From d40d060ee67b7da7567eb0ecf2149df6d7b8f1f1 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Fri, 22 Nov 2024 18:52:57 -0500
Subject: [PATCH] bump regtools version (#7050)

* bump regtools version

* change conda

* fix version

* fix singularity url

---------

Co-authored-by: Lorena Pantano <lorena.pantano@gmail.com>
---
 .../regtools/junctionsextract/environment.yml |  2 +-
 .../nf-core/regtools/junctionsextract/main.nf |  7 ++++---
 .../junctionsextract/tests/main.nf.test.snap  | 20 +++++++++----------
 3 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/regtools/junctionsextract/environment.yml b/modules/nf-core/regtools/junctionsextract/environment.yml
index c8e4700cb36..2b615890f84 100644
--- a/modules/nf-core/regtools/junctionsextract/environment.yml
+++ b/modules/nf-core/regtools/junctionsextract/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::regtools=0.5.0"
+  - "bioconda::regtools=1.0.0"
diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index 7884ab92eca..d2cd32642c0 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -2,10 +2,10 @@ process REGTOOLS_JUNCTIONSEXTRACT {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::regtools=0.5.0"
+    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/b6/b6c0653189b95b22e16038f61ade205a865857f54eeae9ba0184490a1834f7c9/data' :
-        'community.wave.seqera.io/library/regtools:0.5.0--b9a260c4c898354a' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/14/143bc2dfa40320fbe1e52329953c8508780591835223f4ca492d3206598604a8/data' :
+        'community.wave.seqera.io/library/regtools:1.0.0--461ddf16709a70cf' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -23,6 +23,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
     """
     regtools junctions extract \\
         $args \\
+        -s XS \\
         -o ${prefix}.junc \\
         $bam
 
diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
index 9c365497e5e..cac83a6127e 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                    "versions.yml:md5,5fbc639c97d9eb07a0530b875667a14e"
                 ],
                 "junc": [
                     [
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                    "versions.yml:md5,5fbc639c97d9eb07a0530b875667a14e"
                 ]
             }
         ],
@@ -32,13 +32,13 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-20T13:29:27.373772"
+        "timestamp": "2024-11-21T13:15:36.794996"
     },
     "versions": {
         "content": [
             {
                 "REGTOOLS_JUNCTIONSEXTRACT": {
-                    "regtools": "0.5.0"
+                    "regtools": "1.0.0"
                 }
             }
         ],
@@ -46,7 +46,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-20T13:29:27.448238"
+        "timestamp": "2024-11-21T13:15:36.873402"
     },
     "homo_sapiens - bam-bai": {
         "content": [
@@ -57,11 +57,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                        "test.junc:md5,abcb59fd5c52fb16acf6ecc6528d26b7"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                    "versions.yml:md5,5fbc639c97d9eb07a0530b875667a14e"
                 ],
                 "junc": [
                     [
@@ -69,11 +69,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                        "test.junc:md5,abcb59fd5c52fb16acf6ecc6528d26b7"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
+                    "versions.yml:md5,5fbc639c97d9eb07a0530b875667a14e"
                 ]
             }
         ],
@@ -81,6 +81,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-20T13:29:23.165022"
+        "timestamp": "2024-11-21T13:15:32.656276"
     }
 }
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