d

load model images, don't need double escape

f35c880

restore MSA coverage and PAE container

42b4657

update snapshots

f2e71ac

keiran-rowell-unsw requested a review from jscgh September 29, 2026 01:43

jscgh added 2 commits September 30, 2026 23:59

Rework MultiQC to use stock module and custom content files

5a1e936

Complete to-dos for the generated reports

3c70b51

Sort ranked models, make the embedded config JSON injection-safe, de-duplicate model images and fix rendering for the ipTM/ipSAE/chainwise tables.

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Fix multiline version emissions which crashed MQC 1.35

a56fc83

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Drop deprecated modes, restore upstream template elements, fix report…

a4a242c

… downloads

jscgh approved these changes Oct 1, 2026

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jscgh merged commit 0bef7bc into dev Oct 1, 2026
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Bulk MultiQC reporting as a pipeline-installed Python module - #45

Bulk MultiQC reporting as a pipeline-installed Python module#45
jscgh merged 36 commits into
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multiqc_bulk_report

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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