From 5e58fbfb71ee6d39d7b9cfd8841116d40ac4af2b Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 17 Dec 2024 15:16:29 +0100
Subject: [PATCH 01/16] use docker containers for fusioninspector,
 fusioncatcher and starfusion

---
 modules/local/fusioncatcher/detect/main.nf        |  3 +--
 modules/local/fusioncatcher/download/main.nf      |  3 +--
 modules/local/fusioninspector/environment.yml     |  7 +------
 modules/local/fusioninspector/main.nf             |  2 +-
 modules/local/starfusion/build/environment.yml    |  7 +------
 modules/local/starfusion/build/main.nf            |  2 +-
 modules/local/starfusion/detect/environment.yml   |  7 +------
 modules/local/starfusion/detect/main.nf           |  2 +-
 modules/local/starfusion/download/environment.yml |  7 +------
 modules/local/starfusion/download/main.nf         |  2 +-
 workflows/build_references.nf                     | 10 +++++-----
 11 files changed, 15 insertions(+), 37 deletions(-)

diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf
index 9a092846..d2c6b929 100644
--- a/modules/local/fusioncatcher/detect/main.nf
+++ b/modules/local/fusioncatcher/detect/main.nf
@@ -2,8 +2,7 @@ process FUSIONCATCHER {
     tag "$meta.id"
     label 'process_high'
 
-    conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"
+    container "docker.io/rannickscilifelab/fusioncatcher:1.34"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/fusioncatcher/download/main.nf b/modules/local/fusioncatcher/download/main.nf
index 65a73607..f11491b9 100644
--- a/modules/local/fusioncatcher/download/main.nf
+++ b/modules/local/fusioncatcher/download/main.nf
@@ -2,8 +2,7 @@ process FUSIONCATCHER_DOWNLOAD {
     tag "fusioncatcher_download"
     label 'process_medium'
 
-    conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/fusioncatcher:1.33--4733482b637ef92f"
+    container "docker.io/rannickscilifelab/fusioncatcher:1.34"
 
     output:
     path "*"                , emit: reference
diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
index 06a9828a..77187e8b 100644
--- a/modules/local/fusioninspector/environment.yml
+++ b/modules/local/fusioninspector/environment.yml
@@ -2,9 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::dfam=3.7
-  - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
index ae05ceb4..b91d37c9 100644
--- a/modules/local/fusioninspector/main.nf
+++ b/modules/local/fusioninspector/main.nf
@@ -3,7 +3,7 @@ process FUSIONINSPECTOR {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container 'trinityctat/fusioninspector:2.10.0'
 
     input:
     tuple val(meta), path(reads), path(fusion_list)
diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
index 06a9828a..77187e8b 100644
--- a/modules/local/starfusion/build/environment.yml
+++ b/modules/local/starfusion/build/environment.yml
@@ -2,9 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::dfam=3.7
-  - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index 6ac3c694..9212cdaf 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -2,7 +2,7 @@ process STARFUSION_BUILD {
     tag 'star-fusion'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container 'docker.io/trinityctat/starfusion:1.14.0'
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
index 06a9828a..77187e8b 100644
--- a/modules/local/starfusion/detect/environment.yml
+++ b/modules/local/starfusion/detect/environment.yml
@@ -2,9 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::dfam=3.7
-  - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index 27396770..94342e99 100644
--- a/modules/local/starfusion/detect/main.nf
+++ b/modules/local/starfusion/detect/main.nf
@@ -3,7 +3,7 @@ process STARFUSION {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container 'docker.io/trinityctat/starfusion:1.14.0'
 
     input:
     tuple val(meta), path(reads), path(junction)
diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
index 06a9828a..77187e8b 100644
--- a/modules/local/starfusion/download/environment.yml
+++ b/modules/local/starfusion/download/environment.yml
@@ -2,9 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::dfam=3.7
-  - bioconda::hmmer=3.4
-  - bioconda::star-fusion=1.7.0
-  - bioconda::trinity=2.15.2
-  - bioconda::samtools=1.21
-  - bioconda::star=2.7.11b
+  - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index d0668486..735764c9 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -2,7 +2,7 @@ process STARFUSION_DOWNLOAD {
     tag 'star-fusion'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/dfam_hmmer_samtools_star-fusion_pruned:5694d82381bf039e'
+    container 'docker.io/trinityctat/starfusion:1.14.0'
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference
diff --git a/workflows/build_references.nf b/workflows/build_references.nf
index 4886a7bb..baf2ee26 100644
--- a/workflows/build_references.nf
+++ b/workflows/build_references.nf
@@ -44,14 +44,14 @@ workflow BUILD_REFERENCES {
     GATK4_CREATESEQUENCEDICTIONARY(ENSEMBL_DOWNLOAD.out.primary_assembly)
 
 
-    RRNATRANSCRIPTS(ENSEMBL_DOWNLOAD.out.gtf.map{ meta, gtf -> [ gtf ] })
+    RRNATRANSCRIPTS(ENSEMBL_DOWNLOAD.out.gtf.map{ it -> [ it[1] ] })
     BEDOPS_CONVERT2BED(RRNATRANSCRIPTS.out.rrna_gtf.map{ it -> [[id:it.Name], it] })
     GATK4_BEDTOINTERVALLIST(BEDOPS_CONVERT2BED.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict)
 
-    GFFREAD(ENSEMBL_DOWNLOAD.out.gtf, ENSEMBL_DOWNLOAD.out.primary_assembly.map { meta, fasta -> [ fasta ] })
+    GFFREAD(ENSEMBL_DOWNLOAD.out.gtf, ENSEMBL_DOWNLOAD.out.primary_assembly.map { it -> [ it[1] ] })
 
     if (!params.skip_salmon_index){
-        SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ meta, fasta -> [ fasta ] }, GFFREAD.out.gffread_fasta.map{ meta, gffread_fasta -> [ gffread_fasta ] })
+        SALMON_INDEX(ENSEMBL_DOWNLOAD.out.primary_assembly.map{ it -> [ it[1] ] }, GFFREAD.out.gffread_fasta.map{ it -> [ it[1] ] })
     }
 
     if (params.starindex || params.all || params.starfusion || params.arriba) {
@@ -75,9 +75,9 @@ workflow BUILD_REFERENCES {
     }
 
     if (params.starfusion_build){
-        UCSC_GTFTOGENEPRED(ENSEMBL_DOWNLOAD.out.chrgtf)
+        UCSC_GTFTOGENEPRED(ENSEMBL_DOWNLOAD.out.gtf)
     } else {
-        UCSC_GTFTOGENEPRED(STARFUSION_DOWNLOAD.out.chrgtf)
+        UCSC_GTFTOGENEPRED(STARFUSION_DOWNLOAD.out.gtf)
     }
     if (params.fusionreport || params.all) {
         FUSIONREPORT_DOWNLOAD()

From 081249ad824b0a89aeecba37a16dcbc58b00c308 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 17 Dec 2024 15:45:24 +0100
Subject: [PATCH 02/16] update changelog

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a5c881c3..7816df5a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560)
 - Add nf-test to local subworkflow: `QC_WORKFLOW` [#568](https://github.com/nf-core/rnafusion/pull/568)
 - Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572)
-- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#572](https://github.com/nf-core/rnafusion/pull/577)
+- Add nf-test to local module: `FUSIONREPORT_DETECT`. Improve `FUSIONREPORT_DOWNLOAD` module [#577](https://github.com/nf-core/rnafusion/pull/577)
 - Add nf-test to local subworkflow: `ARRIBA_WORKFLOW` [#578](https://github.com/nf-core/rnafusion/pull/578)
 
 ### Changed
@@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541)
 - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548)
 - Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581)
+- Use docker.io instead of wave as to keep supporting singularity in the transition period [#588](https://github.com/nf-core/rnafusion/pull/588)
 
 ### Fixed
 

From 33f4b57edf548d98fb05b7279dd2f8aab7a57d10 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:04:26 +0100
Subject: [PATCH 03/16] revert change

---
 workflows/build_references.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/build_references.nf b/workflows/build_references.nf
index baf2ee26..9f7ce633 100644
--- a/workflows/build_references.nf
+++ b/workflows/build_references.nf
@@ -55,7 +55,7 @@ workflow BUILD_REFERENCES {
     }
 
     if (params.starindex || params.all || params.starfusion || params.arriba) {
-        STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf )
+        STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.chrgtf )
     }
 
     if (params.arriba || params.all) {
@@ -68,7 +68,7 @@ workflow BUILD_REFERENCES {
 
     if (params.starfusion || params.all) {
         if (params.starfusion_build){
-            STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf )
+            STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.chrgtf )
         } else {
             STARFUSION_DOWNLOAD()
         }

From ff69a60b84d2e4ff2c635e571f78fc08aec77979 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 17 Dec 2024 16:06:40 +0100
Subject: [PATCH 04/16] revert change

---
 workflows/build_references.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/workflows/build_references.nf b/workflows/build_references.nf
index 9f7ce633..3b88a47f 100644
--- a/workflows/build_references.nf
+++ b/workflows/build_references.nf
@@ -55,7 +55,7 @@ workflow BUILD_REFERENCES {
     }
 
     if (params.starindex || params.all || params.starfusion || params.arriba) {
-        STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.chrgtf )
+        STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf )
     }
 
     if (params.arriba || params.all) {
@@ -68,16 +68,16 @@ workflow BUILD_REFERENCES {
 
     if (params.starfusion || params.all) {
         if (params.starfusion_build){
-            STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.chrgtf )
+            STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.primary_assembly, ENSEMBL_DOWNLOAD.out.gtf )
         } else {
             STARFUSION_DOWNLOAD()
         }
     }
 
     if (params.starfusion_build){
-        UCSC_GTFTOGENEPRED(ENSEMBL_DOWNLOAD.out.gtf)
+        UCSC_GTFTOGENEPRED(ENSEMBL_DOWNLOAD.out.chrgtf)
     } else {
-        UCSC_GTFTOGENEPRED(STARFUSION_DOWNLOAD.out.gtf)
+        UCSC_GTFTOGENEPRED(STARFUSION_DOWNLOAD.out.chrgtf)
     }
     if (params.fusionreport || params.all) {
         FUSIONREPORT_DOWNLOAD()

From b7383ebaf52c8a157e365c251e6e120f37746e71 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 17 Dec 2024 17:08:06 +0100
Subject: [PATCH 05/16] test to see if dependencies are working with
 starfusion1.14 onluy

---
 modules/local/fusioninspector/main.nf     | 4 +++-
 modules/local/starfusion/build/main.nf    | 4 +++-
 modules/local/starfusion/detect/main.nf   | 4 +++-
 modules/local/starfusion/download/main.nf | 4 +++-
 4 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
index b91d37c9..8745b0e3 100644
--- a/modules/local/fusioninspector/main.nf
+++ b/modules/local/fusioninspector/main.nf
@@ -3,7 +3,9 @@ process FUSIONINSPECTOR {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container 'trinityctat/fusioninspector:2.10.0'
+    container "${ 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'}"
 
     input:
     tuple val(meta), path(reads), path(fusion_list)
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index 9212cdaf..15b5517a 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -2,7 +2,9 @@ process STARFUSION_BUILD {
     tag 'star-fusion'
 
     conda "${moduleDir}/environment.yml"
-    container 'docker.io/trinityctat/starfusion:1.14.0'
+    container "${ 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'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index 94342e99..38a88112 100644
--- a/modules/local/starfusion/detect/main.nf
+++ b/modules/local/starfusion/detect/main.nf
@@ -3,7 +3,9 @@ process STARFUSION {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container 'docker.io/trinityctat/starfusion:1.14.0'
+    container "${ 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'}"
 
     input:
     tuple val(meta), path(reads), path(junction)
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index 735764c9..6defb6cd 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -2,7 +2,9 @@ process STARFUSION_DOWNLOAD {
     tag 'star-fusion'
 
     conda "${moduleDir}/environment.yml"
-    container 'docker.io/trinityctat/starfusion:1.14.0'
+    container "${ 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'}"
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference

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 06/16] 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)

From bf05cb766954979dd741a315c2018585df9fb5d0 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:52:16 +0100
Subject: [PATCH 07/16] update bin path

---
 modules/local/starfusion/build/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index 05ca3089..47b881c0 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -14,7 +14,6 @@ process STARFUSION_BUILD {
     path "*"  , emit: reference
 
     script:
-    def binPath = (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1)  ? "prep_genome_lib.pl" : "/usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl"
     """
     export TMPDIR=/tmp
     wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
@@ -26,7 +25,7 @@ process STARFUSION_BUILD {
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p --no-check-certificate
     gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
-    $binPath \\
+    prep_genome_lib.pl \\
         --genome_fa $fasta \\
         --gtf $gtf \\
         --annot_filter_rule AnnotFilterRule.pm \\

From 235a7529b6e93db0d2553a86805a7a14c3ba9761 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 15:47:49 +0100
Subject: [PATCH 08/16] bin path to prep_genome_lib not working with
 singularity wave container, reverting to galaxy and specifying path

---
 modules/local/starfusion/build/main.nf  | 5 +++--
 modules/local/starfusion/detect/main.nf | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index 47b881c0..38d27832 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -3,7 +3,7 @@ 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/f8/f804c086cee338c315fbc51faf0c37de360b047b47c33388716962eb3467b087/data':
+        'https://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
         'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
 
     input:
@@ -14,6 +14,7 @@ process STARFUSION_BUILD {
     path "*"  , emit: reference
 
     script:
+    def binPath = (workflow.profile.tokenize(',').intersect(['singularity']).size() >= 1)  ?  "/usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl" : "prep_genome_lib.pl"
     """
     export TMPDIR=/tmp
     wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
@@ -25,7 +26,7 @@ process STARFUSION_BUILD {
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p --no-check-certificate
     gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
-    prep_genome_lib.pl \\
+    $binPath \\
         --genome_fa $fasta \\
         --gtf $gtf \\
         --annot_filter_rule AnnotFilterRule.pm \\
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index 84a57d21..c95e3926 100644
--- a/modules/local/starfusion/detect/main.nf
+++ b/modules/local/starfusion/detect/main.nf
@@ -4,7 +4,7 @@ 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/f8/f804c086cee338c315fbc51faf0c37de360b047b47c33388716962eb3467b087/data':
+        'https://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
         'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
 
     input:

From a0698b1f08e0643283e6a4bb80633098aca7e408 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 16:17:21 +0100
Subject: [PATCH 09/16] propagate container of starfusion to fusioninspector

---
 modules/local/fusioninspector/environment.yml     | 6 ++++++
 modules/local/fusioninspector/main.nf             | 4 ++--
 modules/local/starfusion/build/environment.yml    | 2 +-
 modules/local/starfusion/detect/environment.yml   | 2 +-
 modules/local/starfusion/download/environment.yml | 6 ++++++
 modules/local/starfusion/download/main.nf         | 4 ++--
 6 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
index 77187e8b..757544ca 100644
--- a/modules/local/fusioninspector/environment.yml
+++ b/modules/local/fusioninspector/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=2.7.9
+  - bioconda::trinity=2.8.5
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
index 8745b0e3..53a0bb45 100644
--- a/modules/local/fusioninspector/main.nf
+++ b/modules/local/fusioninspector/main.nf
@@ -4,8 +4,8 @@ process FUSIONINSPECTOR {
 
     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://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
 
     input:
     tuple val(meta), path(reads), path(fusion_list)
diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
index eacee484..757544ca 100644
--- a/modules/local/starfusion/build/environment.yml
+++ b/modules/local/starfusion/build/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - bioconda::minimap2=2.28
   - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
-  - bioconda::star=2.7.11a
+  - bioconda::star=2.7.9
   - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
index eacee484..757544ca 100644
--- a/modules/local/starfusion/detect/environment.yml
+++ b/modules/local/starfusion/detect/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - bioconda::minimap2=2.28
   - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
-  - bioconda::star=2.7.11a
+  - bioconda::star=2.7.9
   - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
index 77187e8b..757544ca 100644
--- a/modules/local/starfusion/download/environment.yml
+++ b/modules/local/starfusion/download/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=2.7.9
+  - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index 6defb6cd..19cad44b 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -3,8 +3,8 @@ process STARFUSION_DOWNLOAD {
 
     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://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference

From b2a075bc0e0f43ac296685b605e2f56e0322265f Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 16:19:47 +0100
Subject: [PATCH 10/16] update star

---
 modules/local/fusioninspector/environment.yml     | 2 +-
 modules/local/starfusion/build/environment.yml    | 2 +-
 modules/local/starfusion/detect/environment.yml   | 2 +-
 modules/local/starfusion/download/environment.yml | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
index 757544ca..f5d21d5a 100644
--- a/modules/local/fusioninspector/environment.yml
+++ b/modules/local/fusioninspector/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - bioconda::minimap2=2.28
   - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
-  - bioconda::star=2.7.9
+  - bioconda::star=2.7.11b
   - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
index 757544ca..f5d21d5a 100644
--- a/modules/local/starfusion/build/environment.yml
+++ b/modules/local/starfusion/build/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - bioconda::minimap2=2.28
   - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
-  - bioconda::star=2.7.9
+  - bioconda::star=2.7.11b
   - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
index 757544ca..f5d21d5a 100644
--- a/modules/local/starfusion/detect/environment.yml
+++ b/modules/local/starfusion/detect/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - bioconda::minimap2=2.28
   - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
-  - bioconda::star=2.7.9
+  - bioconda::star=2.7.11b
   - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
index 757544ca..f5d21d5a 100644
--- a/modules/local/starfusion/download/environment.yml
+++ b/modules/local/starfusion/download/environment.yml
@@ -7,5 +7,5 @@ dependencies:
   - bioconda::minimap2=2.28
   - bioconda::samtools=1.6
   - bioconda::star-fusion=1.14.0
-  - bioconda::star=2.7.9
+  - bioconda::star=2.7.11b
   - bioconda::trinity=2.8.5

From 853e48d9e9ca66aac81fe1ba6d78f65f599802bc Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 16:22:22 +0100
Subject: [PATCH 11/16] update changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7816df5a..b281d82f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541)
 - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548)
 - Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581)
-- Use docker.io instead of wave as to keep supporting singularity in the transition period [#588](https://github.com/nf-core/rnafusion/pull/588)
+- Use docker.io and galaxy containers for fusioncatcher and starfusion (incl. fusioninspector) instead of wave as they are not functional on wave [#588](https://github.com/nf-core/rnafusion/pull/588)
 
 ### Fixed
 

From 9cad032e4a706c2a79dca951a6361a348bff2f1d Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Dec 2024 16:23:45 +0100
Subject: [PATCH 12/16] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b281d82f..1d400fa2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Allow fastq files without a dot before .fn(.gz)/.fastq(.gz) files [#548](https://github.com/nf-core/rnafusion/pull/548)
 - Remove double nested folder introduced in [#577](https://github.com/nf-core/rnafusion/pull/577), [#581](https://github.com/nf-core/rnafusion/pull/581)
 - Use docker.io and galaxy containers for fusioncatcher and starfusion (incl. fusioninspector) instead of wave as they are not functional on wave [#588](https://github.com/nf-core/rnafusion/pull/588)
+- Update STAR-Fusion to 1.14 [#588](https://github.com/nf-core/rnafusion/pull/588)
 
 ### Fixed
 

From a08c02f1d0f7d900e841fe4643d628f0bab8b71e Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 19 Dec 2024 11:19:41 +0100
Subject: [PATCH 13/16] update dependencies

---
 modules/local/starfusion/build/environment.yml    | 4 ----
 modules/local/starfusion/build/main.nf            | 4 ++--
 modules/local/starfusion/detect/environment.yml   | 4 ----
 modules/local/starfusion/detect/main.nf           | 4 ++--
 modules/local/starfusion/download/environment.yml | 4 ----
 modules/local/starfusion/download/main.nf         | 4 ++--
 6 files changed, 6 insertions(+), 18 deletions(-)

diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
index f5d21d5a..18b2407b 100644
--- a/modules/local/starfusion/build/environment.yml
+++ b/modules/local/starfusion/build/environment.yml
@@ -4,8 +4,4 @@ channels:
 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=2.7.11b
-  - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index 38d27832..eba6e2c0 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://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f7977acd75883433483258a1cc21d069a64947af431b26c3fc13c6be62666dfa/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
index f5d21d5a..18b2407b 100644
--- a/modules/local/starfusion/detect/environment.yml
+++ b/modules/local/starfusion/detect/environment.yml
@@ -4,8 +4,4 @@ channels:
 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=2.7.11b
-  - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index c95e3926..691601e9 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://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f7977acd75883433483258a1cc21d069a64947af431b26c3fc13c6be62666dfa/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
 
     input:
     tuple val(meta), path(reads), path(junction)
diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
index f5d21d5a..18b2407b 100644
--- a/modules/local/starfusion/download/environment.yml
+++ b/modules/local/starfusion/download/environment.yml
@@ -4,8 +4,4 @@ channels:
 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=2.7.11b
-  - bioconda::trinity=2.8.5
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index 19cad44b..7dffbf2c 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -3,8 +3,8 @@ process STARFUSION_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f7/f7977acd75883433483258a1cc21d069a64947af431b26c3fc13c6be62666dfa/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference

From 34109cd9ecd754793cf6fdc419e1fcc60dbe1cda Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 19 Dec 2024 11:35:02 +0100
Subject: [PATCH 14/16] update path again

---
 modules/local/starfusion/build/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index eba6e2c0..e106bf80 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -14,7 +14,6 @@ process STARFUSION_BUILD {
     path "*"  , emit: reference
 
     script:
-    def binPath = (workflow.profile.tokenize(',').intersect(['singularity']).size() >= 1)  ?  "/usr/local/src/STAR-Fusion/ctat-genome-lib-builder/prep_genome_lib.pl" : "prep_genome_lib.pl"
     """
     export TMPDIR=/tmp
     wget http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
@@ -26,7 +25,7 @@ process STARFUSION_BUILD {
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m --no-check-certificate
     wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p --no-check-certificate
     gunzip Pfam-A.hmm.gz && hmmpress Pfam-A.hmm
-    $binPath \\
+    prep_genome_lib.pl \\
         --genome_fa $fasta \\
         --gtf $gtf \\
         --annot_filter_rule AnnotFilterRule.pm \\

From 0ea316e94661b472b7e615e8d0233a3690ed6f5a Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 19 Dec 2024 11:57:02 +0100
Subject: [PATCH 15/16] add minimap

---
 modules/local/starfusion/build/environment.yml    | 1 +
 modules/local/starfusion/build/main.nf            | 2 +-
 modules/local/starfusion/detect/environment.yml   | 1 +
 modules/local/starfusion/download/environment.yml | 1 +
 4 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/local/starfusion/build/environment.yml b/modules/local/starfusion/build/environment.yml
index 18b2407b..ef7f9316 100644
--- a/modules/local/starfusion/build/environment.yml
+++ b/modules/local/starfusion/build/environment.yml
@@ -4,4 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
+  - bioconda::minimap2=2.28
   - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index e106bf80..ad35b067 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -3,7 +3,7 @@ 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/f7/f7977acd75883433483258a1cc21d069a64947af431b26c3fc13c6be62666dfa/data' :
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
         'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
 
     input:
diff --git a/modules/local/starfusion/detect/environment.yml b/modules/local/starfusion/detect/environment.yml
index 18b2407b..ef7f9316 100644
--- a/modules/local/starfusion/detect/environment.yml
+++ b/modules/local/starfusion/detect/environment.yml
@@ -4,4 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
+  - bioconda::minimap2=2.28
   - bioconda::star-fusion=1.14.0
diff --git a/modules/local/starfusion/download/environment.yml b/modules/local/starfusion/download/environment.yml
index 18b2407b..ef7f9316 100644
--- a/modules/local/starfusion/download/environment.yml
+++ b/modules/local/starfusion/download/environment.yml
@@ -4,4 +4,5 @@ channels:
 dependencies:
   - bioconda::dfam=3.7
   - bioconda::hmmer=3.4
+  - bioconda::minimap2=2.28
   - bioconda::star-fusion=1.14.0

From 27b3f8b3f198f18ba725ecb3ef6bf82bf42000ed Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Thu, 19 Dec 2024 12:48:30 +0100
Subject: [PATCH 16/16] propagate container/env change

---
 modules/local/fusioninspector/environment.yml | 3 ---
 modules/local/fusioninspector/main.nf         | 4 ++--
 modules/local/starfusion/build/main.nf        | 2 +-
 modules/local/starfusion/detect/main.nf       | 4 ++--
 modules/local/starfusion/download/main.nf     | 4 ++--
 5 files changed, 7 insertions(+), 10 deletions(-)

diff --git a/modules/local/fusioninspector/environment.yml b/modules/local/fusioninspector/environment.yml
index f5d21d5a..ef7f9316 100644
--- a/modules/local/fusioninspector/environment.yml
+++ b/modules/local/fusioninspector/environment.yml
@@ -5,7 +5,4 @@ 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=2.7.11b
-  - bioconda::trinity=2.8.5
diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf
index 53a0bb45..ade7c174 100644
--- a/modules/local/fusioninspector/main.nf
+++ b/modules/local/fusioninspector/main.nf
@@ -4,8 +4,8 @@ process FUSIONINSPECTOR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/star-fusion:1.14.0--hdfd78af_0' :
-        'community.wave.seqera.io/library/dfam_hmmer_minimap2_samtools_pruned:bd39df228dad7086'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
 
     input:
     tuple val(meta), path(reads), path(fusion_list)
diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf
index ad35b067..05abec92 100644
--- a/modules/local/starfusion/build/main.nf
+++ b/modules/local/starfusion/build/main.nf
@@ -4,7 +4,7 @@ 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/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/starfusion/detect/main.nf b/modules/local/starfusion/detect/main.nf
index 691601e9..83b0dc2f 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/f7/f7977acd75883433483258a1cc21d069a64947af431b26c3fc13c6be62666dfa/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
 
     input:
     tuple val(meta), path(reads), path(junction)
diff --git a/modules/local/starfusion/download/main.nf b/modules/local/starfusion/download/main.nf
index 7dffbf2c..989c2420 100644
--- a/modules/local/starfusion/download/main.nf
+++ b/modules/local/starfusion/download/main.nf
@@ -3,8 +3,8 @@ process STARFUSION_DOWNLOAD {
 
     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/f7/f7977acd75883433483258a1cc21d069a64947af431b26c3fc13c6be62666dfa/data' :
-        'community.wave.seqera.io/library/dfam_hmmer_star-fusion:e8fe96707386872f'}"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/be/bed86145102fdf7e381e1a506a4723676f98b4bbe1db5085d02213cef18525c9/data' :
+        'community.wave.seqera.io/library/dfam_hmmer_minimap2_star-fusion:aa3a8e3951498552'}"
 
     output:
     path "ctat_genome_lib_build_dir/*"            , emit: reference