Bump TRGT to 1.5.0 (#7346)

nf-core · Jan 23, 2025 · 9b9d7d0 · 9b9d7d0
1 parent 3d18fc5
commit 9b9d7d0
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Showing 9 changed files with 66 additions and 66 deletions.
diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::trgt=1.2.0"
+  - "bioconda::trgt=1.5.0"
diff --git a/modules/nf-core/trgt/genotype/main.nf b/modules/nf-core/trgt/genotype/main.nf
@@ -4,8 +4,8 @@ process TRGT_GENOTYPE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
-        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/trgt:1.5.0--h9ee0642_0':
+        'biocontainers/trgt:1.5.0--h9ee0642_0' }"
 
     input:
     tuple val(meta) , path(bam), path(bai), val(karyotype)

diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test.snap b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap
@@ -7,46 +7,46 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e"
+                        "test.vcf.gz:md5,e60da9fd3a401595263df8822c3e5044"
                     ]
                 ],
                 "1": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37"
+                        "test.spanning.bam:md5,83cc54729b657edbc30670926c357a5f"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ],
                 "bam": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37"
+                        "test.spanning.bam:md5,83cc54729b657edbc30670926c357a5f"
                     ]
                 ],
                 "vcf": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e"
+                        "test.vcf.gz:md5,e60da9fd3a401595263df8822c3e5044"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T16:07:55.029938504"
+        "timestamp": "2025-01-22T16:47:21.469366302"
     },
     "homo sapiens - [bam,bai,[]], [fa,fai], bed - stub": {
         "content": [
@@ -56,46 +56,46 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                        "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855"
                     ]
                 ],
                 "1": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                        "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ],
                 "bam": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                        "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6"
                     ]
                 ],
                 "vcf": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                        "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T16:08:33.937952067"
+        "timestamp": "2025-01-22T16:48:00.564096612"
     },
     "homo sapiens - [bam,bai,XX], [fa,fai], bed - stub": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ],
                 "bam": [
                     [
@@ -136,15 +136,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T16:16:39.197756426"
+        "timestamp": "2025-01-22T16:47:47.478426582"
     },
     "homo sapiens - [bam,bai,[]], [fa,fai], bed": {
         "content": [
@@ -154,45 +154,45 @@
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                        "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855"
                     ]
                 ],
                 "1": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                        "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ],
                 "bam": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                        "test.spanning.bam:md5,10cf9b7bd685c862d3c7c9fa0b024bb6"
                     ]
                 ],
                 "vcf": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                        "test.vcf.gz:md5,51b46a9ceadc1ad6d34d5780c80ca855"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                    "versions.yml:md5,425fe64c6fa8f505f252664ca4e388b5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T16:08:07.631383773"
+        "timestamp": "2025-01-22T16:47:35.097638611"
     }
 }
diff --git a/modules/nf-core/trgt/merge/environment.yml b/modules/nf-core/trgt/merge/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::trgt=1.2.0"
+  - "bioconda::trgt=1.5.0"
diff --git a/modules/nf-core/trgt/merge/main.nf b/modules/nf-core/trgt/merge/main.nf
@@ -4,8 +4,8 @@ process TRGT_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
-        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/trgt:1.5.0--h9ee0642_0':
+        'biocontainers/trgt:1.5.0--h9ee0642_0' }"
 
     input:
     tuple val(meta) , path(vcfs), path(tbis)

diff --git a/modules/nf-core/trgt/merge/tests/main.nf.test.snap b/modules/nf-core/trgt/merge/tests/main.nf.test.snap
@@ -5,29 +5,29 @@
             "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=1, phased=false, phasedAutodetect=false]",
             2,
             [
-                "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T14:52:26.329527707"
+        "timestamp": "2025-01-22T16:48:39.055002317"
     },
     "homo sapiens - 2 VCFs": {
         "content": [
             "75acbf6205a44ca44d6fc644dda57d82",
             "VcfFile [chromosomes=[chr22], sampleCount=2, variantCount=1, phased=false, phasedAutodetect=false]",
             2,
             [
-                "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T14:39:54.475134386"
+        "timestamp": "2025-01-22T16:48:22.59942164"
     },
     "homo sapiens - 2 VCFs - stub": {
         "content": [
@@ -41,7 +41,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                    "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef"
                 ],
                 "vcf": [
                     [
@@ -52,29 +52,29 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                    "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T15:06:23.198648143"
+        "timestamp": "2025-01-22T16:49:31.819625734"
     },
     "homo sapiens - 1 VCF - --force-single": {
         "content": [
             "6e09773892c37f17e01c9771e8ef2171",
             "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
             1,
             [
-                "versions.yml:md5,ac3a6dca80725cee1bf724975e54c067"
+                "versions.yml:md5,55e68623bd39d3a94346eb612b5d99ef"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-15T15:01:59.765895584"
+        "timestamp": "2025-01-22T16:49:13.2045895"
     }
 }
diff --git a/modules/nf-core/trgt/plot/environment.yml b/modules/nf-core/trgt/plot/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::trgt=1.2.0"
+  - "bioconda::trgt=1.5.0"
diff --git a/modules/nf-core/trgt/plot/main.nf b/modules/nf-core/trgt/plot/main.nf
@@ -4,8 +4,8 @@ process TRGT_PLOT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
-        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/trgt:1.5.0--h9ee0642_0':
+        'biocontainers/trgt:1.5.0--h9ee0642_0' }"
 
     input:
     tuple val(meta) , path(bam), path(bai), path(vcf), path(tbi), val(repeat_id)

diff --git a/modules/nf-core/trgt/plot/tests/main.nf.test.snap b/modules/nf-core/trgt/plot/tests/main.nf.test.snap
@@ -3,26 +3,26 @@
         "content": [
             "test.png",
             [
-                "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c"
+                "versions.yml:md5,280ac168a069db522950dce55feddbae"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-18T13:58:28.083155724"
+        "timestamp": "2025-01-22T16:50:04.133470512"
     },
     "homo sapiens - [bam, bai, vcf, TEST], fasta, fai, bed": {
         "content": [
             "test_TEST.png",
             [
-                "versions.yml:md5,24cc939a0b88728bae8a2102feaf542c"
+                "versions.yml:md5,280ac168a069db522950dce55feddbae"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-18T13:57:59.291774232"
+        "timestamp": "2025-01-22T16:49:48.231158363"
     }
 }