update environments

sequana · Dec 20, 2023 · de4f76d · de4f76d
1 parent 6b6c433
commit de4f76d
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Showing 2 changed files with 19 additions and 2 deletions.
diff --git a/environment.yml b/environment.yml
@@ -0,0 +1,19 @@
+name: mapper
+
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - bwa
+  - samtools
+  - pigz
+  - fastqc
+  - sambamba
+  - pip:
+    - sequana
+    - cutadapt
+    - atropos
+
+
diff --git a/sequana_pipelines/quality_control/tools.txt b/sequana_pipelines/quality_control/tools.txt
@@ -1,8 +1,6 @@
 - bwa
 - sambamba
 - samtools
-- kraken2
-- ktImportText
 - fastqc
 - pigz
 - cutadapt