From c70900f908b5da5a1372270e029af91426441042 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 11 Jun 2024 16:38:25 -0500
Subject: [PATCH] build: Update to use commity.wave.seqera.io

---
 modules/nf-core/bowtie/align/environment.yml  | 7 +++----
 modules/nf-core/bowtie/align/main.nf          | 2 +-
 modules/nf-core/bowtie/build/environment.yml  | 7 +++----
 modules/nf-core/samtools/view/environment.yml | 7 +++----
 modules/nf-core/samtools/view/main.nf         | 2 +-
 5 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml
index fb5d7c1ef12..b48471c1022 100644
--- a/modules/nf-core/bowtie/align/environment.yml
+++ b/modules/nf-core/bowtie/align/environment.yml
@@ -1,8 +1,7 @@
-name: bowtie_align
+name: bowtie_samtools
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::bowtie=1.3.0
-  - bioconda::samtools=1.16.1
+  - bioconda::bowtie=1.3.1
+  - bioconda::samtools=1.20
diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf
index 54af8c40728..35b80d2c26d 100644
--- a/modules/nf-core/bowtie/align/main.nf
+++ b/modules/nf-core/bowtie/align/main.nf
@@ -3,7 +3,7 @@ process BOWTIE_ALIGN {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "nf-core/modules/bowtie_align:bowtie_align--d797c0ccd2d330fd"
+    container "community.wave.seqera.io/library/bowtie_samtools:772b3bee982574e4"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/bowtie/build/environment.yml b/modules/nf-core/bowtie/build/environment.yml
index 3b6490b87e5..b48471c1022 100644
--- a/modules/nf-core/bowtie/build/environment.yml
+++ b/modules/nf-core/bowtie/build/environment.yml
@@ -1,8 +1,7 @@
-name: bowtie_build
+name: bowtie_samtools
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::bowtie=1.3.0
-  - bioconda::samtools=1.16.1
+  - bioconda::bowtie=1.3.1
+  - bioconda::samtools=1.20
diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
index f75f7c5e62a..1c255c63d7f 100644
--- a/modules/nf-core/samtools/view/environment.yml
+++ b/modules/nf-core/samtools/view/environment.yml
@@ -1,10 +1,9 @@
-name: samtools_view
+name: htslib_samtools
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  # renovate: datasource=conda depName=bioconda/samtools
-  - bioconda::samtools=1.20
   # renovate: datasource=conda depName=bioconda/htslib
   - bioconda::htslib=1.20
+  # renovate: datasource=conda depName=bioconda/samtools
+  - bioconda::samtools=1.20
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 3a42de1cf42..3f273468d5c 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -3,7 +3,7 @@ process SAMTOOLS_VIEW {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "nf-core/modules/samtools_view:samtools_view--033f764f39eb1f2d"
+    container "community.wave.seqera.io/library/htslib_samtools:1.20--11a4e6daa46930ec"
 
     input:
     tuple val(meta), path(input), path(index)