Ewing cell typing part 3 #134
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jashapiro
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Mar 7, 2025
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This looks good, and I overall like your approach. I suggested a change to get the library ids with groovy instead though, as it adds a bit more flexibility if file names change for some reason (like your change to not compressing).
I also don't think you need to filter both input channels, but I do think maybe it makes sense to filter in the main workflow? I can't decide, to be honest.
| @@ -18,6 +18,7 @@ params{ | |||
| cell_type_ewings_msigdb_list = 'https://raw.githubusercontent.com/AlexsLemonade/OpenScPCA-analysis/refs/tags/v0.2.2/analyses/cell-type-ewings/references/msigdb-gene-sets.tsv' | |||
| cell_type_ewings_ews_high_list = 'https://raw.githubusercontent.com/AlexsLemonade/OpenScPCA-analysis/refs/tags/v0.2.2/analyses/cell-type-ewings/references/gene_signatures/aynaud-ews-targets.tsv' | |||
| cell_type_ewings_ews_low_list = 'https://raw.githubusercontent.com/AlexsLemonade/OpenScPCA-analysis/refs/tags/v0.2.2/analyses/cell-type-ewings/references/gene_signatures/wrenn-nt5e-genes.tsv' | |||
| cell_type_ewings_marker_gene_file = 'https://raw.githubusercontent.com/AlexsLemonade/OpenScPCA-analysis/refs/tags/v0.2.2/analyses/cell-type-ewings/references/gene_signatures/tumor-cell-state-markers.tsv' | |||
| cell_type_ewings_marker_gene_file = 'https://raw.githubusercontent.com/AlexsLemonade/OpenScPCA-analysis/refs/tags/v0.2.2/analyses/cell-type-ewings/references/tumor-cell-state-markers.tsv' | |||
| cell_type_ewings_auc_thresholds_file = "${projectDir}/modules/cell-type-ewings/resources/auc-thresholds.tsv" | |||
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I can't quite decide if this file should be a parameter, but I think it is fine to leave it as one.
| // combine aucell and gene set output with consensus cell types | ||
| assign_ch = ewing_aucell.out | ||
| // join by sample ID and project ID | ||
| .join(consensus_ch, by: [0, 1]) // sample id, project id, aucell, mean exp, consensus, consensus gene exp |
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Join drops non-matches, which is why we shouldn't need to pre-filter the consensus_ch
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
jashapiro
reviewed
Mar 11, 2025
jashapiro
reviewed
Mar 11, 2025
| @@ -4,7 +4,7 @@ | |||
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| process ewing_aucell { | |||
| container params.cell_type_ewing_container | |||
| tag "${project_id}" | |||
| tag "${sample_id}" | |||
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Very minor, but can an you also update this in cell-type-consensus?
jashapiro
reviewed
Mar 11, 2025
Co-authored-by: Joshua Shapiro <josh.shapiro@ccdatalab.org>
jashapiro
reviewed
Mar 11, 2025
modules/cell-type-ewings/main.nf
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| path(celltype_assignment_output_files) | ||
| script: | ||
| library_ids = aucell_files.collect{(it.name =~ /SCPCL\d{6}/)[0]} | ||
| celltype_assignment_output_files = library_ids.collect{"${it}_ewing-aucell-results.tsv"} |
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My bad, again.
Suggested change
| celltype_assignment_output_files = library_ids.collect{"${it}_ewing-aucell-results.tsv"} | |
| celltype_assignment_output_files = library_ids.collect{"${it}_ewing-celltype-assignments.tsv"} |
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Closes #129
This PR adds running the cell type assignment script to the
cell-type-ewingsmain workflow and should be the last PR to complete that module.cell-type-consensusmodule as input. I chose to filter to the correct samples inmain.nfin the root of this repo so that the Ewing module only takes in the correct samples rather than everything. Are we okay with this choice or would we prefer to filter within the Ewing module workflow?