From 54f3e3c07d444a95ab3198b5efff5cf25b18889b Mon Sep 17 00:00:00 2001 From: remomomo Date: Thu, 19 May 2022 16:34:22 +0200 Subject: [PATCH] switched to using ln -s -r instead of absolute paths --- Snakefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Snakefile b/Snakefile index 8bd31b9..d91b4ce 100644 --- a/Snakefile +++ b/Snakefile @@ -80,7 +80,7 @@ rule link_genotypes: run: if not os.path.isdir('data/genotypes'): os.makedirs('data/genotypes') - shell('ln -s "$(readlink -f {input.bim})" {output.bim} && ln -s "$(readlink -f {input.fam})" {output.fam} && ln -s "$(readlink -f {input.bed})" {output.bed}') + shell('ln -s -r "{input.bim}" {output.bim} && ln -s -r "{input.fam}" {output.fam} && ln -s -r "{input.bed}" {output.bed}') rule link_reference: input: @@ -90,7 +90,7 @@ rule link_reference: run: if not os.path.isdir('data/reference'): os.makedirs('data/reference') - shell('ln -s "$(readlink -f {input})" {output}') + shell('ln -s -r "{input}" {output}') rule link_gene_annotation: input: @@ -100,7 +100,7 @@ rule link_gene_annotation: run: if not os.path.isdir('data/reference'): os.makedirs('data/reference') - shell('ln -s "$(readlink -f {input})" {output}') + shell('ln -s -r "{input}" {output}') rule link_all: # checks if all the input files are present and links some of them to the working directory