bwamem_index fix #581

eduard-watchmaker · 2025-12-02T18:13:36Z

mistake in the bwamem_index schema

@sateeshperi sorry for missing this one!

github-actions · 2025-12-02T18:15:44Z

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

Posted for pipeline commit a717f8d

+| ✅ 234 tests passed       |+
#| ❔   7 tests were ignored |#

Details

❔ Tests ignored:

files_exist - File is ignored: lib/nfcore_external_java_deps.jar
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: .github/workflows/ci.yml
files_unchanged - File ignored due to lint config: assets/nf-core-methylseq_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-methylseq_logo_dark.png
modules_config - modules_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/CONTRIBUTING.md
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-methylseq_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-methylseq_logo_light.png
files_exist - File found: docs/images/nf-core-methylseq_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.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-methylseq_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/WorkflowMethylseq.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: .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: 4.2.0dev
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.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.aligner= bismark
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.nextseq_trim= 0
nextflow_config - Config default value correct: params.num_mismatches= 0.6
nextflow_config - Config default value correct: params.no_overlap= true
nextflow_config - Config default value correct: params.ignore_r1= 0
nextflow_config - Config default value correct: params.ignore_r2= 2
nextflow_config - Config default value correct: params.ignore_3prime_r1= 0
nextflow_config - Config default value correct: params.ignore_3prime_r2= 2
nextflow_config - Config default value correct: params.min_depth= 0
nextflow_config - Config default value correct: params.trim_OT= 0,0,10,0
nextflow_config - Config default value correct: params.trim_OB= 0,0,10,0
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/methylseq/
nf_test_content - 'tests/targeted_sequencing_variants.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/targeted_sequencing_variants.nf.test' contains outdir parameter
nf_test_content - 'tests/bwamem_taps.nf.test' contains outdir parameter
nf_test_content - 'tests/bwamem_taps.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/default.nf.test' contains outdir parameter
nf_test_content - 'tests/index_downloads.nf.test' contains outdir parameter
nf_test_content - 'tests/index_downloads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bismark_hisat_variants.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bismark_hisat_variants.nf.test' contains outdir parameter
nf_test_content - 'tests/bismark_variants.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bismark_variants.nf.test' contains outdir parameter
nf_test_content - 'tests/bwameth_variants.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bwameth_variants.nf.test' contains outdir parameter
nf_test_content - 'tests/bwameth_use_gpu.nf.test' contains outdir parameter
nf_test_content - 'tests/bwameth_use_gpu.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 - 'tests/nextflow.config' contains pipelines_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/CONTRIBUTING.md 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/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 - 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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings 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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.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: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test-gpu.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: update-gpu-snapshot.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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.
base_config - PRESEQ_LCEXTRAP found in conf/base.config and Nextflow scripts.
base_config - BISMARK_ALIGN found in conf/base.config and Nextflow scripts.
base_config - BISMARK_DEDUPLICATE found in conf/base.config and Nextflow scripts.
base_config - BISMARK_METHYLATIONEXTRACTOR found in conf/base.config and Nextflow scripts.
base_config - BWAMETH_ALIGN found in conf/base.config and Nextflow scripts.
base_config - PARABRICKS_FQ2BAMMETH found in conf/base.config and Nextflow scripts.
base_config - PARABRICKS_FQ2BAM found in conf/base.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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2025-12-06 18:33:29

- add BWA-MEM alignment configuration - Update GitHub link for Eduard Casas - replace logo image in assets

sateeshperi · 2025-12-03T10:45:23Z

hold till upstream module changes: nf-core/modules#9496

nextflow.config

…m subwf

- Refactor version output to include process name and command used for version retrieval. - Remove legacy versions.yml file generation in favor of structured output.

eduard-watchmaker · 2025-12-03T18:47:35Z

I can't figure out what's going on with the MULTIQC (it hangs and doesnt finish) so I'd suggest rolling back that update, merge this branch and then separately figuring out what's going on with this update and add a hot fix

- Implemented a mechanism to merge topic channel versions into the main versions file upon workflow completion. - Updated the software version output to include both main and topic versions in separate YAML files.

- Bump NFT_VER from 0.9.2 to 0.9.3 - Bump NXF_VER from 24.10.5 to 25.04.0

eduard-watchmaker · 2025-12-05T16:18:28Z

Should we ignore the 25.04 tests and merge @sateeshperi ?

sateeshperi · 2025-12-06T11:14:47Z

Cannot ignore the tests. A fix for multiqc is in works. will be resolved soon

sateeshperi · 2025-12-06T15:27:17Z

fixed tests. just need to update the gpu snapshot now

eduard-watchmaker · 2025-12-06T18:14:27Z

@nf-core-bot update gpu snapshot path: tests/bwameth_use_gpu.nf.test

eduard-watchmaker · 2025-12-06T18:49:43Z

fixed tests. just need to update the gpu snapshot now

I just updated them, let me know if there is anything else I can do to help! Thanks @sateeshperi

bwamem_index fix

a6e08a9

eduard-watchmaker requested a review from a team as a code owner December 2, 2025 18:13

eduard-watchmaker requested a review from sateeshperi December 2, 2025 18:13

Merge branch 'dev' into bwamem_fix

daa0571

fix: refine SAMTOOLS_SORT process settings

617d0a3

- add BWA-MEM alignment configuration - Update GitHub link for Eduard Casas - replace logo image in assets

sateeshperi linked an issue Dec 3, 2025 that may be closed by this pull request

--aligner bwameth samtools sort bam incorrectly named with deduplicated prefix #580

Closed

eduard-watchmaker commented Dec 3, 2025

View reviewed changes

nextflow.config Show resolved Hide resolved

sateeshperi and others added 4 commits December 3, 2025 21:54

Update fasta_index_methylseq, fastq_align_dedup_bismark/bwameth/bwame…

d1127da

…m subwf

chore: Update software version tracking in FastQC and MultiQC processes

4b8cee3

- Refactor version output to include process name and command used for version retrieval. - Remove legacy versions.yml file generation in favor of structured output.

chore: re-install bam_methyldackel and bam_taps_conversion

15ae2ab

Remove version channel output after adding topic

73ed560

sateeshperi added 3 commits December 4, 2025 11:22

fix: update version tracking and output for nf-core methylseq workflow

1957d21

- Implemented a mechanism to merge topic channel versions into the main versions file upon workflow completion. - Updated the software version output to include both main and topic versions in separate YAML files.

chore: update changelog

0a12198

chore: update GPU snapshot workflow versions

33f8db4

- Bump NFT_VER from 0.9.2 to 0.9.3 - Bump NXF_VER from 24.10.5 to 25.04.0

new gpu snapshot

a717f8d

eduard-watchmaker enabled auto-merge December 6, 2025 18:49

sateeshperi approved these changes Dec 7, 2025

View reviewed changes

eduard-watchmaker merged commit 7f30dbf into dev Dec 7, 2025
99 checks passed

sateeshperi deleted the bwamem_fix branch December 7, 2025 02:35

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bwamem_index fix #581

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❔ Tests ignored:

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nf-core pipelines lint overall result: Passed ✅

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✅ Tests passed:

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eduard-watchmaker commented Dec 2, 2025 •

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