Try fixing samtools merge numpy issue

moiexpositoalonsolab · Nov 27, 2024 · 0121447 · 0121447
1 parent 4fc3386
commit 0121447
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git 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
@@ -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"