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Improve celltype-specific rankgenesgroups implementation #217

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14 changes: 5 additions & 9 deletions subworkflows/local/per_group.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,32 +4,28 @@ include { LIANA_RANKAGGREGATE } from '../../modules/local/liana/rankaggregate

workflow PER_GROUP {
take:
ch_h5ad_both // channel: [ integration, h5ad ]
ch_h5ad_with_neighbors // channel: [ integration, h5ad ]
ch_h5ad_no_neighbors // channel: [ merged, h5ad ]
ch_h5ad_with_neighbors // channel: [ meta, h5ad ], anndata objects with neighbors, one per embedding and annotation
ch_h5ad_no_neighbors // channel: [ meta, h5ad ], anndata objects without neighbors, one per annotation

main:
ch_versions = Channel.empty()
ch_uns = Channel.empty()
ch_multiqc_files = Channel.empty()

ch_with_neighbors = ch_h5ad_both.mix(ch_h5ad_with_neighbors)
ch_no_neighbors = ch_h5ad_both.mix(ch_h5ad_no_neighbors)

SCANPY_PAGA(ch_with_neighbors)
SCANPY_PAGA(ch_h5ad_with_neighbors)
ch_versions = ch_versions.mix(SCANPY_PAGA.out.versions)
// ch_obsp = ch_obsp.mix(SCANPY_PAGA.out.obsp)
ch_uns = ch_uns.mix(SCANPY_PAGA.out.uns)
ch_multiqc_files = ch_multiqc_files.mix(SCANPY_PAGA.out.multiqc_files)

if (!params.skip_liana) {
LIANA_RANKAGGREGATE(ch_no_neighbors)
LIANA_RANKAGGREGATE(ch_h5ad_no_neighbors)
ch_versions = ch_versions.mix(LIANA_RANKAGGREGATE.out.versions)
ch_uns = ch_uns.mix(LIANA_RANKAGGREGATE.out.uns)
}

if (!params.skip_rankgenesgroups) {
SCANPY_RANKGENESGROUPS(ch_no_neighbors)
SCANPY_RANKGENESGROUPS(ch_h5ad_no_neighbors)
ch_versions = ch_versions.mix(SCANPY_RANKGENESGROUPS.out.versions)
ch_uns = ch_uns.mix(SCANPY_RANKGENESGROUPS.out.uns)
ch_multiqc_files = ch_multiqc_files.mix(SCANPY_RANKGENESGROUPS.out.multiqc_files)
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15 changes: 12 additions & 3 deletions workflows/scdownstream.nf
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Expand Up @@ -153,10 +153,19 @@ workflow SCDOWNSTREAM {
ch_versions = ch_versions.mix(PSEUDOBULKING.out.versions)
}

ch_h5ad_both = CLUSTER.out.h5ad_clustering.map { meta, h5ad -> [meta + [obs_key: "${meta.id}_leiden"], h5ad] }

PER_GROUP(
CLUSTER.out.h5ad_clustering.map { meta, h5ad -> [meta + [obs_key: "${meta.id}_leiden"], h5ad] },
CLUSTER.out.h5ad_neighbors.map { meta, h5ad -> [meta + [obs_key: grouping_col], h5ad] },
ch_label_grouping.map { meta, h5ad -> [meta + [obs_key: grouping_col], h5ad] },
// Run on each clustering resolution for each embedding
ch_h5ad_both.mix(
// And on the label column for each embedding
CLUSTER.out.h5ad_neighbors.map { meta, h5ad -> [meta + [obs_key: grouping_col], h5ad] }
),
// Run on each clustering (there is one clustering per embedding and resolution)
ch_h5ad_both.mix(
// And on the label column
ch_label_grouping.map { meta, h5ad -> [meta + [obs_key: grouping_col], h5ad] }
),
)
ch_versions = ch_versions.mix(PER_GROUP.out.versions)
ch_uns = ch_uns.mix(PER_GROUP.out.uns)
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