From 1416a55e40bdf426f2112878f6bb468af3722cf2 Mon Sep 17 00:00:00 2001 From: Bilal Shaikh Date: Tue, 4 Jun 2024 12:52:54 -0400 Subject: [PATCH 1/2] fix: use derived input for star_index the file path for the -sjdbGTFfile parameter was hardcoded to 'resources/genome.gtf' which causes execution to fail due to missing files on remote execution environments without a shared filesystem (such as kubernetes) This derives the filepath correctly from the input property to fix this issue --- workflow/rules/ref.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk index 9be480ba..8ee0fd6b 100644 --- a/workflow/rules/ref.smk +++ b/workflow/rules/ref.smk @@ -63,7 +63,7 @@ rule star_index: directory("resources/star_genome"), threads: 4 params: - extra="--sjdbGTFfile resources/genome.gtf --sjdbOverhang 100", + extra= lambda wc, input: f'--sjdbGTFfile {input.annotation} --sjdbOverhang 100', log: "logs/star_index_genome.log", cache: True From a900e727332afae956b5bf3689c96a804a5bd2a4 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 5 Jun 2024 17:10:35 +0200 Subject: [PATCH 2/2] chore: make the formatter happy --- workflow/rules/ref.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk index 8ee0fd6b..685c49b2 100644 --- a/workflow/rules/ref.smk +++ b/workflow/rules/ref.smk @@ -63,7 +63,7 @@ rule star_index: directory("resources/star_genome"), threads: 4 params: - extra= lambda wc, input: f'--sjdbGTFfile {input.annotation} --sjdbOverhang 100', + extra=lambda wc, input: f"--sjdbGTFfile {input.annotation} --sjdbOverhang 100", log: "logs/star_index_genome.log", cache: True