From 0121447aa1ec0ac1464217f367e80bcd53138dc0 Mon Sep 17 00:00:00 2001
From: Lucas Czech <luc.czech@gmail.com>
Date: Wed, 27 Nov 2024 02:49:54 +0100
Subject: [PATCH] Try fixing samtools merge numpy issue

---
 workflow/envs/samtools.yaml | 8 ++++----
 workflow/rules/mapping.smk  | 6 ++++++
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml
index 05e4deb..bf98624 100644
--- a/workflow/envs/samtools.yaml
+++ b/workflow/envs/samtools.yaml
@@ -4,9 +4,9 @@ channels:
   - bioconda
 dependencies:
   # Python
-  # - python ==3.12
-  # - pandas ==2.2.2
-  # - numpy  ==2.0.0
+  - python ==3.12
+  - pandas ==2.2.2
+  - numpy  ==2.0.0
   # Tools
   - bioconda::samtools ==1.20
-  # - snakemake-wrapper-utils ==0.6.2
+  - snakemake-wrapper-utils ==0.6.2
diff --git a/workflow/rules/mapping.smk b/workflow/rules/mapping.smk
index d7f282d..97d0d01 100644
--- a/workflow/rules/mapping.smk
+++ b/workflow/rules/mapping.smk
@@ -23,6 +23,8 @@ rule bam_index:
         "logs/mapping/samtools-index/_" + "{prefix}.log",
     group:
         "mapping_extra"
+    conda:
+        "../envs/samtools.yaml"
     wrapper:
         "0.51.3/bio/samtools/index"
 
@@ -143,6 +145,10 @@ rule merge_sample_unit_bams:
     threads: config["params"]["samtools"]["merge-threads"]
     log:
         "logs/mapping/samtools-merge/{sample}.log",
+    conda:
+        # Need our own env again, because of conflicting numpy and pandas version...
+        # Probably the cause of https://github.com/moiexpositoalonsolab/grenepipe/issues/58
+        "../envs/samtools.yaml"
     wrapper:
         "v3.13.6/bio/samtools/merge"