Fix aws test by ggabernet · Pull Request #479 · nf-core/airrflow

ggabernet · 2026-06-05T02:58:27Z

PR checklist

Fix aws

github-actions · 2026-06-05T03:00:03Z

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

Posted for pipeline commit 011431c

+| ✅ 281 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  28 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
local_component_structure - rename_fastq.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - gunzip.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - merge_UMI.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - unzip_cellrangerdb.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fetch_databases.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - parse_logs.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - prepare_trust4_reference.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - validate_igblast_db.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - samplesheet_check.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - rename_file.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - unzip_db.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - fastqc_postassembly.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - presto_sans_umi.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - databases.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - sc_raw_input.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - vdj_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - novel_alleles_and_genotyping.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - translate_embed.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - clonal_analysis.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - bulk_qc_and_filter.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - assembled_input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - fastq_input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - sequence_assembly.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - presto_umi.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - repertoire_analysis_reporting.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - single_cell_qc_and_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - rnaseq_input.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
nextflow_config - nextflow_config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
schema_params - schema_params

❔ 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/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-airrflow_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-airrflow_logo_light.png
files_exist - File found: docs/images/nf-core-airrflow_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-airrflow_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/WorkflowAirrflow.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
nf_test_content - 'tests/test_maskprimers_extract.nf.test' contains outdir parameter
nf_test_content - 'tests/test_maskprimers_extract.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_maskprimers_extract.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_embeddings_H.nf.test' contains outdir parameter
nf_test_content - 'tests/test_embeddings_H.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_embeddings_H.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_rnaseq_bulk.nf.test' contains outdir parameter
nf_test_content - 'tests/test_rnaseq_bulk.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_rnaseq_bulk.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_rnaseq_sc.nf.test' contains outdir parameter
nf_test_content - 'tests/test_rnaseq_sc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_rnaseq_sc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_nocluster.nf.test' contains outdir parameter
nf_test_content - 'tests/test_nocluster.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_nocluster.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_assembled_mm.nf.test' contains outdir parameter
nf_test_content - 'tests/test_assembled_mm.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_assembled_mm.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fetch_airrc_imgt.nf.test' contains outdir parameter
nf_test_content - 'tests/test_fetch_airrc_imgt.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fetch_airrc_imgt.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_10x_sc.nf.test' contains outdir parameter
nf_test_content - 'tests/test_10x_sc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_10x_sc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_embeddings_HL.nf.test' contains outdir parameter
nf_test_content - 'tests/test_embeddings_HL.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_embeddings_HL.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_reassign_false.nf.test' contains outdir parameter
nf_test_content - 'tests/test_reassign_false.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_reassign_false.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_no_umi.nf.test' contains outdir parameter
nf_test_content - 'tests/test_no_umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_no_umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_nebnext_umi.nf.test' contains outdir parameter
nf_test_content - 'tests/test_nebnext_umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_nebnext_umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_tcr.nf.test' contains outdir parameter
nf_test_content - 'tests/test_tcr.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_tcr.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_maskprimers_align.nf.test' contains outdir parameter
nf_test_content - 'tests/test_maskprimers_align.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_maskprimers_align.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_assembled_hs.nf.test' contains outdir parameter
nf_test_content - 'tests/test_assembled_hs.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_assembled_hs.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_takara_smartseq_umi_bcr.nf.test' contains outdir parameter
nf_test_content - 'tests/test_takara_smartseq_umi_bcr.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_takara_smartseq_umi_bcr.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_genotyping.nf.test' contains outdir parameter
nf_test_content - 'tests/test_genotyping.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_genotyping.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fetchimgt.nf.test' contains outdir parameter
nf_test_content - 'tests/test_fetchimgt.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_fetchimgt.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/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-airrflow_logo_light.png matches the template
files_unchanged - docs/images/nf-core-airrflow_logo_light.png matches the template
files_unchanged - docs/images/nf-core-airrflow_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: 26.04.1, Config: 26.04.1
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'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awstest.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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
modules_config - SAMPLESHEET_CHECK_ASSEMBLED found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
modules_config - VALIDATE_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_POSTASSEMBLY found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FILE_ found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_FILTERSEQ found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_UMI_R1 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_UMI_R2 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ALIGN_PRIMERS found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ALIGN_CREGION found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_UMI_R1 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_UMI_R2 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_EXTRACT_R1 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_EXTRACT_R2 found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_CLUSTERSETS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSE_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PAIRSEQ_CLUSTERSETS found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_BUILDCONSENSUS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_BUILDCONSENSUS_ALIGN_RACE found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_BUILDCONSENSUS_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_POSTCONSENSUS_PAIRSEQ found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ASSEMBLEPAIRS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ASSEMBLEPAIRS_SEQUENTIAL found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_ASSEMBLEPAIRS_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_COLLAPSE_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_PRIMERS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_CREGION found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_PARSEHEADERS_METADATA found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_CREGION found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_COLLAPSESEQ_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_SPLITSEQ_UMI found in conf/modules.config and Nextflow scripts.
modules_config - PRESTO_SPLITSEQ_SANS_UMI found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_DATABASES found in conf/modules.config and Nextflow scripts.
modules_config - VALIDATE_IGBLAST_DB found in conf/modules.config and Nextflow scripts.
modules_config - UNZIP_DB found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_CONVERTDB_FASTA_FROM_AIRR found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_ASSIGNGENES found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_MAKEDB found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_QUALITY found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_PARSEDB_SELECT_LOCUS found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_PARSEDB_SPLIT found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_JUNCTION_MOD3 found in conf/modules.config and Nextflow scripts.
modules_config - ADD_META_TO_TAB found in conf/modules.config and Nextflow scripts.
modules_config - CHANGEO_CREATEGERMLINES found in conf/modules.config and Nextflow scripts.
modules_config - REMOVE_CHIMERIC found in conf/modules.config and Nextflow scripts.
modules_config - DETECT_CONTAMINATION found in conf/modules.config and Nextflow scripts.
modules_config - COLLAPSE_DUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - SINGLE_CELL_QC found in conf/modules.config and Nextflow scripts.
modules_config - NOVEL_ALLELE_INFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - REASSIGN_ALLELES_NOVEL found in conf/modules.config and Nextflow scripts.
modules_config - CLONAL_ASSIGNMENT_GENOTYPING found in conf/modules.config and Nextflow scripts.
modules_config - BAYESIAN_GENOTYPE_INFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - REASSIGN_ALLELES_GENOTYPE found in conf/modules.config and Nextflow scripts.
modules_config - FIND_CLONAL_THRESHOLD found in conf/modules.config and Nextflow scripts.
modules_config - REPORT_THRESHOLD found in conf/modules.config and Nextflow scripts.
modules_config - CLONAL_ASSIGNMENT found in conf/modules.config and Nextflow scripts.
modules_config - REPERTOIRE_ANALYSIS found in conf/modules.config and Nextflow scripts.
modules_config - DOWSER_LINEAGES found in conf/modules.config and Nextflow scripts.
modules_config - AMULETY_TRANSLATE found in conf/modules.config and Nextflow scripts.
modules_config - AMULETY_EMBED_ANTIBERTA2 found in conf/modules.config and Nextflow scripts.
modules_config - AMULETY_EMBED_ANTIBERTY found in conf/modules.config and Nextflow scripts.
modules_config - AMULETY_EMBED_BALMPAIRED found in conf/modules.config and Nextflow scripts.
modules_config - AMULETY_EMBED_ESM2 found in conf/modules.config and Nextflow scripts.
modules_config - AIRRFLOW_REPORT found in conf/modules.config and Nextflow scripts.
modules_config - PARSE_LOGS found in conf/modules.config and Nextflow scripts.
modules_config - REPORT_FILE_SIZE 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: 4.0.2
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 4.0.2
Run at 2026-06-05 14:10:57

Fix aws

try fix aws test

ggabernet and others added 7 commits June 4, 2026 22:03

fix params

67edd9c

Merge pull request #477 from ggabernet/dev

2a094f5

Fix aws

fix params

d3fb192

Apply suggestion from @ggabernet

2407b20

Merge pull request #478 from ggabernet/dev

c313775

Fix aws

update param

0a9a956

fix params

f046a31

ggabernet added 4 commits June 4, 2026 23:00

Merge pull request #480 from ggabernet/dev

7dcb033

Fix aws

try fix aws test

9803838

merge upstream

2f35b06

Merge pull request #481 from ggabernet/dev

011431c

try fix aws test

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Fix aws test#479

Fix aws test#479
ggabernet wants to merge 11 commits into
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ggabernet commented Jun 5, 2026

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github-actions Bot commented Jun 5, 2026 •

edited

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ggabernet commented Jun 5, 2026

PR checklist

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github-actions Bot commented Jun 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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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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github-actions Bot commented Jun 5, 2026 •

edited

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