Release 2.1 ! by muffato · Pull Request #266 · sanger-tol/readmapping

muffato · 2026-09-18T15:59:20Z

PR checklist

Test PR - test CI with new nextflow version

Merge main to dev

Fix fasta filename

…reprocess modules

Template update for nf-core/tools version 4.1.0 (main to dev)

…rameters

Extra additions to the pimms branch

Preserve PG lines

Support PiMmS

Metro map

github-actions · 2026-09-18T16:02:42Z

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

Posted for pipeline commit cedb0e6

+| ✅ 231 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config
local_component_structure - change_name.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - convert_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - merge_output.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - align_short.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - align_long.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-readmapping_logo_light.png
files_exist - File is ignored: assets/methods_description_template.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: docs/images/nf-core-readmapping_logo_dark.png
files_exist - File is ignored: docs/images/nf-core-readmapping_logo_light.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: tower.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config default ignored: params.pacbio_adapter
nextflow_config - Config default ignored: params.pacbio_adapter_yaml
files_unchanged - File ignored due to lint config: .gitattributes
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-readmapping_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-readmapping_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-readmapping_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/readmapping/readmapping/.github/workflows/awstest.yml
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: 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/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: 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/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: conf/base.config
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-readmapping_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/WorkflowReadmapping.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 2.1.0
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.alignment_format= cram
nextflow_config - Config default value correct: params.compression= crumble
nextflow_config - Config default value correct: params.window_size= 1000
nextflow_config - Config default value correct: params.short_aligner= bwamem2
nextflow_config - Config default value correct: params.long_reads_map_chunk_size= 10000
nextflow_config - Config default value correct: params.short_reads_map_chunk_size= 10000
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.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/uli_no_lima.nf.test' contains outdir parameter
nf_test_content - 'tests/uli_no_lima.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/uli_no_lima.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/pimms.nf.test' contains outdir parameter
nf_test_content - 'tests/pimms.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/pimms.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/uli.nf.test' contains outdir parameter
nf_test_content - 'tests/uli.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/uli.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/amplifi.nf.test' contains outdir parameter
nf_test_content - 'tests/amplifi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/amplifi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/short_aligner_minimap2.nf.test' contains outdir parameter
nf_test_content - 'tests/short_aligner_minimap2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/short_aligner_minimap2.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/untrim.nf.test' contains outdir parameter
nf_test_content - 'tests/untrim.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/untrim.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 - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - assets/email_template.txt 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
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_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: pr-comment.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: branch.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: sanger_test.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - BLAST_BLASTN found in conf/base.config and Nextflow scripts.
base_config - BLOBTK_DEPTH found in conf/base.config and Nextflow scripts.
base_config - BLOBTK_DEPTH found in conf/base.config and Nextflow scripts.
base_config - BWAMEM2_INDEX found in conf/base.config and Nextflow scripts.
base_config - CONVERT_CRAM found in conf/base.config and Nextflow scripts.
base_config - CRUMBLE found in conf/base.config and Nextflow scripts.
base_config - FASTQC found in conf/base.config and Nextflow scripts.
base_config - LIMA found in conf/base.config and Nextflow scripts.
base_config - MINIMAP2_INDEX found in conf/base.config and Nextflow scripts.
base_config - MULTIQC found in conf/base.config and Nextflow scripts.
base_config - PBMARKDUP found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_ADDREPLACERG found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_CRAM found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_STATS found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_ found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_ found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_ found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_FASTQ found in conf/base.config and Nextflow scripts.
base_config - SAMTOOLS_INDEX found in conf/base.config and Nextflow scripts.
base_config - FASTXALIGN_MINIMAP2ALIGN found in conf/base.config and Nextflow scripts.
base_config - FASTXALIGN_PYFASTXINDEX found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - BLAST_BLASTN found in conf/modules.config and Nextflow scripts.
modules_config - BLOBTK_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - BGZIP_BEDGRAPH found in conf/modules.config and Nextflow scripts.
modules_config - CHANGE_NAME found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_CRAM found in conf/modules.config and Nextflow scripts.
modules_config - CRUMBLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - GAWK_MODIFY_YAML_BARCODE found in conf/modules.config and Nextflow scripts.
modules_config - HIFITRIMMER_PROCESSBLAST found in conf/modules.config and Nextflow scripts.
modules_config - HIFITRIMMER_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - LIMA found in conf/modules.config and Nextflow scripts.
modules_config - BLAST_MAKEBLASTDB found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - PBMARKDUP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_ADDREPLACERG found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_IDXSTATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGEDUP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_REHEADER found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.1.0
rocrate_readme_sync - RO-Crate 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
version_consistency - Version tags are consistent: manifest.version = 2.1.0, nfcore_yml.version = 2.1.0

Run details

nf-core/tools version 4.1.0
Run at 2026-09-25 16:28:42

There was a typo but anyway we don't want this column in the samplesheet. Otherwise we're not able to nullify the option on the command-line for the uli_no_lima test. The pimms samplesheet makes use of this column so we still test it works as an override.

…ndices

I didn't touch samtools when embedded in one of the multi-tool containers, for instance blast/blastn and the alignment modules. That explains why there are still some 1.23.1 occurrences in the snapshots.

(except the two nf-core utils* ones which should stay in sync with the template) No output/version change

Fixed the 4.1.0 template merge

Stub runs and modules update

sainsachiko and others added 30 commits May 15, 2026 18:46

Merge pull request #243 from sanger-tol/main

58234e7

Fix BigDecimal error

cace3af

Removed fixed nextflow version for test download

81e9af5

Merge pull request #244 from sanger-tol/ci-new-nf-ver

6f9ddc0

Test PR - test CI with new nextflow version

Merge pull request #251 from sanger-tol/main

acbfdd5

Merge main to dev

Fix fasta filename

1825895

Merge pull request #252 from sanger-tol/fasta-fn

b4dc76e

Fix fasta filename

Template update for nf-core/tools version 4.1.0

a2de6bc

Update Pacbio_preprocess module

da0ecc9

Update fastx_map_long_reads

374a156

Install cram_map_long_reads

8d0432d

Update cramalign modules

64b39a3

Adjust align_long and align_short to be compatible with new mapping/p…

572a821

…reprocess modules

Update nf-test & snapshots

f2ca590

Remove FASTQC_FILTERED

aaad545

Removed path to command in CL for tests

5df8fbc

Add script to bin

ce8a110

Remove unneccesary scripts

3019431

Add resource for cramalign_minimapalign

9d67d29

Update test snapshots

5f70906

Forgot to change FILTERBAM to TRIM in base.config

cb1f747

Merge pull request #256 from sanger-tol/main

4b224e0

Template update for nf-core/tools version 4.1.0 (main to dev)

Add function to sanitize BAM/CRAM headers

3fbdecc

Fix prettier

753aafb

Force timezone for nf-test

ade6d90

Update LICENSE

a483301

Sort BAM files before merging

3e62eab

Sort BAM before merging for stable order of PG lines

c27cd0e

Fix warning params not used

e90a794

Merge pull request #257 from sanger-tol/update-nf-test

37414d9

muffato and others added 14 commits September 11, 2026 01:47

Made the tests as identical as possible, to simplify maintenance

28897d7

Don't need to test CRAM and crumble on the alternative libraries / pa…

95440be

…rameters

Moved parameters to the profile themselves

095ff77

Correct spelling and case

223f90c

Merge pull request #264 from sanger-tol/mm49_pimms

1246cf2

Extra additions to the pimms branch

Update alignment modules

6f470d5

Update snapshots

fb873b2

Fix broken PG chain

78477ee

Merge pull request #254 from sanger-tol/pg_lines

7da004c

Preserve PG lines

Merge branch 'dev' into pimms

068357a

Merge pull request #265 from sanger-tol/pimms

738284b

Support PiMmS

Merge branch 'dev' into metro_map

c83dcbb

Updated the RO-Crate

51650cf

Merge pull request #261 from sanger-tol/metro_map

591936a

Metro map

muffato self-assigned this Sep 18, 2026

muffato added 14 commits September 23, 2026 10:22

Merge remote-tracking branch 'origin/TEMPLATE' into for_release

2764503

Made all tests look the same

223db4d

These files don't exist in the template any more

d6784a4

Unnecessary column

f30aaf0

There was a typo but anyway we don't want this column in the samplesheet. Otherwise we're not able to nullify the option on the command-line for the uli_no_lima test. The pimms samplesheet makes use of this column so we still test it works as an override.

Switched bgziptabix to the sanger-tol version, which builds TBI+CSI i…

5b44540

…ndices

Updated all the standalone samtools modules

04237d6

I didn't touch samtools when embedded in one of the multi-tool containers, for instance blast/blastn and the alignment modules. That explains why there are still some 1.23.1 occurrences in the snapshots.

Innocuous patch update

7d4498d

crumble update (move to topic version !)

063ac52

gawk module update

475e15e

Updated blobtk depth

d887b03

Updated all remaining modules

c795d26

(except the two nf-core utils* ones which should stay in sync with the template) No output/version change

Local modules within their own directory should be called main.nf

390b713

Merge pull request #267 from sanger-tol/template_fix

15546f1

Fixed the 4.1.0 template merge

Merge pull request #268 from sanger-tol/stub_modules_update

cedb0e6

Stub runs and modules update

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Release 2.1 ! - #266

Release 2.1 !#266
muffato wants to merge 109 commits into
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muffato commented Sep 18, 2026

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muffato commented Sep 18, 2026

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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Milestone

Development

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github-actions Bot commented Sep 18, 2026 •

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