From 0d4f0108e205be974fe9370fecf5caa56d2dcee3 Mon Sep 17 00:00:00 2001 From: Sid Cox Date: Fri, 13 Dec 2024 11:00:33 -0500 Subject: [PATCH] remove bam_base_name from CreateFragments task --- pipelines/skylab/atac/atac.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl index 3290d22498..0a55334c15 100644 --- a/pipelines/skylab/atac/atac.wdl +++ b/pipelines/skylab/atac/atac.wdl @@ -625,7 +625,7 @@ task CreateFragmentFile { if peakcalling_bool: print("Peak calling starting...") - atac_data = snap.read("~{bam_base_name}.metrics.h5ad") + atac_data = snap.read("~{input_id}.metrics.h5ad") # Calculate and plot the size distribution of fragments print("Calculating fragment size distribution") @@ -706,7 +706,7 @@ task CreateFragmentFile { atac_data_mod.uns[key] = atac_data_mod.uns[key].to_pandas() print("Write into h5ad file") - atac_data_mod.write_h5ad("~{bam_base_name}.peaks.h5ad") + atac_data_mod.write_h5ad("~{input_id}.peaks.h5ad") print("test") CODE