added csi_index to atac

broadinstitute · Jan 21, 2025 · 0cf1ab7 · 0cf1ab7
1 parent 256b324
commit 0cf1ab7
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/pipelines/skylab/paired_tag/PairedTag.wdl b/pipelines/skylab/paired_tag/PairedTag.wdl
@@ -33,7 +33,7 @@ workflow PairedTag {
         Boolean count_exons = false
         File gex_whitelist = if cloud_provider == "gcp" then "gs://gcp-public-data--broad-references/RNA/resources/arc-v1/737K-arc-v1_gex.txt" else "https://datasetpublicbroadref.blob.core.windows.net/dataset/RNA/resources/arc-v1/737K-arc-v1_gex.txt?sv=2020-04-08&si=prod&sr=c&sig=DQxmjB4D1lAfOW9AxIWbXwZx6ksbwjlNkixw597JnvQ%3D"
 
-        String? soloMultiMappers = "Uniform"
+        String? soloMultiMappers = "EM"
         # ATAC inputs
         # Array of input fastq files
         Array[File] atac_r1_fastq
@@ -153,6 +153,7 @@ workflow PairedTag {
     }
 
     File atac_fragment_out = select_first([ParseBarcodes.atac_fragment_tsv,Atac_preindex.fragment_file])
+    File atac_fragment_index_out = select_first([ParseBarcodes.atac_fragment_tsv_tbi,Atac_preindex.fragment_file_index])
     File atac_h5ad_out = select_first([ParseBarcodes.atac_h5ad_file, Atac_preindex.snap_metrics])
 
     output {
@@ -164,6 +165,7 @@ workflow PairedTag {
         File fragment_file_atac = atac_fragment_out
         File snap_metrics_atac = atac_h5ad_out
         File atac_library_final = Atac_preindex.library_metrics_file
+        File fragment_file_index_atac = atac_fragment_index_out
 
         # optimus outputs
         File genomic_reference_version_gex = Optimus.genomic_reference_version