feat: Salmon-tximport meta-wrapper pathvars update #4665
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📝 WalkthroughWalkthroughAdds a declarative Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Snakemake as SMK
participant MetaWrapper as MW
participant Tools
rect rgba(200,230,255,0.5)
note right of SMK: config + meta.pathvars resolved
User->>SMK: run workflow (module salmon_tximport)
SMK->>MW: expand rules with placeholders
end
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SMK->>Tools: salmon_decoy_sequences(inputs: <transcriptome_sequence>,<genome_sequence>)
Tools-->>SMK: gentrome, decoys -> saved under <resources>
SMK->>Tools: salmon_index_gentrome(inputs: <resources>/gentrome.fasta,decoys)
Tools-->>SMK: index files -> <resources>/salmon_gentrome_index/
SMK->>Tools: salmon_quant_reads(inputs: <reads_r1>,<reads_r2>, index:<resources>/salmon_gentrome_index/, gtf:<genome_annotation>)
Tools-->>SMK: per-sample quant outputs -> <results>/pseudo_mapping/{per}/...
SMK->>Tools: tximport(inputs: per-sample quant from <results>, tx2gene:<tx_to_gene>)
Tools-->>SMK: txi -> <results>/tximport/SummarizedExperimentObject.RDS
end
note over SMK: Logs written under <logs> paths
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Actionable comments posted: 2
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⛔ Files ignored due to path filters (8)
meta/bio/salmon_tximport/test/reads/S1.fastq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S1_R1.fq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S1_R2.fq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S2.fastq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S2_R1.fq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S2_R2.fq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S3.fastq.gzis excluded by!**/*.gzmeta/bio/salmon_tximport/test/reads/S4.fastq.gzis excluded by!**/*.gz
📒 Files selected for processing (8)
meta/bio/salmon_tximport/meta.yaml(1 hunks)meta/bio/salmon_tximport/meta_wrapper.smk(5 hunks)meta/bio/salmon_tximport/test/Snakefile(1 hunks)meta/bio/salmon_tximport/test/config.yaml(1 hunks)meta/bio/salmon_tximport/test/resources/genome.fasta.fai(1 hunks)meta/bio/salmon_tximport/test/resources/transcriptome.fasta(1 hunks)meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai(1 hunks)test_wrappers.py(1 hunks)
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test_wrappers.py
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🔇 Additional comments (7)
meta/bio/salmon_tximport/test/resources/transcriptome.fasta.fai (1)
1-2: LGTM: Test resource file is correctly formatted.The FASTA index file follows the standard
.faiformat and provides appropriate test data for the pathvars-based configuration system.meta/bio/salmon_tximport/test/resources/genome.fasta.fai (1)
1-1: LGTM: Genome index file is correctly formatted.The FASTA index file is properly structured and aligns with the new pathvars configuration for test resources.
meta/bio/salmon_tximport/test/config.yaml (1)
1-9: LGTM: Test configuration properly defines pathvars mappings.The pathvars configuration aligns with the schema defined in
meta.yamland provides appropriate test resource paths.test_wrappers.py (1)
1104-1104: LGTM: Test expectation updated to match new pathvars structure.The path correctly reflects the new results-prefixed output location defined in the meta-wrapper.
meta/bio/salmon_tximport/test/resources/transcriptome.fasta (1)
1-5: LGTM: Test sequences updated appropriately.The FASTA sequences have been updated and their lengths match the corresponding
.faiindex file entries (transcript1: 49bp, transcript2: 81bp).meta/bio/salmon_tximport/test/Snakefile (1)
6-13: LGTM: Configuration properly integrated into test workflow.The addition of
configfileand the block-stylemeta_wrapperwith explicitconfigsection correctly enables the pathvars-based configuration system.meta/bio/salmon_tximport/meta_wrapper.smk (1)
1-89: LGTM: Placeholder-based parameterization for salmon rules is well-implemented.The
salmon_decoy_sequences,salmon_index_gentrome, andsalmon_quant_readsrules correctly use pathvars placeholders (<transcriptome_sequence>,<genome_sequence>,<resources>,<logs>,<reads_r1>,<reads_r2>,<genome_annotation>,<per>) to enable user configuration without code modification.
1 participant
This PR tries to make salmon-tximport meta-wrapper accessible through
pathvars. Yet, I'd like to get some advice on how to proceed smoothly with theexpandkeyword and thepathvars. But the meta-wrapper wouldn't work if user does not modify the last rule : for now, I still list samples within theexpandfunction.QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
Tests