From 13d9cfcb5f2ec2d2bdfcde0061ead14ec943516b Mon Sep 17 00:00:00 2001 From: Yiming Yang Date: Mon, 18 Jul 2022 10:59:22 -0700 Subject: [PATCH] Fix cyclic dependency on cluster.output_h5ad used for both input and output variable name --- workflows/cumulus/cumulus.wdl | 6 +++--- workflows/cumulus/cumulus_tasks.wdl | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/cumulus/cumulus.wdl b/workflows/cumulus/cumulus.wdl index 92ccca71..20d4f257 100644 --- a/workflows/cumulus/cumulus.wdl +++ b/workflows/cumulus/cumulus.wdl @@ -386,8 +386,8 @@ workflow cumulus { backend = backend } - if (length(cluster.output_h5ad) > 0) { - scatter (focus_h5ad in cluster.output_h5ad) { + if (length(cluster.output_h5ad_file) > 0) { + scatter (focus_h5ad in cluster.output_h5ad_file) { String focus_prefix = basename(focus_h5ad, ".h5ad") if (perform_de_analysis) { @@ -493,7 +493,7 @@ workflow cumulus { File? output_aggr_zarr = aggregate_matrices.output_zarr File output_zarr = cluster.output_zarr File output_cluster_log = cluster.output_log - Array[File] output_h5ad = cluster.output_h5ad + Array[File] output_h5ad_file = cluster.output_h5ad_file Array[File] output_filt_xlsx = cluster.output_filt_xlsx Array[File] output_filt_plot = cluster.output_filt_plot Array[File] output_hvf_plot = cluster.output_hvf_plot diff --git a/workflows/cumulus/cumulus_tasks.wdl b/workflows/cumulus/cumulus_tasks.wdl index c5996ea3..a5233143 100644 --- a/workflows/cumulus/cumulus_tasks.wdl +++ b/workflows/cumulus/cumulus_tasks.wdl @@ -376,7 +376,7 @@ task run_cumulus_cluster { output { File output_zarr = "~{output_name}.zarr.zip" - Array[File] output_h5ad = glob("~{output_name}.*.h5ad") + Array[File] output_h5ad_file = glob("~{output_name}.*.h5ad") Array[File] output_filt_xlsx = glob("~{output_name}.*.filt.xlsx") Array[File] output_filt_plot = glob("~{output_name}.*.filt.*.pdf") Array[File] output_hvf_plot = glob("~{output_name}.*.hvf.pdf")