added utils env

metagenlab · Apr 26, 2024 · 3a7e8cf · 3a7e8cf
1 parent c811b49
commit 3a7e8cf
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Showing 5 changed files with 8 additions and 23 deletions.
diff --git a/mess/workflow/envs/pigz.yml b/mess/workflow/envs/pigz.yml
diff --git a/mess/workflow/envs/sed.yml b/mess/workflow/envs/sed.yml
diff --git a/mess/workflow/envs/tar.yml b/mess/workflow/envs/tar.yml
diff --git a/mess/workflow/envs/curl.yml → mess/workflow/envs/utils.yml b/mess/workflow/envs/curl.yml → mess/workflow/envs/utils.yml
@@ -1,6 +1,9 @@
-name: curl
+name: utils
 channels:
   - conda-forge
   - defaults
 dependencies:
+  - tar >=1.34
+  - sed >=4.7
+  - pigz >=2.8
   - curl >=8.7.1
diff --git a/mess/workflow/rules/processing/reads.smk b/mess/workflow/rules/processing/reads.smk
@@ -107,7 +107,7 @@ if BAM:
             mem=str(config.resources.sml.mem) + "MB",
             time=config.resources.sml.time,
         conda:
-            os.path.join(dir.env, "sed.yml")
+            os.path.join(dir.env, "utils.yml")
         shell:
             """
             sed 's/ref/{params.seqname}/g' {input.maf} > {output}
@@ -247,7 +247,7 @@ if BAM:
             mem=str(config.resources.sml.mem) + "MB",
             time=config.resources.sml.time,
         conda:
-            os.path.join(dir.env, "curl.yml")
+            os.path.join(dir.env, "utils.yml")
         shell:
             """
             curl https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz \\
@@ -273,7 +273,7 @@ if BAM:
         log:
             os.path.join(dir.out.logs, "wget", "taxdump.log"),
         conda:
-            os.path.join(dir.env, "tar.yml")
+            os.path.join(dir.env, "utils.yml")
         shell:
             """
             tar -xzvf {input} -C {params.dir} &> {log}
@@ -381,7 +381,7 @@ rule compress_contig_fastqs:
         time=config.resources.sml.time,
     threads: config.resources.sml.cpu
     conda:
-        os.path.join(dir.env, "pigz.yml")
+        os.path.join(dir.env, "utils.yml")
     shell:
         """
         pigz -p {threads} {input}