From 43966349e82228e008a5a84463a241ba588a02d3 Mon Sep 17 00:00:00 2001
From: Jorge Langa <6546145+jlanga@users.noreply.github.com>
Date: Mon, 15 Apr 2024 14:48:33 +0200
Subject: [PATCH] feat: update envs

---
 workflow/envs/fst.yml         | 14 ++++++--------
 workflow/envs/generic.yml     |  4 +---
 workflow/envs/hp.yml          | 12 +++++-------
 workflow/envs/mpileup.yml     |  8 +++-----
 workflow/envs/popoolation.yml | 10 ++++------
 workflow/envs/qc.yml          |  8 +++-----
 workflow/envs/raw.yml         |  4 +---
 workflow/envs/sync.yml        |  8 +++-----
 8 files changed, 26 insertions(+), 42 deletions(-)

diff --git a/workflow/envs/fst.yml b/workflow/envs/fst.yml
index b167c71..6ff54f8 100644
--- a/workflow/envs/fst.yml
+++ b/workflow/envs/fst.yml
@@ -1,13 +1,11 @@
-# Environment for fst subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - python>=3.5
-  - perl=5.22.0
-  - numpy=1.24.3
-  - pigz=2.6
-  - r-tidyverse=2.0.0
-  - r-argparse=2.2.2
+  - python =3.12.2
+  - perl =5.32.1
+  - numpy =1.26.4
+  - pigz =2.8
+  - r-tidyverse =2.0.0
+  - r-argparse =2.2.3
diff --git a/workflow/envs/generic.yml b/workflow/envs/generic.yml
index 5238b59..2841e13 100644
--- a/workflow/envs/generic.yml
+++ b/workflow/envs/generic.yml
@@ -1,8 +1,6 @@
-# Environment for generic subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - samtools=1.17.0
+  - samtools =1.19.2
diff --git a/workflow/envs/hp.yml b/workflow/envs/hp.yml
index d3499ec..d85ac40 100644
--- a/workflow/envs/hp.yml
+++ b/workflow/envs/hp.yml
@@ -1,12 +1,10 @@
-# Environment for hp subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - python>=3.5
-  - pigz=2.6
-  - r-tidyverse=2.0.0
-  - r-argparse=2.2.2
-  - numpy=1.24.3
+  - python =3.12.2
+  - pigz =2.8
+  - r-tidyverse =2.0.0
+  - r-argparse =2.2.3
+  - numpy =1.26.4
diff --git a/workflow/envs/mpileup.yml b/workflow/envs/mpileup.yml
index f81e07f..03199bf 100644
--- a/workflow/envs/mpileup.yml
+++ b/workflow/envs/mpileup.yml
@@ -1,10 +1,8 @@
-# Environment for mpileup subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - samtools=1.17.0
-  - python>=3
-  - perl=5.22.0
+  - samtools =1.19.2
+  - python =3.12.2
+  - perl =5.32.1
diff --git a/workflow/envs/popoolation.yml b/workflow/envs/popoolation.yml
index 14e8416..fbedb75 100644
--- a/workflow/envs/popoolation.yml
+++ b/workflow/envs/popoolation.yml
@@ -1,11 +1,9 @@
-# Environment for popoolation subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - perl=5.22.0
-  - pigz=2.6
-  - r-tidyverse=2.0.0
-  - r-argparse=2.2.2
+  - perl =5.32.1
+  - pigz =2.8
+  - r-tidyverse =2.0.0
+  - r-argparse =2.2.3
diff --git a/workflow/envs/qc.yml b/workflow/envs/qc.yml
index 4cc8a2f..541212e 100644
--- a/workflow/envs/qc.yml
+++ b/workflow/envs/qc.yml
@@ -1,10 +1,8 @@
-# Environment for qc subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - trimmomatic=0.36  # Greater than 0.36 breaks the process substitution trick
-  - gzip=1.12
-  - pigz=2.6
+  - trimmomatic =0.39
+  - gzip =1.13
+  - pigz =2.8
diff --git a/workflow/envs/raw.yml b/workflow/envs/raw.yml
index c71e91d..0cb21bc 100644
--- a/workflow/envs/raw.yml
+++ b/workflow/envs/raw.yml
@@ -1,8 +1,6 @@
-# Environment for raw subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - gzip=1.12
+  - gzip =1.13
diff --git a/workflow/envs/sync.yml b/workflow/envs/sync.yml
index 6ef0bf1..130e485 100644
--- a/workflow/envs/sync.yml
+++ b/workflow/envs/sync.yml
@@ -1,10 +1,8 @@
-# Environment for sync subworkflow
----
 channels:
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - perl=5.22.0
-  - pigz=2.6
-  - openjdk=20.0.0
+  - perl =5.32.1
+  - pigz =2.8
+  - openjdk =21.0.2