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adding cell calls as output of merge star outputs for calling cells #1361

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adding cell calls as output of merge star outputs for calling cells #1361

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3af3631
adding cell calls as output of merge star outputs for calling cells
ekiernan Aug 20, 2024
0b3ad39
fixing syntax
ekiernan Aug 20, 2024
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2 changes: 2 additions & 0 deletions pipelines/skylab/optimus/Optimus.wdl
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Expand Up @@ -246,6 +246,7 @@ workflow Optimus {
input_name_metadata_field = input_name_metadata_field,
annotation_file = annotations_gtf,
library_metrics = MergeStarOutputs.library_metrics,
cellbarcodes = MergeStarOutputs.outputbarcodes,
cell_metrics = CellMetrics.cell_metrics,
gene_metrics = GeneMetrics.gene_metrics,
sparse_count_matrix = MergeStarOutputs.sparse_counts,
Expand Down Expand Up @@ -281,6 +282,7 @@ workflow Optimus {
input_name_metadata_field = input_name_metadata_field,
annotation_file = annotations_gtf,
library_metrics = MergeStarOutputs.library_metrics,
cellbarcodes = MergeStarOutputs.outputbarcodes,
cell_metrics = CellMetrics.cell_metrics,
gene_metrics = GeneMetrics.gene_metrics,
sparse_count_matrix = MergeStarOutputs.sparse_counts,
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3 changes: 3 additions & 0 deletions tasks/skylab/H5adUtils.wdl
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Expand Up @@ -16,6 +16,7 @@ task OptimusH5adGeneration {
String? input_name_metadata_field
# gene annotation file in GTF format
File annotation_file
File? cellbarcodes
File? library_metrics
# the file "merged-cell-metrics.csv.gz" that contains the cellwise metrics
File cell_metrics
Expand Down Expand Up @@ -172,6 +173,8 @@ task SingleNucleusOptimusH5adOutput {
File gene_id_exon
# library-level metrics
File? library_metrics
# Cell calls from starsolo in TSV format
File? cellbarcodes

String pipeline_version

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1 change: 1 addition & 0 deletions tasks/skylab/StarAlign.wdl
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Expand Up @@ -619,6 +619,7 @@ task MergeStarOutput {
File? cell_reads_out = "~{input_id}.star_metrics.tar"
File? library_metrics="~{input_id}_library_metrics.csv"
File? mtx_files ="~{input_id}.mtx_files.tar"
File? outputbarcodes = "outputbarcodes.tsv"
}
}

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