From e95a84a367e3ba26aa642dc0b8a15e6f23d5d349 Mon Sep 17 00:00:00 2001
From: tdurand <theo.durand@etu.uca.fr>
Date: Wed, 29 Jun 2022 09:27:16 +0200
Subject: [PATCH] Add better input on rule orthofinder parse and orthofinder
---
snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/snakefile b/snakefile
index a318519..dd3a91c 100644
--- a/snakefile
+++ b/snakefile
@@ -711,7 +711,7 @@ rule add_caz_to_gff:
rule orthofinder:
threads: get_threads("orthofinder", 10)
input:
- prot_files = expand(f"{output_dir}1_PROTEIN_SORTED/{{samples}}.fasta", samples = PROTEIN)
+ prot_files = expand(rules.rename_protein.output.sorted_protein, samples = PROTEIN)
params:
dir_prot = f"{output_dir}1_PROTEIN_SORTED/",
dir_out = f"{output_dir}7_ORTHOFINDER/",
@@ -745,7 +745,7 @@ rule orthofinder:
rule orthofinder_parse:
threads: get_threads("orthofinder_parse", 1)
input:
- orthogroups_table= f"{output_dir}7_ORTHOFINDER/Results_orthofinder/Orthogroups/Orthogroups.GeneCount.tsv"
+ orthogroups_table= rules.orthofinder.output.orthogroups_table
params:
strain_name = f"{{samples}}",
path_seq = f"{output_dir}7_ORTHOFINDER/Results_orthofinder/Orthogroup_Sequences/"
--
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