From a67cc0f6f14d6905f9d18a861ef82fef4e08975d Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 09:51:42 +0100
Subject: [PATCH] add dependencies explicitly

---
 modules/local/starfusion/build/environment.yml  | 6 ++++++
 modules/local/starfusion/build/main.nf          | 4 ++--
 modules/local/starfusion/detect/environment.yml | 6 ++++++
 modules/local/starfusion/detect/main.nf         | 4 ++--
 4 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
index 77187e8b..eacee484 100644
--- a/modules/local/starfusion/build/environment.yml
+++ b/modules/local/starfusion/build/environment.yml
@@ -2,4 +2,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::minimap2=2.28
+  - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
+  - bioconda::star=2.7.11a
+  - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index 15b5517a..05ca3089 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -3,8 +3,8 @@ process STARFUSION_BUILD {
 
     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/f0/f0bf770bcc7a7af4c9b7a83a88a191bb9e9875759e1985030268df9ffa27dde6/data':
-        'community.wave.seqera.io/library/star-fusion:4d0a3a362520dfa6'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f804c086cee338c315fbc51faf0c37de360b047b47c33388716962eb3467b087/data':
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
index 77187e8b..eacee484 100644
--- a/modules/local/starfusion/detect/environment.yml
+++ b/modules/local/starfusion/detect/environment.yml
@@ -2,4 +2,10 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  - bioconda::dfam=3.7
+  - bioconda::hmmer=3.4
+  - bioconda::minimap2=2.28
+  - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
+  - bioconda::star=2.7.11a
+  - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index 38a88112..84a57d21 100644
--- a/modules/local/starfusion/detect/main.nf
+++ b/modules/local/starfusion/detect/main.nf
@@ -4,8 +4,8 @@ process STARFUSION {
 
     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/f0/f0bf770bcc7a7af4c9b7a83a88a191bb9e9875759e1985030268df9ffa27dde6/data':
-        'community.wave.seqera.io/library/star-fusion:4d0a3a362520dfa6'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f8/f804c086cee338c315fbc51faf0c37de360b047b47c33388716962eb3467b087/data':
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
 
     input:
     tuple val(meta), path(reads), path(junction)