Merge pull request #324 from nf-core/modules-update

Update deeparg/deepbgc versions
nf-core · Dec 13, 2023 · 38da7c2 · 38da7c2
2 parents bb2f4a8 + 38c9787
commit 38da7c2
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,14 +8,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz)
+- [#324](https://github.com/nf-core/funcscan/pull/324) Removed separate DeepARG test profile because database download is now stable. (by @jasmezz)
 
 ### `Fixed`
 
 ### `Dependencies`
 
 | Tool    | Previous version | New version |
 | ------- | ---------------- | ----------- |
-| MultiQC | 1.15             | 1.17        |
+| DeepARG | 1.0.2            | 1.0.4       |
+| DeepBGC | 0.1.30           | 0.1.31      |
+| MultiQC | 1.15             | 1.18        |
 
 ### `Deprecated`
 

diff --git a/conf/test.config b/conf/test.config
@@ -29,8 +29,6 @@ params {
     arg_fargene_hmmmodel    = 'class_a,class_b_1_2'
     // Database download regularly fails due to server downtime
     // Tested instead with -profile test_deeparg to allow checking of other tools
-    arg_skip_deeparg        = true
-
 
     run_amp_screening       = true
 }
diff --git a/conf/test_deeparg.config b/conf/test_deeparg.config
diff --git a/modules.json b/modules.json
@@ -7,173 +7,173 @@
                 "nf-core": {
                     "abricate/run": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "ampcombi": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "ampir": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "amplify/predict": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "b15e8f066db9071996e83c0bec4a5d1a6e0b7b65",
                         "installed_by": ["modules"]
                     },
                     "amrfinderplus/run": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "amrfinderplus/update": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "antismash/antismashlite": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "antismash/antismashlitedownloaddatabases": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bioawk": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/bioawk/bioawk.diff"
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f",
+                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
                         "installed_by": ["modules"]
                     },
                     "deeparg/downloaddata": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "045be63d4c76c2cf4e7ca263e8c2b5fbce2ab070",
                         "installed_by": ["modules"]
                     },
                     "deeparg/predict": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "045be63d4c76c2cf4e7ca263e8c2b5fbce2ab070",
                         "installed_by": ["modules"]
                     },
                     "deepbgc/download": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f315f85d9ac6c321f6e3596493fd61019340df2a",
                         "installed_by": ["modules"]
                     },
                     "deepbgc/pipeline": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "f315f85d9ac6c321f6e3596493fd61019340df2a",
                         "installed_by": ["modules"]
                     },
                     "fargene": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "2506084773f9fa01b65b25058cd5a010f87395b4",
                         "installed_by": ["modules"]
                     },
                     "gecco/run": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hamronization/abricate": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hamronization/amrfinderplus": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hamronization/deeparg": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hamronization/fargene": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hamronization/rgi": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hamronization/summarize": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "macrel/contigs": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "pyrodigal": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "rgi/main": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/abricate/run/environment.yml b/modules/nf-core/abricate/run/environment.yml
diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml
diff --git a/modules/nf-core/ampir/environment.yml b/modules/nf-core/ampir/environment.yml
diff --git a/modules/nf-core/amplify/predict/environment.yml b/modules/nf-core/amplify/predict/environment.yml
diff --git a/modules/nf-core/amplify/predict/meta.yml b/modules/nf-core/amplify/predict/meta.yml
diff --git a/modules/nf-core/amrfinderplus/run/environment.yml b/modules/nf-core/amrfinderplus/run/environment.yml
diff --git a/modules/nf-core/amrfinderplus/update/environment.yml b/modules/nf-core/amrfinderplus/update/environment.yml
diff --git a/modules/nf-core/antismash/antismashlite/environment.yml b/modules/nf-core/antismash/antismashlite/environment.yml
diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml
diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml
diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml
diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/deeparg/downloaddata/environment.yml b/modules/nf-core/deeparg/downloaddata/environment.yml
diff --git a/modules/nf-core/deeparg/downloaddata/main.nf b/modules/nf-core/deeparg/downloaddata/main.nf
diff --git a/modules/nf-core/deeparg/downloaddata/meta.yml b/modules/nf-core/deeparg/downloaddata/meta.yml