feat (closes #7246): add new component: leafcutter/differentialsplicing by JTL-lab · Pull Request #12271 · nf-core/modules

JTL-lab · 2026-07-07T20:28:35Z

PR Description

This PR adds a new module leafcutter/differentialsplicing for running Leafcutter differential splicing analysis to determine statistically significant junction usage changes between biological conditions of interest. This module relies on the new Python reimplementation of Leafcutter (leafcutter-ds) here (also documented in the meta.yml).

PR checklist

Closes #7246

…lsplicing

…ot, set python environment hash variable

SPPearce · 2026-07-14T06:00:26Z

+                { assert snapshot(
+                    process.out.findAll { key, val -> key.startsWith('versions') },
+                    process.out.cluster_significance.collect { file(it[1]).getName() },
+                    process.out.effect_sizes.collect { file(it[1]).getName() }
+                ).match() },
+                // Check non-deterministic files exist
+                { assert file(process.out.cluster_significance[0][1]).exists() },
+                { assert file(process.out.effect_sizes[0][1]).exists() }


Try this:

Suggested change

{ assert snapshot(

process.out.findAll { key, val -> key.startsWith('versions') },

process.out.cluster_significance.collect { file(it[1]).getName() },

process.out.effect_sizes.collect { file(it[1]).getName() }

).match() },

// Check non-deterministic files exist

{ assert file(process.out.cluster_significance[0][1]).exists() },

{ assert file(process.out.effect_sizes[0][1]).exists() }

{ assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cluster_significance", "effect_sizes"])).match()}

SPPearce · 2026-07-14T06:01:21Z

+process {
+
+    withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
+        ext.args = '--min_samples_per_group 2 --min_samples_per_intron 2 --num_threads 1'


Shouldn't need num_threads in here, that should already be in the tool?

SPPearce · 2026-07-14T06:01:39Z

+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export USER=\${USER:-nobody}


Is this required?

Not strictly required, but useful for reproducibility with PyTorch. I have changed this to be set only within main.nf.test rather than main.nf, and opted to include a note in meta.yml to users about this as an FYI.

…sts, removed redundant --num_threads param in test config args, move container options set in main.nf to main.nf.test and add note in meta.yml

JTL-lab · 2026-07-28T18:43:56Z

Hi @SPPearce, thank you very much for your review and suggestions. I have addressed your feedback in my latest commit. Please let me know if anything else is needed to merge. Thank you!

SPPearce · 2026-07-29T08:40:29Z

+maintainers:
+  - "@JTL-lab"
+notes:
+  - This module uses PyTorch for statistical analysis. When running in containers, you may need to set environment variables in your pipeline configuration for reproducibility. For example, `containerOptions = '--env USER=nobody --env PYTHONHASHSEED=0 --env CUBLAS_WORKSPACE_CONFIG=:4096:8'` (Docker) or `containerOptions = '--env USER=nobody,PYTHONHASHSEED=0,CUBLAS_WORKSPACE_CONFIG=:4096:8'` (Singularity/Apptainer).


There are definitely several modules that set PYTHONHASHSEED directly in the code, that seems important.
Can you explain why the others are required?

CUBLAS_WORKSPACE_CONFIG=:4096:8 is for reproducibility with PyTorch CUDA (more detail here), upon rereview though CUDA isn't currently implemented (might be in the future, in which case this would be best practice to include) so we could omit this from meta.yml for now.

For USER=nobody, this is to resolve an issue to my understanding caused by an internal PyTorch cache initialization call where if the USER env variable isn't set it throws an OSError, which in Leafcutter differential splicing happens when the multiprocessing workers are being called and the cache directory paths are being constructed, e.g.

Test Process LEAFCUTTER_DIFFERENTIALSPLICING │ │ │ │ Test [8fb16eda] 'homo_sapiens - bam - differential splicing' FAILED (19.617s) │ │ │ │ Assertion failed: │ │ │ │ 2 of 2 assertions failed │ │ │ │ Nextflow stdout: │ │ │ │ ERROR ~ Error executing process > 'LEAFCUTTER_DIFFERENTIALSPLICING (test_ds)' │ │ │ │ Caused by: │ │ Process `LEAFCUTTER_DIFFERENTIALSPLICING (test_ds)` terminated with an error exit status (1) │ │ │ │ │ │ Command executed: │ │ │ │ leafcutter-ds \ │ │ test_ds_perind_numers.counts.gz \ │ │ groups_file.txt \ │ │ --output_prefix test_ds_results \ │ │ --num_threads 4 \ │ │ --min_samples_per_group 2 --min_samples_per_intron 2 │ │ │ │ Command exit status: │ │ 1 │ │ │ │ Command output: │ │ Loading counts from test_ds_perind_numers.counts.gz │ │ Loading metadata from groups_file.txt │ │ Settings: Namespace(counts_file='test_ds_perind_numers.counts.gz', groups_file='groups_file.txt', baseline_group='Control', │ │ output_prefix='test_ds_results', max_cluster_size=inf, min_samples_per_intron=2, min_samples_per_group=2, min_coverage=20, min_unique_vals=10, │ │ exon_file=None, init='brr', timeit=False, num_threads=4) │ │ Running differential splicing analysis... │ │ │ │ Command error: │ │ optimizer = MyLBFGS(params, **lbfgs_kwargs) #lr=0.05, max_iter=inner_iterations, tolerance_grad=1e-4, history_size = 20) │ │ File "/usr/local/lib/python3.13/site-packages/torch/optim/lbfgs.py", line 272, in __init__ │ │ super().__init__(params, defaults) │ │ ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^ │ │ File "/usr/local/lib/python3.13/site-packages/torch/optim/optimizer.py", line 408, in __init__ │ │ self.add_param_group(cast(dict, param_group)) │ │ ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ │ │ File "/usr/local/lib/python3.13/site-packages/torch/_compile.py", line 47, in inner │ │ import torch._dynamo │ │ File "/usr/local/lib/python3.13/site-packages/torch/_dynamo/__init__.py", line 13, in <module> │ │ from . import ( │ │ ...<6 lines>... │ │ ) │ │ File "/usr/local/lib/python3.13/site-packages/torch/_dynamo/aot_compile.py", line 17, in <module> │ │ from torch._dynamo.package import SystemInfo │ │ File "/usr/local/lib/python3.13/site-packages/torch/_dynamo/package.py", line 1173, in <module> │ │ DynamoCache = DiskDynamoCache(os.path.join(cache_dir(), "dynamo")) │ │ ~~~~~~~~~^^ │ │ File "/usr/local/lib/python3.13/site-packages/torch/_dynamo/package.py", line 1170, in cache_dir │ │ return cache_dir() │ │ File "/usr/local/lib/python3.13/site-packages/torch/_inductor/runtime/cache_dir_utils.py", line 17, in cache_dir │ │ os.environ["TORCHINDUCTOR_CACHE_DIR"] = cache_dir = default_cache_dir() │ │ ~~~~~~~~~~~~~~~~~^^ │ │ File "/usr/local/lib/python3.13/site-packages/torch/_inductor/runtime/cache_dir_utils.py", line 23, in default_cache_dir │ │ sanitized_username = re.sub(r'[\\/:*?"<>|]', "_", getpass.getuser()) │ │ ~~~~~~~~~~~~~~~^^ │ │ File "/usr/local/lib/python3.13/getpass.py", line 175, in getuser │ │ raise OSError('No username set in the environment') from e │ │ OSError: No username set in the environment │ │ """ │ │ │ │ The above exception was the direct cause of the following exception: │ │ │ │ Traceback (most recent call last): │ │ File "/usr/local/bin/leafcutter-ds", line 10, in <module> │ │ sys.exit(leafcutter_ds()) │ │ ~~~~~~~~~~~~~^^ │ │ File "/usr/local/lib/python3.13/site-packages/leafcutter/__main__.py", line 12, in leafcutter_ds │ │ run_path(str(script_pth), run_name="__main__") │ │ ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ │ │ File "<frozen runpy>", line 287, in run_path │ │ File "<frozen runpy>", line 98, in _run_module_code │ │ File "<frozen runpy>", line 88, in _run_code │ │ File "/usr/local/lib/python3.13/site-packages/leafcutter/differential_splicing/leafcutter_ds.py", line 128, in <module> │ │ res = differential_splicing(counts, meta["group"], confounders = confounders, max_cluster_size = args.max_cluster_size, │ │ min_samples_per_intron = args.min_samples_per_intron, min_samples_per_group = args.min_samples_per_group, min_coverage = args.min_coverage, init = │ │ args.init, device = "cpu", num_cores = args.num_threads, timeit = args.timeit) │ │ File "/usr/local/lib/python3.13/site-packages/leafcutter/differential_splicing/differential_splicing.py", line 230, in differential_splicing │ │ pool_results = list(pool.imap(task_task, _cluster_iter(), chunksize=max(1, len(cluster_ids) // (num_cores * 8)))) │ │ File "/usr/local/lib/python3.13/multiprocessing/pool.py", line 873, in next │ │ raise value │ │ OSError: No username set in the environment │

I was thinking I could potentially ask the main leafcutter-ds developer to set a fallback for os.environ['USER'] in the code to make it more container-friendly. But for now in the interim maybe we opt to keep PYTHONHASHSEED=0, omit CUBLAS_WORKSPACE_CONFIG=:4096:8, keep --env USER=nobody (could hypothetically be any string val, Pytorch just needs it set to something so just following Unix convention) in containerOptions, and include a clearer note in meta.yml about the purpose of these?

Happy to make these changes asap if you are in agreement, just let me know!

The more transparent pattern is to set in the bash with a default if it's not set.

export USER="\${USER:-nobody}" export PYTHONHASHSEED=0 leafcutter-ds \

I have implemented @mahesh-panchal's suggested pattern. Please let me know if there is anything else required to merge. Thank you both for the feedback!

Edit: I am seeing several failing checks for my latest commit 8333804, but these seem unrelated to the refactor and notably the failures are all related to DUCKDB_TABLE2PARQUET snapshot mismatches across all test profiles.. For example, for the nf-test \ x64 | singularity | 1 test:

Run NFT_WORKDIR=~ 🚀 nf-test 0.9.5 https://www.nf-test.com/ Please cite: https://doi.org/10.1093/gigascience/giaf130 (c) 2021 - 2026 Lukas Forer and Sebastian Schoenherr Load .nf-test/plugins/nft-anndata/0.4.1/nft-anndata-0.4.1.jar Load .nf-test/plugins/nft-bam/0.6.1/nft-bam-0.6.1.jar Load .nf-test/plugins/nft-csv/0.1.0/nft-csv-0.1.0.jar Load .nf-test/plugins/nft-compress/0.1.0/nft-compress-0.1.0.jar Load .nf-test/plugins/nft-fastq/0.1.0/nft-fastq-0.1.0.jar Load .nf-test/plugins/nft-utils/0.0.9/nft-utils-0.0.9.jar Load .nf-test/plugins/nft-vcf/1.0.7/nft-vcf-1.0.7.jar nf-test runs in CI mode. Test Process ANGSD_DOSAF Test [5e64d21f] 'angsd - GL 1 - doSAF 1' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-5e64d21f7d64ffcb3f8e7e3193366a29.nf` [pensive_legentil] DSL2 - revision: 4bcd289e53 > Pulling Singularity image https://depot.galaxyproject.org/singularity/angsd:0.940--h13024bc_4 [cache /home/runner/work/modules/modules/.singularity/depot.galaxyproject.org-singularity-angsd-0.940--h13024bc_4.img] > [df/30feba] Submitted process > ANGSD_DOSAF (FIN) PASSED (15.793s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Process BISMARK_ALIGN Test [6e05a7f7] 'bowtie2 | paired-end | sarscov2 genome [fasta]' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-6e05a7f7c8d0af067b53e3954e150b6d.nf` [tiny_gutenberg] DSL2 - revision: 3ebdd28580 > WARN: Unknown directive `params` for process `BISMARK_GENOMEPREPARATION` > WARN: Unknown directive `params` for process `BISMARK_ALIGN` > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bd/bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-bd-bddea334e6ccbce005ce540214747acf822b040185d2198220dcfbb4b258c331-data.img] > [6c/3f3545] Submitted process > BISMARK_GENOMEPREPARATION (BismarkIndex/genome.fasta) > [83/99c9d7] Submitted process > BISMARK_ALIGN (test) PASSED (12.581s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Process DUCKDB_TABLE2PARQUET Test [c3b78b2c] 'csv - stub' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-c3b78b2c31a37dfdda2803f306594bc6.nf` [loquacious_sammet] DSL2 - revision: 35f4d8c2b9 > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/68/68261e24307fdf80b9988d6fd13cf3551735e6dc0e7e38003259f7d8efa84cdb/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-68-68261e24307fdf80b9988d6fd13cf3551735e6dc0e7e38003259f7d8efa84cdb-data.img] > [21/941646] Submitted process > DUCKDB_TABLE2PARQUET (test) java.lang.RuntimeException: Different Snapshot: --- /tmp/expected12306652735755230492json 2026-07-30 15:31:25.890398238 +0000 +++ /tmp/found8756876436986920248json 2026-07-30 15:31:25.891459980 +0000 @@ -1,20 +1,5 @@ [ { - "0": [ - [ - { - "id": "test" - }, - "test.parquet:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "DUCKDB_TABLE2PARQUET", - "duckdb", - "1.5.5" - ] - ], "parquet": [ [ { FAILED (6.14s) Assertion failed: 1 of 2 assertions failed Nextflow stdout: N E X T F L O W ~ version 25.10.2 Launching `/home/runner/work/modules/modules/.nf-test-c3b78b2c31a37dfdda2803f306594bc6.nf` [loquacious_sammet] DSL2 - revision: 35f4d8c2b9 Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/68/68261e24307fdf80b9988d6fd13cf3551735e6dc0e7e38003259f7d8efa84cdb/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-68-68261e24307fdf80b9988d6fd13cf3551735e6dc0e7e38003259f7d8efa84cdb-data.img] [21/941646] Submitted process > DUCKDB_TABLE2PARQUET (test) Nextflow stderr: Nextflow 26.04.6 is available - Please consider updating your version to it Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Process FGUMI_EXTRACT Test [ad3f3ca0] 'homo_sapiens - [fastq1, fastq2]' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-ad3f3ca0272bb9684ee513822a93bfef.nf` [angry_avogadro] DSL2 - revision: ce97306aba > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/64/64e8f594b6f0dd879bc5abbe4ca70b6b761e1920e407d9e1c7d27b89004aac34/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-64-64e8f594b6f0dd879bc5abbe4ca70b6b761e1920e407d9e1c7d27b89004aac34-data.img] > [8a/f67cef] Submitted process > FGUMI_EXTRACT (test) PASSED (7.103s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Process FGUMI_SIMPLEXMETRICS Test [8b936acc] 'homo_sapiens - grouped bam - stub' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-8b936acccaf2535dcea2923ebc102380.nf` [irreverent_kilby] DSL2 - revision: 9fa204a04e > [88/9ecde4] Submitted process > FGUMI_SIMPLEXMETRICS (test) PASSED (5.12s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Process HMMER_ESLSFETCHINDEX Test [eba2dea3] 'sarscov2 - fasta - stub' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-eba2dea3132534a1882290a6b1163ea8.nf` [elated_murdock] DSL2 - revision: b8c738c3b8 > Pulling Singularity image https://depot.galaxyproject.org/singularity/hmmer:3.4--hb6cb901_4 [cache /home/runner/work/modules/modules/.singularity/depot.galaxyproject.org-singularity-hmmer-3.4--hb6cb901_4.img] > [0f/529b53] Submitted process > HMMER_ESLSFETCHINDEX (test) PASSED (25.618s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Process TAR Test [7c38ef1d] 'sarscov2 - genome - db - kraken2 - .gz' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-7c38ef1def83f33981fdaf869bc19bce.nf` [fervent_albattani] DSL2 - revision: f18e5b15dc > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-52-52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa-data.img] > [59/f6b6a1] Submitted process > UNTAR (kraken2.tar.gz) > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/98/98946ea8217c35441352a94f3e0cd1dfa24137c323e8b0f5dfcb3123b465d0b1/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-98-98946ea8217c35441352a94f3e0cd1dfa24137c323e8b0f5dfcb3123b465d0b1-data.img] > [dc/ed3da4] Submitted process > TAR (test) PASSED (6.991s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. Test Subworkflow FASTQ_ALIGN_DEDUP_BISMARK Test [650a6bfe] 'Params: bismark paired-end | cytosine_report' > Nextflow 26.04.6 is available - Please consider updating your version to it > N E X T F L O W ~ version 25.10.2 > Launching `/home/runner/work/modules/modules/.nf-test-650a6bfed4b9797d6c7a7fe77946f6e3.nf` [exotic_faggin] DSL2 - revision: a06673991a > [8b/ac253c] Submitted process > BOWTIE2 (Bowtie2_Index.tar.gz) > [d1/2b4ace] Submitted process > HISAT2 (Hisat2_Index.tar.gz) > [d7/237ec6] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_ALIGN (test) > [b6/ac7ace] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_DEDUPLICATE (test) > [d7/b6a8d6] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_METHYLATIONEXTRACTOR (test) > Pulling Singularity image https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e9/e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859/data [cache /home/runner/work/modules/modules/.singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-e9-e994bf4eb3731150511a14f5706b7bdfd64df1b6d40898fff334286c027e0859-data.img] > [9f/28c498] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_REPORT (test) > [58/48d703] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_SUMMARY > [59/6565e5] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_COVERAGE2CYTOSINE (test) > [f7/ab0431] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:SAMTOOLS_SORT (test) > [bc/04756b] Submitted process > FASTQ_ALIGN_DEDUP_BISMARK:SAMTOOLS_INDEX (test) PASSED (12.713s) Snapshots: Obsolete snapshots can only be checked if all tests of a file are executed successful. FAILURE: Executed 8 tests in 92.073s (1 failed) Wrote TAP report to file test.tap Error: Process completed with exit code 1.

Just wanted to flag in case there is something broader going on with CI.

Thanks for flagging the duckdb issue btw, I fixed that in a separate PR after you highlighted it.

…nf for better transparency as recommended, update meta.yml with note on what is set and why

…best practices

… main.nf.test per nf-core docs best practices

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

JTL-lab and others added 3 commits July 7, 2026 16:19

feat (closes nf-core#7246): add new component: leafcutter/differentia…

eda8ca9

…lsplicing

fix: update main.nf.test for non-deterministic outputs, update snapsh…

58b53d4

…ot, set python environment hash variable

Merge branch 'master' into leafcutter/differentialsplicing

b92aec7

JTL-lab enabled auto-merge July 8, 2026 18:55

Merge branch 'master' into leafcutter/differentialsplicing

9a7cce3

SPPearce reviewed Jul 14, 2026

View reviewed changes

JTL-lab and others added 2 commits July 28, 2026 14:36

refactor, fix: incorporated cleaner syntax with sanitizeOutput for te…

e80e3b3

…sts, removed redundant --num_threads param in test config args, move container options set in main.nf to main.nf.test and add note in meta.yml

Merge branch 'master' into leafcutter/differentialsplicing

70047f9

JTL-lab mentioned this pull request Jul 28, 2026

new module: leafcutter/differential_splicing #7246

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JTL-lab added 2 commits July 28, 2026 23:56

fix: increase pullTimeout for singularity in test profile

d17cd67

refactor: add EOF space to nextflow.config for test profile

b28f3a7

SPPearce reviewed Jul 29, 2026

View reviewed changes

JTL-lab and others added 2 commits July 30, 2026 11:23

refactor: move environment variables from test config to module main.…

8333804

…nf for better transparency as recommended, update meta.yml with note on what is set and why

Merge branch 'master' into leafcutter/differentialsplicing

04cb43c

mahesh-panchal reviewed Jul 31, 2026

View reviewed changes

Comment thread modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config

JTL-lab added 2 commits August 1, 2026 13:25

docs: update tools section of meta.yml with args_id per nf-core docs …

b4a7945

…best practices

refactor: move ext.args from nextflow.config to be with test input in…

b048a4f

… main.nf.test per nf-core docs best practices

SPPearce reviewed Aug 2, 2026

View reviewed changes

Comment thread modules/nf-core/leafcutter/differentialsplicing/main.nf Outdated

Update modules/nf-core/leafcutter/differentialsplicing/main.nf

bea36d8

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

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