rename

broadinstitute · Jan 31, 2025 · 328ec9a · 328ec9a
1 parent c664618
commit 328ec9a
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
@@ -164,7 +164,6 @@ workflow ATAC {
     if (peak_calling) {
       call PeakCalling {
         input:
-          bam = BWAPairedEndAlignment.bam_aligned_output,
           annotations_gtf = annotations_gtf,
           metrics_h5ad = CreateFragmentFile.Snap_metrics,
           chrom_sizes = chrom_sizes,
@@ -793,8 +792,8 @@ task PeakCalling {
           atac_data_mod.uns[key] = atac_data_mod.uns[key].to_pandas()
 
     print("Write into h5ad file")
-    atac_data_mod.write_h5ad("~{output_base_name}.cellbybin.h5ad")
-    peak_matrix.write_h5ad("~{output_base_name}.cellbypeak.h5ad")
+    atac_data_mod.write_h5ad("~{base_name}.cellbybin.h5ad")
+    peak_matrix.write_h5ad("~{base_name}.cellbypeak.h5ad")
      
     CODE
   >>>