From 3a7e8cfd21a0e695f64008e8c4c4ad1911aa7927 Mon Sep 17 00:00:00 2001
From: farchaab <farid.chaabane@chuv.ch>
Date: Fri, 26 Apr 2024 11:51:05 +0200
Subject: [PATCH] added utils env

---
 mess/workflow/envs/pigz.yml                | 6 ------
 mess/workflow/envs/sed.yml                 | 6 ------
 mess/workflow/envs/tar.yml                 | 6 ------
 mess/workflow/envs/{curl.yml => utils.yml} | 5 ++++-
 mess/workflow/rules/processing/reads.smk   | 8 ++++----
 5 files changed, 8 insertions(+), 23 deletions(-)
 delete mode 100644 mess/workflow/envs/pigz.yml
 delete mode 100644 mess/workflow/envs/sed.yml
 delete mode 100644 mess/workflow/envs/tar.yml
 rename mess/workflow/envs/{curl.yml => utils.yml} (55%)

diff --git a/mess/workflow/envs/pigz.yml b/mess/workflow/envs/pigz.yml
deleted file mode 100644
index ad08a20..0000000
--- a/mess/workflow/envs/pigz.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: pigz
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - pigz >=2.8
diff --git a/mess/workflow/envs/sed.yml b/mess/workflow/envs/sed.yml
deleted file mode 100644
index 7ecbf80..0000000
--- a/mess/workflow/envs/sed.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: sed
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - sed >=4.7
diff --git a/mess/workflow/envs/tar.yml b/mess/workflow/envs/tar.yml
deleted file mode 100644
index 8f84537..0000000
--- a/mess/workflow/envs/tar.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: tar
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - tar >=1.34
diff --git a/mess/workflow/envs/curl.yml b/mess/workflow/envs/utils.yml
similarity index 55%
rename from mess/workflow/envs/curl.yml
rename to mess/workflow/envs/utils.yml
index bc8bf08..dfdc22e 100644
--- a/mess/workflow/envs/curl.yml
+++ b/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
index e04ecd5..9974c74 100644
--- 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}