feat(simpleaf): add simpleaf/multiplexquant module#11724
Open
an-altosian wants to merge 2 commits into
Open
Conversation
New module wrapping `simpleaf multiplex-quant` for sample-multiplexed single-cell libraries (10x Chromium Fixed RNA Profiling / Flex). The subcommand auto-resolves probe set + sample-BC TSV + cell-BC whitelist from the chemistry preset (e.g. `10x-flexv1-gex-3p` + `--organism human`), builds a piscem probe index when one is not supplied, maps reads, performs hierarchical cell+sample barcode correction, collates, and quantifies — emitting a count matrix whose barcodes are prefixed with the demultiplexed sample name. - Inputs: reads + chemistry, optional pre-built index + t2g, optional probe-set / sample-BC TSV / cell-BC whitelist overrides, resolution mode. - Outputs: af_map, af_quant, h5ad (optional), probe_t2g.tsv (optional), auto-built probe_index (optional), per-tool topic-channel versions for alevin-fry / piscem / simpleaf. - Container: Seqera Wave simpleaf 0.25.0 (bundles alevin-fry 0.15.0, piscem 0.20.0). Matches the simpleaf/index and simpleaf/quant modules on the parallel Wave-migration branch. Tests: - Real test using auto-resolution path with the singleplex Flex Kidney FASTQs from nf-core/test-datasets (chr22 subset). - Stub test exercising channel shape. nf-core modules lint: 0 failures.
SPPearce
requested changes
May 24, 2026
| tuple val(meta), path("${prefix}/probe_index/index") , emit: probe_index, optional: true | ||
| tuple val("${task.process}"), val('alevin-fry'), eval("alevin-fry --version | sed 's/alevin-fry //'"), topic: versions, emit: versions_alevin_fry | ||
| tuple val("${task.process}"), val('piscem'), eval("piscem --version | sed 's/piscem //'"), topic: versions, emit: versions_piscem | ||
| tuple val("${task.process}"), val('simpleaf'), eval("ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'"), topic: versions, emit: versions_simpleaf |
Contributor
There was a problem hiding this comment.
I think that the ALEVIN_FRY_HOME environment variable should be inherited by this part as well.
Suggested change
| tuple val("${task.process}"), val('simpleaf'), eval("ALEVIN_FRY_HOME=. simpleaf --version | sed 's/simpleaf //'"), topic: versions, emit: versions_simpleaf | |
| tuple val("${task.process}"), val('simpleaf'), eval("simpleaf --version | sed 's/simpleaf //'"), topic: versions, emit: versions_simpleaf |
Comment on lines
+77
to
+101
| // `simpleaf multiplex-quant` requires both reads and a chemistry preset (or, with extra | ||
| // ext.args, a --geometry override + --cell-bc-list). Only the mainstream case is enforced | ||
| // here; non-default geometries can still be set via ext.args. | ||
| def mappingArgs(chemistry, reads) { | ||
| if (!reads) error "Missing read files; could not proceed." | ||
| if (!chemistry) error "Missing chemistry; could not proceed." | ||
|
|
||
| def (forward, reverse) = reads.collate(2).transpose() | ||
| return """--chemistry ${chemistry} \\ | ||
| --reads1 ${forward.join(',')} \\ | ||
| --reads2 ${reverse.join(',')}""" | ||
| } | ||
|
|
||
| // Build optional reference-override flags. With none of these set, simpleaf auto-downloads | ||
| // a probe set + sample BC TSV based on the chemistry preset and (if also provided in ext.args) | ||
| // `--organism`. Any combination of overrides is allowed. | ||
| def referenceArgs(index, probe_set, sample_bc_list, cell_bc_list, t2g_map) { | ||
| def parts = [] | ||
| if (index) parts << "--index ${index}" | ||
| if (probe_set) parts << "--probe-set ${probe_set}" | ||
| if (sample_bc_list) parts << "--sample-bc-list ${sample_bc_list}" | ||
| if (cell_bc_list) parts << "--cell-bc-list ${cell_bc_list}" | ||
| if (t2g_map) parts << "--t2g-map ${t2g_map}" | ||
| return parts.join(' \\\n ') | ||
| } |
Contributor
There was a problem hiding this comment.
This is very non-standard, compared to just doing them one at a time.
| def mapping_args = mappingArgs(chemistry, reads) | ||
| def reference_args = referenceArgs(index, probe_set, sample_bc_list, cell_bc_list, t2g_map) | ||
|
|
||
| meta = meta2 + meta3 + meta |
Contributor
There was a problem hiding this comment.
Why are you doing this? We just take the first meta. I think this is pipeline-specific.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds a new
simpleaf/multiplexquantmodule wrappingsimpleaf multiplex-quantfor sample-multiplexed single-cell libraries (10x Chromium Fixed RNA Profiling / Flex). End-to-end: auto-resolves probe set + sample-BC TSV from a chemistry preset, optionally builds a piscem probe index, maps reads withpiscem map-sc, performs hierarchical cell-BC + sample-BC correction, collates, and quantifies — emitting barcodes prefixed by demultiplexed sample name.alevin-fry,piscem,simpleaf),process_mediumlabel, stub block, meta-merge across input channels.(meta, chemistry, reads),(meta2, index, t2g_map),(meta3, probe_set, sample_bc_list, cell_bc_list),resolution. The middle two channels are fully optional ([]for any element) — empty inputs fall back to chemistry-preset auto-resolution.simpleaf 0.25.0/piscem 0.20.0/alevin-fry 0.15.0viacommunity.wave.seqera.io/library/simpleaf:0.25.0--b9f96d8b71a01864.Validation
nf-test:flex - auto(end-to-end via Wave container) andflex - auto - stubpass locally on Docker.Test plan
nf-test test modules/nf-core/simpleaf/multiplexquant/tests/main.nf.test --profile dockerpassesnf-core modules lint simpleaf/multiplexquantpasses (expected Wave-container lint warnings as in feat(simpleaf): bump to 0.25.0 with Seqera Wave container and topic-channel versions #11696)