Merge pull request #249 from adamrtalbot/update_modules_to_use_test_path

Update modules to use absolute path data
nf-core · Jan 14, 2024 · 8a55a59 · 8a55a59
2 parents ea0a0a3 + 30031c0
commit 8a55a59
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #243](https://github.com/nf-core/fetchngs/pull/243) - Fixes for [PR #238](https://github.com/nf-core/fetchngs/pull/238)
 - [PR #246](https://github.com/nf-core/fetchngs/pull/246) - Handle dark/light mode for logo in GitHub README properly
 - [PR #248](https://github.com/nf-core/fetchngs/pull/248) - Update pipeline level test data path to use mirror on s3
+- [PR #249](https://github.com/nf-core/fetchngs/pull/249) - Update modules which includes absolute paths for test data, making module level test compatible within the pipeline.
 
 ### Software dependencies
 

diff --git a/modules.json b/modules.json
@@ -7,22 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "20e78a9868eaa69c8cac91152397def32374b807",
                         "installed_by": ["modules"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "bdfd7bc8d2e5a93531e14bd94c4128d9a72a2435",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {
@@ -41,7 +41,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "c81784b47d44464b35e04220e00051bb5be27524",
+                        "git_sha": "524ccbab145985b26eb7daa6e551af486dab2100",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {

diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/nf-core/custom/sratoolsncbisettings/environment.yml
diff --git a/modules/nf-core/custom/sratoolsncbisettings/main.nf b/modules/nf-core/custom/sratoolsncbisettings/main.nf
diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test.snap
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml