From ff870d40b303cae174040269b712c06089c67db6 Mon Sep 17 00:00:00 2001
From: Zachary Nolen <zachary.nolen@biol.lu.se>
Date: Mon, 30 Sep 2024 11:06:03 +0200
Subject: [PATCH] Make a param with the input file order list for bamlists

This will force a rerun of the rule. I am not quite sure why it wouldn't before. The code should change if input order changes, but maybe Snakemake doesn't look inside input list expansions when determining code changes?
---
 workflow/rules/3.0_genotype_likelihoods.smk | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/workflow/rules/3.0_genotype_likelihoods.smk b/workflow/rules/3.0_genotype_likelihoods.smk
index e6b78ad..3041608 100644
--- a/workflow/rules/3.0_genotype_likelihoods.smk
+++ b/workflow/rules/3.0_genotype_likelihoods.smk
@@ -19,10 +19,14 @@ rule angsd_makeBamlist:
         "logs/datasets/{dataset}/bamlists/{dataset}.{ref}_{population}{dp}.log",
     container:
         shell_container
+    params:
+        sampord=lambda w, input: f"{input.bams}",
     shell:
         """
-        (readlink -f {input.bams} > {output}
-        truncate -s -1 {output}) 2> {log}
+        (
+        echo "BAM order: {params.sampord}" > {log}
+        readlink -f {input.bams} > {output} 2>> {log}
+        truncate -s -1 {output}) 2>> {log}
         """