Add sentieon star #1590

FriederikeHanssen · 2025-08-12T08:07:35Z

This PR add Sentieon support for STAR. The output of sentieon is equivalent to STAR. For this three modules where added:

SENTIEON_STARALIGN, that is added as additional option for STAR_ALIGN
SENTIEON_RSEMPREPAREREFERNCES, that is added as additional option for RSEM_PREPAREREFERENCES
SENTIEON_RSEMCALCULATEEXPRESSIONS, that is added as additional option for RSEM_CALCULATEEXPRESSION

Since Sentieon needs a number of things to be able to ping the license server, the respective scripts, and environment variables were added to :

bin/
the CI/CD workflows in .github
all test configs

Additional tests to test these changes were added for the individual subworkflows align and rsem, as well as 2 new pipeline level tests, one expanding the default one (star & salmon) with sentieon enabled, one that is testing star_rsem directly.

The usage docs on how to enable sentieon were added.

PR checklist

nf-core-bot · 2025-08-12T08:08:09Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

nextflow_schema.json

github-actions · 2025-08-12T08:10:11Z

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

Posted for pipeline commit f228324

+| ✅ 290 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
pipeline_todos - TODO string in base.config: Check the defaults for all processes
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 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
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
_

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
nextflow_config - Config default ignored: params.ribo_database_manifest
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
multiqc_config - multiqc_config
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
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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
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files_exist - File found: README.md
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files_exist - File found: conf/test.config
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files_exist - File not found check: .github/workflows/push_dockerhub.yml
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nextflow_config - Found nf-schema plugin
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nextflow_config - Config variable found: timeline.enabled
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nextflow_config - Config variable found: process.cpus
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nextflow_config - Config variable found: validation.help.beforeText
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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
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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 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: 3.20.0dev
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.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.gtf_extra_attributes= gene_name
nextflow_config - Config default value correct: params.gtf_group_features= gene_id
nextflow_config - Config default value correct: params.featurecounts_group_type= gene_biotype
nextflow_config - Config default value correct: params.featurecounts_feature_type= exon
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.trimmer= trimgalore
nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
nextflow_config - Config default value correct: params.umi_dedup_tool= umitools
nextflow_config - Config default value correct: params.umitools_extract_method= string
nextflow_config - Config default value correct: params.umitools_grouping_method= directional
nextflow_config - Config default value correct: params.aligner= star_salmon
nextflow_config - Config default value correct: params.pseudo_aligner_kmer_size= 31
nextflow_config - Config default value correct: params.min_mapped_reads= 5.0
nextflow_config - Config default value correct: params.kallisto_quant_fraglen= 200
nextflow_config - Config default value correct: params.kallisto_quant_fraglen_sd= 200
nextflow_config - Config default value correct: params.stranded_threshold= 0.8
nextflow_config - Config default value correct: params.unstranded_threshold= 0.1
nextflow_config - Config default value correct: params.extra_fqlint_args= --disable-validator P001
nextflow_config - Config default value correct: params.deseq2_vst= true
nextflow_config - Config default value correct: params.rseqc_modules= bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
nextflow_config - Config default value correct: params.bracken_precision= S
nextflow_config - Config default value correct: params.skip_bbsplit= true
nextflow_config - Config default value correct: params.skip_preseq= 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.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/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/
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nf_test_content - 'tests/kallisto.nf.test' contains outdir parameter
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nf_test_content - 'tests/kallisto.nf.test' contains outdir parameter
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nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_default.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_default.nf.test' snapshots a 'versions.yml' file
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nf_test_content - 'tests/umi.nf.test' contains outdir parameter
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nf_test_content - 'tests/umi.nf.test' contains outdir parameter
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nf_test_content - 'tests/min_mapped_reads.nf.test' contains outdir parameter
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nf_test_content - 'tests/min_mapped_reads.nf.test' snapshots a 'versions.yml' file
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nf_test_content - 'tests/sentieon_star_rsem.nf.test' contains outdir parameter
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nf_test_content - 'tests/star_rsem.nf.test' contains outdir parameter
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nf_test_content - 'tests/salmon.nf.test' contains outdir parameter
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nf_test_content - 'tests/skip_qc.nf.test' contains outdir parameter
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nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
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actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
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readme - README Nextflow minimum version badge matched config. Badge: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
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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.
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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-08-14 09:38:36

subworkflows/local/prepare_genome/tests/main.nf.test

maxulysse

Llooking good, @pinin4fjords covered most of the questions already.
There are some minor typos left

Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>

edmundmiller

Looks great to me!

Might have to revisit how we're testing Sentieon vs what we're supporting.

We could probably have a util for it in nf-core-utils 🤔

docs/usage.md

pinin4fjords

Nice clean solution, feel free to merge when you've sorted the tests, and sorry for my diversion ;-)

subworkflows/local/align_star/main.nf

subworkflows/local/quantify_rsem/main.nf

FriederikeHanssen added 4 commits August 11, 2025 15:03

install sentieon/staralign

807fd19

add args to sentieon_align_star

7636eb6

add sentieon secrets to ci

c02c684

add sentieon secrets

8c8599d

maxulysse reviewed Aug 12, 2025

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

revert changes from schema builder

82c38be

FriederikeHanssen added 22 commits August 12, 2025 08:23

snapshots

fddcc5b

add auth_mech env var

a4dace5

sentieon star uses old style args

f4f5a18

add more env vars

1f044f5

fix versions checksum

9f2f8ce

Merge branch 'dev' into add_sentieon_star

9452604

fix version

fc3cab4

snapshots

0799db8

refactor code since sentieon star uses same syntax as igenomes star

ff9b53a

add license usage docs

e0351a6

update changelog

411645c

add complete pipeline test with sentieon

f96bdc7

checksum order

6163917

test out symlinking sentieon star in rsem

752e85d

add tests for symlinking star in rsem

476d022

add sentieon env vars to subworkflow test

26703b9

update version chcksum

c3ff26a

add stub test

a6958f5

add pipeline level test

679d699

add sentieon license vars to pipeline level tests

f55fccc

replace local module with nf-core module

5be778d

update module name in configs

59978b6

maxulysse reviewed Aug 13, 2025

View reviewed changes

subworkflows/local/prepare_genome/tests/main.nf.test Outdated Show resolved Hide resolved

maxulysse reviewed Aug 13, 2025

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subworkflows/local/prepare_genome/tests/main.nf.test Outdated Show resolved Hide resolved

maxulysse approved these changes Aug 13, 2025

View reviewed changes

maxulysse and others added 5 commits August 13, 2025 17:58

Merge branch 'dev' into add_sentieon_star

3bc2151

Apply suggestions from code review

ddfbee8

Co-authored-by: Jonathan Manning <[email protected]> Co-authored-by: Maxime U Garcia <[email protected]>

move license script to .github.actions

d0c7eba

fix comment alignment

43abdc7

rename use_sentieon to use_sentieon_star

9450a5c

edmundmiller assigned FriederikeHanssen Aug 13, 2025

edmundmiller added this to nf-core infrastructure projects Aug 13, 2025

edmundmiller added the sentieon label Aug 13, 2025

edmundmiller approved these changes Aug 13, 2025

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edmundmiller mentioned this pull request Aug 13, 2025

Sentieon License helper functions nf-core/nf-core-utils#9

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FriederikeHanssen added 9 commits August 14, 2025 06:37

test process name reassignment

9e00a4d

test renaming

74f7d4d

revert process renaming tests

107f668

assign output name

5f45235

Address reviews from @pinin4fjords & reduce one level of if statements

3cf1b7b

add link to modules tested to address review by @edmundmiller

c0bfbd2

simplify logic

e81774e

clean up code

9c108af

fix syntax error

b33be90

pinin4fjords approved these changes Aug 14, 2025

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FriederikeHanssen added 4 commits August 14, 2025 08:51

propagate changes from #1573 to a number of other tests

195550b

set multi_channel initialisation to null

d6d32cb

fix order

fda153f

more odering

f228324

FriederikeHanssen merged commit 75ded6e into dev Aug 14, 2025
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github-project-automation bot moved this to Done in nf-core infrastructure projects Aug 14, 2025

FriederikeHanssen deleted the add_sentieon_star branch August 14, 2025 09:55

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Add sentieon star #1590

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FriederikeHanssen commented Aug 12, 2025 •

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❗ Test warnings:

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Add sentieon star #1590

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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FriederikeHanssen commented Aug 12, 2025 •

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