From de93e7a9e2ae8468e443679c19973db900988df3 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 17:42:39 +0100
Subject: [PATCH 01/23] dysgu

---
 modules/nf-core/dysgu/environment.yml | 2 +-
 modules/nf-core/dysgu/main.nf         | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/dysgu/environment.yml b/modules/nf-core/dysgu/environment.yml
index f3b35f5ac4f..cbf7a7668df 100644
--- a/modules/nf-core/dysgu/environment.yml
+++ b/modules/nf-core/dysgu/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - dysgu
+  - dysgu=1.6.5
diff --git a/modules/nf-core/dysgu/main.nf b/modules/nf-core/dysgu/main.nf
index 6aa1deea958..00677d3782b 100644
--- a/modules/nf-core/dysgu/main.nf
+++ b/modules/nf-core/dysgu/main.nf
@@ -4,8 +4,8 @@ process DYSGU {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/dysgu:48830f55112c399e':
-        'community.wave.seqera.io/library/dysgu:faf71ac972284412' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3a8406b0443d7ed75cd1ff9a687b2f7dd6d30e5ce91d79a8e3c9372bebab5e19/data':
+        'community.wave.seqera.io/library/dysgu:1.6.5--69cfa1b1db5c2aec' }"
 
     input:
     tuple val(meta), path(input), path(index)

From f74b133064522805759ec6765e98971512cee94b Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 17:59:26 +0100
Subject: [PATCH 02/23] cellbender/merge

---
 modules/nf-core/cellbender/merge/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/cellbender/merge/main.nf b/modules/nf-core/cellbender/merge/main.nf
index 58a631e6e4d..f5d47b8a2ca 100644
--- a/modules/nf-core/cellbender/merge/main.nf
+++ b/modules/nf-core/cellbender/merge/main.nf
@@ -4,8 +4,8 @@ process CELLBENDER_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/cellbender:0.3.0--c4addb97ab2d83fe':
-        'community.wave.seqera.io/library/cellbender:0.3.0--41318a055fc3aacb' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/055d333b219227f029403ab8591440367f659968eced58b79bdb67c33f30d1e5/data':
+        'community.wave.seqera.io/library/cellbender:0.3.0--d6088f41c6eb0a0f' }"
 
     input:
     tuple val(meta), path(filtered), path(unfiltered), path(cellbender_h5)

From 1f719724a7c3eb1fcc1716cc686ff8f91241131f Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:03:48 +0100
Subject: [PATCH 03/23] annotsv/annotsv

---
 modules/nf-core/annotsv/annotsv/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/annotsv/annotsv/main.nf b/modules/nf-core/annotsv/annotsv/main.nf
index d6ef0cb03bc..95545b72604 100644
--- a/modules/nf-core/annotsv/annotsv/main.nf
+++ b/modules/nf-core/annotsv/annotsv/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_ANNOTSV {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     input:
     tuple val(meta), path(sv_vcf), path(sv_vcf_index), path(candidate_small_variants)

From a690e3504febb99d083a5e54d46aa9906a15a887 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:09:23 +0100
Subject: [PATCH 04/23] foldmason/easymsa

---
 modules/nf-core/foldmason/easymsa/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf
index b4870da0d10..ec7b86b8f59 100644
--- a/modules/nf-core/foldmason/easymsa/main.nf
+++ b/modules/nf-core/foldmason/easymsa/main.nf
@@ -4,7 +4,7 @@ process FOLDMASON_EASYMSA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-            'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03':
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/067e6389ab95497b753ba1deabaa6acbce25b99c8cfcf39c06d5c1af42fd7751/data':
             'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }"
 
 

From 34dbf17ed389daa02525bc3fda4d6df721a30cfa Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:13:39 +0100
Subject: [PATCH 05/23] scvitools/scar

---
 modules/nf-core/scvitools/scar/environment.yml | 3 ++-
 modules/nf-core/scvitools/scar/main.nf         | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/scvitools/scar/environment.yml b/modules/nf-core/scvitools/scar/environment.yml
index 42881dd7b8f..b40a1c25591 100644
--- a/modules/nf-core/scvitools/scar/environment.yml
+++ b/modules/nf-core/scvitools/scar/environment.yml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - conda-forge::scvi-tools=1.2.0
   - conda-forge::jaxlib=0.4.31
+  - conda-forge::scvi-tools=1.2.0
diff --git a/modules/nf-core/scvitools/scar/main.nf b/modules/nf-core/scvitools/scar/main.nf
index db9dcfc4215..6bdfcd86af6 100644
--- a/modules/nf-core/scvitools/scar/main.nf
+++ b/modules/nf-core/scvitools/scar/main.nf
@@ -4,7 +4,7 @@ process SCVITOOLS_SCAR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/scvi-tools:1.2.0--adbeb4160de8b08e':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b999caba5a5a6bc19bd324d9f1ac28e092a750140b453071956ebc304b7c4aa/data':
         'community.wave.seqera.io/library/scvi-tools:1.2.0--680d378b86801b8a' }"
 
     input:

From eb9e3f51416291ca1d69d0abc98667bb4770a152 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:19:33 +0100
Subject: [PATCH 06/23] scvitools/solo

---
 modules/nf-core/scvitools/solo/environment.yml | 3 ++-
 modules/nf-core/scvitools/solo/main.nf         | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/scvitools/solo/environment.yml b/modules/nf-core/scvitools/solo/environment.yml
index 42881dd7b8f..b40a1c25591 100644
--- a/modules/nf-core/scvitools/solo/environment.yml
+++ b/modules/nf-core/scvitools/solo/environment.yml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - conda-forge::scvi-tools=1.2.0
   - conda-forge::jaxlib=0.4.31
+  - conda-forge::scvi-tools=1.2.0
diff --git a/modules/nf-core/scvitools/solo/main.nf b/modules/nf-core/scvitools/solo/main.nf
index f4d7403087b..7e62d6afec3 100644
--- a/modules/nf-core/scvitools/solo/main.nf
+++ b/modules/nf-core/scvitools/solo/main.nf
@@ -6,7 +6,7 @@ process SCVITOOLS_SOLO {
     conda "${moduleDir}/environment.yml"
     container "${ task.ext.use_gpu ? 'docker.io/nicotru/scvitools-gpu:cuda-12' :
         workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/scvi-tools:1.2.0--adbeb4160de8b08e':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9b999caba5a5a6bc19bd324d9f1ac28e092a750140b453071956ebc304b7c4aa/data':
         'community.wave.seqera.io/library/scvi-tools:1.2.0--680d378b86801b8a' }"
 
     input:

From 3a6389b7eb8df931dd0793c2b40855133c01c00d Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:24:26 +0100
Subject: [PATCH 07/23] upp/align

---
 modules/nf-core/upp/align/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/upp/align/main.nf b/modules/nf-core/upp/align/main.nf
index 1b254ea4727..c0e4a8dac98 100644
--- a/modules/nf-core/upp/align/main.nf
+++ b/modules/nf-core/upp/align/main.nf
@@ -4,8 +4,8 @@ process UPP_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sepp_pigz:d72591720d0277b1':
-        'community.wave.seqera.io/library/sepp_pigz:ea6dbc7704a2e251' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/80/800667a716528cc6d655da1885d38f9d10385a184e0b1165985ae12034ff5f1d/data':
+        'community.wave.seqera.io/library/sepp_pigz:8f996974b960fc41' }"
 
     input:
     tuple val(meta) , path(fasta)

From 8f650fcc8a3eccee9334c14112c333360a2eec66 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:34:21 +0100
Subject: [PATCH 08/23] annotsv/installannotations

---
 modules/nf-core/annotsv/installannotations/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/annotsv/installannotations/main.nf b/modules/nf-core/annotsv/installannotations/main.nf
index 371e1bbf5b9..a56bdf7c345 100644
--- a/modules/nf-core/annotsv/installannotations/main.nf
+++ b/modules/nf-core/annotsv/installannotations/main.nf
@@ -4,8 +4,8 @@ process ANNOTSV_INSTALLANNOTATIONS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/annotsv:3.4.2--141a0ee560de1897' :
-        'community.wave.seqera.io/library/annotsv:3.4.2--010fa21247b5b64b' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b2/b202e030802ec909556961b542f15e0b37583755cebf08e899b3042a44f93ddb/data' :
+        'community.wave.seqera.io/library/annotsv:3.4.2--6e6cee83703bd24c' }"
 
     output:
     path "AnnotSV_annotations", emit: annotations

From a7a4bc659ce462cb835749df29de8106d1103f76 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:50:18 +0100
Subject: [PATCH 09/23] tcoffee/consensus

---
 modules/nf-core/tcoffee/consensus/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/tcoffee/consensus/main.nf b/modules/nf-core/tcoffee/consensus/main.nf
index 7205db903e5..d0567b8d01b 100644
--- a/modules/nf-core/tcoffee/consensus/main.nf
+++ b/modules/nf-core/tcoffee/consensus/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_CONSENSUS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/t-coffee_pigz:f47b85d70360f1a0':
-        'community.wave.seqera.io/library/t-coffee_pigz:6c9b2f8b97ee55e5' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5e/5e5c1c07cc0099dacea172348bc78f9a9baab592ce3ece89873703b9e963d269/data':
+        'community.wave.seqera.io/library/t-coffee_pigz:c98a6c87c62d9df6' }"
 
 
     input:

From 5d53f4a0391ee38f1a87c9e1ca51c1227dfdc4ed Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 18:53:36 +0100
Subject: [PATCH 10/23] untarfiles

---
 modules/nf-core/untarfiles/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/untarfiles/main.nf b/modules/nf-core/untarfiles/main.nf
index bae7838c49b..117b68954bd 100644
--- a/modules/nf-core/untarfiles/main.nf
+++ b/modules/nf-core/untarfiles/main.nf
@@ -10,8 +10,8 @@ process UNTARFILES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/grep_sed_tar:40b34489f8e82876' :
-        'community.wave.seqera.io/library/grep_sed_tar:16f6591cd62505b3' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/88/88e03525287eaeb8bb74114aaee2c67118c1cdcfb99ee52e3ddc71a1acce35d4/data' :
+        'community.wave.seqera.io/library/grep_sed_tar:db2951cd23a1ffde' }"
 
     input:
     tuple val(meta), path(archive)

From 7c559e57a1a8322f889e27585b4b72097dd95a02 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Sat, 21 Dec 2024 20:13:08 +0100
Subject: [PATCH 11/23] eido/convert

---
 modules/nf-core/eido/convert/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/eido/convert/main.nf b/modules/nf-core/eido/convert/main.nf
index 1c1cb06d8bb..1ba02ece565 100644
--- a/modules/nf-core/eido/convert/main.nf
+++ b/modules/nf-core/eido/convert/main.nf
@@ -4,8 +4,8 @@ process EIDO_CONVERT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/eido_peppy:7f50d6891ca1a6d9' :
-        'community.wave.seqera.io/library/eido_peppy:0de9533940828c4d' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4aef51a3d75d6b950bb643ed5ebc1d7243d67bbf3de0410fcaa7d347e8fc0007/data' :
+        'community.wave.seqera.io/library/eido_peppy_setuptools:53ed68799568c4fa' }"
 
     input:
     path samplesheet

From 35643555b0075cec1b0845e4288503644aca0d25 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 13:38:02 +0100
Subject: [PATCH 12/23] sequali

---
 modules/nf-core/sequali/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/sequali/main.nf b/modules/nf-core/sequali/main.nf
index 718c07171c9..768b98ceab1 100644
--- a/modules/nf-core/sequali/main.nf
+++ b/modules/nf-core/sequali/main.nf
@@ -4,7 +4,7 @@ process SEQUALI {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/sequali:0.12.0--c288fa2befb47d0f':
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ed3be5b0d3beb64807ec93b25a80b55abdcdffe684114d12ddef78461dd64e9/data':
         'community.wave.seqera.io/library/sequali:0.12.0--07485bec824d914a' }"
 
     input:

From e525c71b982d6f1f2146987b74c584580d716035 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 13:52:18 +0100
Subject: [PATCH 13/23] samshee

---
 modules/nf-core/samshee/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf
index d40885c4a84..0ec85ae35a3 100644
--- a/modules/nf-core/samshee/main.nf
+++ b/modules/nf-core/samshee/main.nf
@@ -4,8 +4,8 @@ process SAMSHEE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/pip_samshee:6ef3bad21377d60e' :
-        'community.wave.seqera.io/library/pip_samshee:9a11bec0d7c8df27' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3afa0f69cc7ab7e3f9a80582958b8fa33d6673cb914e0f5bdc1c883f61e16073/data' :
+        'community.wave.seqera.io/library/samshee_python:96db61572eca797e' }"
 
     input:
     tuple val(meta), path(samplesheet)

From fe65d2082700bce28dd50ad81981a9331ce864fd Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 14:01:32 +0100
Subject: [PATCH 14/23] narfmap/align

---
 modules/nf-core/narfmap/align/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
index 68001973bd9..f02d5708dc1 100644
--- a/modules/nf-core/narfmap/align/main.nf
+++ b/modules/nf-core/narfmap/align/main.nf
@@ -4,8 +4,8 @@ process NARFMAP_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/narfmap_align:8bad41386eab9997':
-        'community.wave.seqera.io/library/narfmap_align:517a1fed8e4e84c1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a9/a9634de8646d72c54319cc5683949929af4b38e2245b4bc8d28a6666a1f702d6/data':
+        'community.wave.seqera.io/library/narfmap_samtools_pigz:77d0682b7dae0251' }"
 
     input:
     tuple val(meta) , path(reads)

From cf20461a98f5ab32e934159e4a03c0bb5199ec5a Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 14:07:44 +0100
Subject: [PATCH 15/23] purecn/intervalfile

---
 modules/nf-core/purecn/intervalfile/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/purecn/intervalfile/main.nf b/modules/nf-core/purecn/intervalfile/main.nf
index 49434776d0c..83e75cd5ff2 100644
--- a/modules/nf-core/purecn/intervalfile/main.nf
+++ b/modules/nf-core/purecn/intervalfile/main.nf
@@ -4,8 +4,8 @@ process PURECN_INTERVALFILE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:c04754ed02eb7cd3':
-        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:cd51f6d3c90eb24f' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31bad5bbf2277cc9ea746c3c4fd440d1689dd7c8d32d0697b5077f08c084a03e/data':
+        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:bc942848b4c78040' }"
 
     input:
     tuple val(meta), path(target_bed)

From b4ac09712abd1ced390bd682ec173a6474a1499b Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 14:10:29 +0100
Subject: [PATCH 16/23] purecn/normaldb

---
 modules/nf-core/purecn/normaldb/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/purecn/normaldb/main.nf b/modules/nf-core/purecn/normaldb/main.nf
index 9e92e6ae500..b545802b164 100644
--- a/modules/nf-core/purecn/normaldb/main.nf
+++ b/modules/nf-core/purecn/normaldb/main.nf
@@ -4,8 +4,8 @@ process PURECN_NORMALDB {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:c04754ed02eb7cd3':
-        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:cd51f6d3c90eb24f' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/31/31bad5bbf2277cc9ea746c3c4fd440d1689dd7c8d32d0697b5077f08c084a03e/data':
+        'community.wave.seqera.io/library/bioconductor-org.hs.eg.db_bioconductor-purecn_bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_pruned:bc942848b4c78040' }"
 
     input:
     tuple val(meta), path(coverage_files), path(normal_vcf), path(normal_vcf_tbi)

From 7e05e95a6be1fa6de1b2d60420018a08692a790c Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 15:09:00 +0100
Subject: [PATCH 17/23] fix scvitools conda CI

---
 modules/nf-core/scvitools/scar/environment.yml | 1 +
 modules/nf-core/scvitools/solo/environment.yml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/modules/nf-core/scvitools/scar/environment.yml b/modules/nf-core/scvitools/scar/environment.yml
index b40a1c25591..c0df8f5baca 100644
--- a/modules/nf-core/scvitools/scar/environment.yml
+++ b/modules/nf-core/scvitools/scar/environment.yml
@@ -4,4 +4,5 @@ channels:
 
 dependencies:
   - conda-forge::jaxlib=0.4.31
+  - conda-forge::python=3.12.7
   - conda-forge::scvi-tools=1.2.0
diff --git a/modules/nf-core/scvitools/solo/environment.yml b/modules/nf-core/scvitools/solo/environment.yml
index b40a1c25591..c0df8f5baca 100644
--- a/modules/nf-core/scvitools/solo/environment.yml
+++ b/modules/nf-core/scvitools/solo/environment.yml
@@ -4,4 +4,5 @@ channels:
 
 dependencies:
   - conda-forge::jaxlib=0.4.31
+  - conda-forge::python=3.12.7
   - conda-forge::scvi-tools=1.2.0

From 8cfb205d596bca1fd29c2aa8510cca9e4507c04b Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 20:31:29 +0100
Subject: [PATCH 18/23] fix eido/convert conda env

---
 modules/nf-core/eido/convert/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/eido/convert/environment.yml b/modules/nf-core/eido/convert/environment.yml
index de4dc485911..11ca69f4353 100644
--- a/modules/nf-core/eido/convert/environment.yml
+++ b/modules/nf-core/eido/convert/environment.yml
@@ -4,3 +4,4 @@ channels:
 dependencies:
   - conda-forge::eido=0.2.2
   - conda-forge::peppy=0.35.7
+  - conda-forge::setuptools=72.2.0

From e4459ce28976d4c821939210b20412e5bf5d144a Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 25 Dec 2024 21:41:55 +0100
Subject: [PATCH 19/23] fix scvitools/solo conda env

---
 modules/nf-core/scvitools/solo/environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/scvitools/solo/environment.yml b/modules/nf-core/scvitools/solo/environment.yml
index c0df8f5baca..b5a28d3c2f8 100644
--- a/modules/nf-core/scvitools/solo/environment.yml
+++ b/modules/nf-core/scvitools/solo/environment.yml
@@ -3,6 +3,7 @@ channels:
   - bioconda
 
 dependencies:
+  - conda-forge::anndata=0.10.9
   - conda-forge::jaxlib=0.4.31
   - conda-forge::python=3.12.7
   - conda-forge::scvi-tools=1.2.0

From 7fbecdf00c21c77e33ebc12a2d276433ad9cbea7 Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Thu, 26 Dec 2024 12:58:55 +0100
Subject: [PATCH 20/23] Revert "cellbender/merge"

This reverts commit f74b133064522805759ec6765e98971512cee94b.
---
 modules/nf-core/cellbender/merge/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/cellbender/merge/main.nf b/modules/nf-core/cellbender/merge/main.nf
index f5d47b8a2ca..58a631e6e4d 100644
--- a/modules/nf-core/cellbender/merge/main.nf
+++ b/modules/nf-core/cellbender/merge/main.nf
@@ -4,8 +4,8 @@ process CELLBENDER_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/05/055d333b219227f029403ab8591440367f659968eced58b79bdb67c33f30d1e5/data':
-        'community.wave.seqera.io/library/cellbender:0.3.0--d6088f41c6eb0a0f' }"
+        'oras://community.wave.seqera.io/library/cellbender:0.3.0--c4addb97ab2d83fe':
+        'community.wave.seqera.io/library/cellbender:0.3.0--41318a055fc3aacb' }"
 
     input:
     tuple val(meta), path(filtered), path(unfiltered), path(cellbender_h5)

From 32d676f122799cb40d53ae3f53028fe9d964dd0e Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 8 Jan 2025 16:23:48 +0100
Subject: [PATCH 21/23] narfmap_align try old container

---
 modules/nf-core/narfmap/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
index f02d5708dc1..e9b39c9b38d 100644
--- a/modules/nf-core/narfmap/align/main.nf
+++ b/modules/nf-core/narfmap/align/main.nf
@@ -5,7 +5,7 @@ process NARFMAP_ALIGN {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a9/a9634de8646d72c54319cc5683949929af4b38e2245b4bc8d28a6666a1f702d6/data':
-        'community.wave.seqera.io/library/narfmap_samtools_pigz:77d0682b7dae0251' }"
+        'community.wave.seqera.io/library/narfmap_align:517a1fed8e4e84c1' }"
 
     input:
     tuple val(meta) , path(reads)

From 8d68f38c134875d351ce945535298a4eb0f9505d Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 8 Jan 2025 16:56:31 +0100
Subject: [PATCH 22/23] Revert "narfmap_align try old container"

This reverts commit 32d676f122799cb40d53ae3f53028fe9d964dd0e.
---
 modules/nf-core/narfmap/align/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
index e9b39c9b38d..f02d5708dc1 100644
--- a/modules/nf-core/narfmap/align/main.nf
+++ b/modules/nf-core/narfmap/align/main.nf
@@ -5,7 +5,7 @@ process NARFMAP_ALIGN {
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a9/a9634de8646d72c54319cc5683949929af4b38e2245b4bc8d28a6666a1f702d6/data':
-        'community.wave.seqera.io/library/narfmap_align:517a1fed8e4e84c1' }"
+        'community.wave.seqera.io/library/narfmap_samtools_pigz:77d0682b7dae0251' }"
 
     input:
     tuple val(meta) , path(reads)

From 6cdc47486282572a351c5e768f73e551ed53885b Mon Sep 17 00:00:00 2001
From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com>
Date: Wed, 8 Jan 2025 16:56:54 +0100
Subject: [PATCH 23/23] Revert "narfmap/align"

This reverts commit fe65d2082700bce28dd50ad81981a9331ce864fd.
---
 modules/nf-core/narfmap/align/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
index f02d5708dc1..68001973bd9 100644
--- a/modules/nf-core/narfmap/align/main.nf
+++ b/modules/nf-core/narfmap/align/main.nf
@@ -4,8 +4,8 @@ process NARFMAP_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a9/a9634de8646d72c54319cc5683949929af4b38e2245b4bc8d28a6666a1f702d6/data':
-        'community.wave.seqera.io/library/narfmap_samtools_pigz:77d0682b7dae0251' }"
+        'oras://community.wave.seqera.io/library/narfmap_align:8bad41386eab9997':
+        'community.wave.seqera.io/library/narfmap_align:517a1fed8e4e84c1' }"
 
     input:
     tuple val(meta) , path(reads)