Mercurial > repos > dereeper > pangenome_explorer

diff Snakemake_files/Snakefile_pggb_heatmap_upset @ 14:5a5c9a6b047b draft

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author dereeper
date Tue, 10 Dec 2024 16:20:53 +0000
parents e42d30da7a74
children
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line diff
--- a/Snakemake_files/Snakefile_pggb_heatmap_upset	Thu May 30 20:07:55 2024 +0000
+++ b/Snakemake_files/Snakefile_pggb_heatmap_upset	Tue Dec 10 16:20:53 2024 +0000
@@ -53,7 +53,7 @@
         """
         cat outputs/genomes/*fasta >outputs/genomes/all_genomes.fa
         samtools faidx outputs/genomes/all_genomes.fa
-        reference=$(head -1 outputs/genomes/strains.txt | awk '{{print $2}}')
+        reference=$(head -1 outputs/genomes/all_genomes.fa | awk '{{print $2}}')
         pggb -i outputs/genomes/all_genomes.fa -o outputs/pggb_out -V $reference -m
         mv outputs/pggb_out/all_genomes.*smooth.final.gfa {output.gfa}
         mv outputs/pggb_out/all_genomes.*lay.draw.png {output.png1}