From fee031a5f4a6ce2bc24cd77928442558cb9c2736 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <bartlettalexandra@gmail.com>
Date: Tue, 19 Nov 2024 16:40:47 -0500
Subject: [PATCH 01/15] initial commit

---
 .../regtools/junctionsextract/environment.yml |  7 +++
 .../nf-core/regtools/junctionsextract/main.nf | 46 ++++++++++++++
 .../regtools/junctionsextract/meta.yml        | 53 ++++++++++++++++
 .../junctionsextract/tests/main.nf.test       | 63 +++++++++++++++++++
 .../junctionsextract/tests/main.nf.test.snap  | 38 +++++++++++
 .../regtools/junctionsextract/tests/tags.yml  |  2 +
 6 files changed, 209 insertions(+)
 create mode 100644 modules/nf-core/regtools/junctionsextract/environment.yml
 create mode 100644 modules/nf-core/regtools/junctionsextract/main.nf
 create mode 100644 modules/nf-core/regtools/junctionsextract/meta.yml
 create mode 100644 modules/nf-core/regtools/junctionsextract/tests/main.nf.test
 create mode 100644 modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/regtools/junctionsextract/tests/tags.yml

diff --git a/modules/nf-core/regtools/junctionsextract/environment.yml b/modules/nf-core/regtools/junctionsextract/environment.yml
new file mode 100644
index 00000000000..0da59d41268
--- /dev/null
+++ b/modules/nf-core/regtools/junctionsextract/environment.yml
@@ -0,0 +1,7 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "regtools_junctionsextract"
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::regtools=0.5.0"
diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
new file mode 100644
index 00000000000..df150d4811a
--- /dev/null
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -0,0 +1,46 @@
+process REGTOOLS_JUNCTIONSEXTRACT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "bioconda::regtools=0.5.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/regtools:0.5.0--he941832_0' :
+        'biocontainers/regtools:0.5.0--he941832_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+
+    output:
+    tuple val(meta), path("*.junc"), emit: junc
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    regtools junctions extract \\
+        $args \\
+        -o ${prefix}.junc \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        regtools: \$(regtools --version 2>&1 | sed 's/^.*regtools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.junc
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        regtools: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/regtools/junctionsextract/meta.yml b/modules/nf-core/regtools/junctionsextract/meta.yml
new file mode 100644
index 00000000000..d20bda1a05a
--- /dev/null
+++ b/modules/nf-core/regtools/junctionsextract/meta.yml
@@ -0,0 +1,53 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "regtools_junctionsextract"
+description: Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.
+keywords:
+  - regtools
+  - leafcutter
+  - RNA-seq
+  - splicing
+tools:
+  - "regtools":
+      description: "RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context."
+      homepage: "https://regtools.readthedocs.io/en/latest/"
+      documentation: "https://regtools.readthedocs.io/en/latest/#usage"
+      tool_dev_url: "https://github.com/griffithlab/regtools"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.{bam}"
+    - bai:
+        type: file
+        description: Index to sorted BAM file
+        pattern: "*.{bai}"
+
+output:
+  - junc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - junc:
+          type: file
+          description: BED12 file containing exon-exon junctions
+          pattern: "*.{junc}"
+  - versions:
+      - versions:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@abartlett004"
+maintainers:
+  - "@abartlett004"
diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
new file mode 100644
index 00000000000..34550d2a890
--- /dev/null
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
@@ -0,0 +1,63 @@
+// nf-core modules test regtools/junctionsextract
+nextflow_process {
+
+    name "Test Process REGTOOLS_JUNCTIONSEXTRACT"
+    script "../main.nf"
+    process "REGTOOLS_JUNCTIONSEXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "regtools"
+    tag "regtools/junctionsextract"
+
+    test("homo_sapiens - bam-bai") {
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam_bai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.junc).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam-bai - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam'], checkIfExists: true),
+                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam_bai'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.junc).match() }
+            )
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
new file mode 100644
index 00000000000..2c170aaec64
--- /dev/null
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
@@ -0,0 +1,38 @@
+{
+    "homo_sapiens - bam-bai - stub": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-19T16:13:20.817212"
+    },
+    "homo_sapiens - bam-bai": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-19T16:13:16.43357"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/regtools/junctionsextract/tests/tags.yml b/modules/nf-core/regtools/junctionsextract/tests/tags.yml
new file mode 100644
index 00000000000..54cc7fc9211
--- /dev/null
+++ b/modules/nf-core/regtools/junctionsextract/tests/tags.yml
@@ -0,0 +1,2 @@
+regtools/junctionsextract:
+  - "modules/nf-core/regtools/junctionsextract/**"

From a0ca177a83a964ba22995c0f5cc0628e3b56c1a4 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 10:57:47 -0500
Subject: [PATCH 02/15] Update
 modules/nf-core/regtools/junctionsextract/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index df150d4811a..202e3027357 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -12,7 +12,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
 
     output:
     tuple val(meta), path("*.junc"), emit: junc
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when

From f2828aa52762fcf9c19b4eeb19ed600f3050bd61 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 10:58:02 -0500
Subject: [PATCH 03/15] Update
 modules/nf-core/regtools/junctionsextract/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index 202e3027357..d3c1b5d0501 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -33,7 +33,6 @@ process REGTOOLS_JUNCTIONSEXTRACT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.junc

From b69d3344b3304240fb067e961ef58288afb77de0 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 10:58:11 -0500
Subject: [PATCH 04/15] Update
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
index 34550d2a890..62dbcc0087f 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
@@ -1,4 +1,3 @@
-// nf-core modules test regtools/junctionsextract
 nextflow_process {
 
     name "Test Process REGTOOLS_JUNCTIONSEXTRACT"

From a6d4cc520a666b0ce0dcf7706311b8b5922550bf Mon Sep 17 00:00:00 2001
From: Alex Bartlett <bartlettalexandra@gmail.com>
Date: Wed, 20 Nov 2024 11:08:02 -0500
Subject: [PATCH 05/15] more recent fill file path

---
 .../nf-core/regtools/junctionsextract/tests/main.nf.test  | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
index 34550d2a890..380790d9909 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
@@ -18,8 +18,8 @@ nextflow_process {
 
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam_bai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
                     ]
                 """
             }
@@ -44,8 +44,8 @@ nextflow_process {
 
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['test_rna_paired_end_sorted_chr6_bam_bai'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
                     ]
                 """
             }

From 8960d90e3bcc9673ce28522fa3d60aff2f52815b Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 11:25:36 -0500
Subject: [PATCH 06/15] Update
 modules/nf-core/regtools/junctionsextract/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index d3c1b5d0501..2a665e3e040 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -39,7 +39,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        regtools: \$(samtools --version |& sed '1!d ; s/samtools //')
+        regtools: \$(regtools --version 2>&1 | sed 's/^.*regtools //; s/ .*\$//')
     END_VERSIONS
     """
 }

From 25a1f868a357f747c6b5653377497cbf12631edd Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 11:27:54 -0500
Subject: [PATCH 07/15] Update
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
index 487789cc7ff..c25f65deb47 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
@@ -27,7 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.junc).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 

From 7e30e8544454fdcc563765f373c8cbafbe8f34be Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 11:28:08 -0500
Subject: [PATCH 08/15] Update
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
index c25f65deb47..d301fc796f4 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
@@ -53,7 +53,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.junc).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 

From 874f79ca7cc0d14bb6741c49f89717d51d4c536b Mon Sep 17 00:00:00 2001
From: Alex Bartlett <bartlettalexandra@gmail.com>
Date: Wed, 20 Nov 2024 11:32:27 -0500
Subject: [PATCH 09/15] update snapshot to include out not out.junc

---
 .../junctionsextract/tests/main.nf.test.snap  | 70 ++++++++++++++-----
 1 file changed, 52 insertions(+), 18 deletions(-)

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 2c170aaec64..18c58455472 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test.snap
@@ -1,38 +1,72 @@
 {
     "homo_sapiens - bam-bai - stub": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
+                ],
+                "junc": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T16:13:20.817212"
+        "timestamp": "2024-11-20T11:29:52.982213"
     },
     "homo_sapiens - bam-bai": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
+                ],
+                "junc": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.junc:md5,c0ccba2d76e9cb1588ba6d2e18c0742c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T16:13:16.43357"
+        "timestamp": "2024-11-20T11:29:48.572345"
     }
 }
\ No newline at end of file

From 213e52b97d6909972d4ddb48b0f0a1c97a9a9ab8 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 11:57:40 -0500
Subject: [PATCH 10/15] Update
 modules/nf-core/regtools/junctionsextract/environment.yml

Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/environment.yml b/modules/nf-core/regtools/junctionsextract/environment.yml
index 0da59d41268..c8e4700cb36 100644
--- a/modules/nf-core/regtools/junctionsextract/environment.yml
+++ b/modules/nf-core/regtools/junctionsextract/environment.yml
@@ -1,5 +1,4 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "regtools_junctionsextract"
 channels:
   - conda-forge
   - bioconda

From cb8a955258eb3a95e2be166552ae7fd138125a11 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 11:58:03 -0500
Subject: [PATCH 11/15] Update
 modules/nf-core/regtools/junctionsextract/main.nf

Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index 2a665e3e040..78e61475aa0 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -4,7 +4,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
 
     conda "bioconda::regtools=0.5.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/regtools:0.5.0--he941832_0' :
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b6c0653189b95b22e16038f61ade205a865857f54eeae9ba0184490a1834f7c9/data' :
         'biocontainers/regtools:0.5.0--he941832_0' }"
 
     input:

From bbe3ebeede5137a6c395c445849dacb31de4a222 Mon Sep 17 00:00:00 2001
From: Alex Bartlett <74612800+abartlett004@users.noreply.github.com>
Date: Wed, 20 Nov 2024 11:58:14 -0500
Subject: [PATCH 12/15] Update
 modules/nf-core/regtools/junctionsextract/main.nf

Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
---
 modules/nf-core/regtools/junctionsextract/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index 78e61475aa0..c65e65ac3be 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -5,7 +5,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
     conda "bioconda::regtools=0.5.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/b6/b6c0653189b95b22e16038f61ade205a865857f54eeae9ba0184490a1834f7c9/data' :
-        'biocontainers/regtools:0.5.0--he941832_0' }"
+        'community.wave.seqera.io/library/regtools:0.5.0--b9a260c4c898354a' }"
 
     input:
     tuple val(meta), path(bam), path(bai)

From 7f83705e434b0e227bc1e3d4799c29f5aaa28eca Mon Sep 17 00:00:00 2001
From: Alex Bartlett <bartlettalexandra@gmail.com>
Date: Wed, 20 Nov 2024 13:09:31 -0500
Subject: [PATCH 13/15] fix meta.yml

---
 .../nf-core/regtools/junctionsextract/meta.yml   | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/regtools/junctionsextract/meta.yml b/modules/nf-core/regtools/junctionsextract/meta.yml
index d20bda1a05a..66e494a4b06 100644
--- a/modules/nf-core/regtools/junctionsextract/meta.yml
+++ b/modules/nf-core/regtools/junctionsextract/meta.yml
@@ -1,7 +1,7 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "regtools_junctionsextract"
-description: Extract exon-exon junctions from an RNAseq BAM file. The output is a BED file in the BED12 format.
+description: Extract exon-exon junctions from an RNAseq BAM file. The output is a
+  BED file in the BED12 format.
 keywords:
   - regtools
   - leafcutter
@@ -9,11 +9,13 @@ keywords:
   - splicing
 tools:
   - "regtools":
-      description: "RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context."
+      description: "RegTools is a set of tools that integrate DNA-seq and RNA-seq data
+        to help interpret mutations in a regulatory and splicing context."
       homepage: "https://regtools.readthedocs.io/en/latest/"
       documentation: "https://regtools.readthedocs.io/en/latest/#usage"
       tool_dev_url: "https://github.com/griffithlab/regtools"
       licence: ["MIT"]
+      identifier: biotools:regtools
 
 input:
   - - meta:
@@ -37,16 +39,16 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - junc:
+      - "*.junc":
           type: file
-          description: BED12 file containing exon-exon junctions
+          description: |
+            BED12 file containing exon-exon "regtools_junctionsextract"
           pattern: "*.{junc}"
   - versions:
-      - versions:
+      - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
-
 authors:
   - "@abartlett004"
 maintainers:

From f75790e6cdd7fb3cd553d994192824846edd618f Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Wed, 20 Nov 2024 13:23:49 -0600
Subject: [PATCH 14/15] test: Add versions check

---
 modules/nf-core/regtools/junctionsextract/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
index d301fc796f4..fbbf55e1ad5 100644
--- a/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
+++ b/modules/nf-core/regtools/junctionsextract/tests/main.nf.test
@@ -53,7 +53,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match() },
+                { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }
             )
         }
 

From 3a185f6dbffb8bee159725a57733154c0ed25f20 Mon Sep 17 00:00:00 2001
From: "Edmund Miller (aider)" <git@edmundmiller.dev>
Date: Wed, 20 Nov 2024 13:28:45 -0600
Subject: [PATCH 15/15] fix: Update regtools version extraction regex in
 junctionsextract module

---
 .../nf-core/regtools/junctionsextract/main.nf |  4 +--
 .../junctionsextract/tests/main.nf.test.snap  | 26 ++++++++++++++-----
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/regtools/junctionsextract/main.nf b/modules/nf-core/regtools/junctionsextract/main.nf
index c65e65ac3be..7884ab92eca 100644
--- a/modules/nf-core/regtools/junctionsextract/main.nf
+++ b/modules/nf-core/regtools/junctionsextract/main.nf
@@ -28,7 +28,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        regtools: \$(regtools --version 2>&1 | sed 's/^.*regtools //; s/ .*\$//')
+        regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
     END_VERSIONS
     """
 
@@ -39,7 +39,7 @@ process REGTOOLS_JUNCTIONSEXTRACT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        regtools: \$(regtools --version 2>&1 | sed 's/^.*regtools //; s/ .*\$//')
+        regtools: \$(regtools --version 2>&1 | grep "Version:" | sed 's/Version:\t//')
     END_VERSIONS
     """
 }
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 18c58455472..9c365497e5e 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,b2432b2a81fb72994ef780a8e979d853"
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
                 ],
                 "junc": [
                     [
@@ -24,7 +24,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
                 ]
             }
         ],
@@ -32,7 +32,21 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-20T11:29:52.982213"
+        "timestamp": "2024-11-20T13:29:27.373772"
+    },
+    "versions": {
+        "content": [
+            {
+                "REGTOOLS_JUNCTIONSEXTRACT": {
+                    "regtools": "0.5.0"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T13:29:27.448238"
     },
     "homo_sapiens - bam-bai": {
         "content": [
@@ -47,7 +61,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
                 ],
                 "junc": [
                     [
@@ -59,7 +73,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b2432b2a81fb72994ef780a8e979d853"
+                    "versions.yml:md5,b8a1d662548217fc4607214fb7b4f42c"
                 ]
             }
         ],
@@ -67,6 +81,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-20T11:29:48.572345"
+        "timestamp": "2024-11-20T13:29:23.165022"
     }
 }
\ No newline at end of file