From 7d7f4c6bdfb295becc77fcfd9f60e439c24ac237 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Mon, 4 Nov 2024 13:48:07 -0500 Subject: [PATCH 1/2] Update nextflow option --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 57f00948..a8f81ab0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,7 +78,7 @@ profiles { standard { process.executor = 'local' docker.enabled = true - docker.userEmulation = true + docker.fixOwnership = true } // AWS batch profile with autoscaling disk batch { From 15010588030b04e2963a0d9008c53ba65c6857e0 Mon Sep 17 00:00:00 2001 From: Joshua Shapiro Date: Mon, 4 Nov 2024 13:52:14 -0500 Subject: [PATCH 2/2] increase cell count requirement --- modules/export-anndata.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/export-anndata.nf b/modules/export-anndata.nf index 89d1aa5d..2e8d94b8 100644 --- a/modules/export-anndata.nf +++ b/modules/export-anndata.nf @@ -61,7 +61,7 @@ workflow sce_to_anndata { // number of cells are stored in each metadata.json file .filter{ def cells = Utils.getMetaVal(file(it[3]), "${it[2]}_cells"); - cells == '' || cells > 1 // if no cell count, keep file for testing, otherwise require at least 2 cells + cells == '' || cells > 2 // if no cell count, keep file for testing, otherwise require at least 3 cells } // remove metadata.json file from tuple .map{it.dropRight(1)}