Update all nf-core modules and subworkflows

nf-core · Jan 8, 2024 · 20769af · 20769af
1 parent c135899
commit 20769af
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Showing 42 changed files with 690 additions and 1,507 deletions.
diff --git a/modules.json b/modules.json
@@ -7,23 +7,22 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
-                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
-                        "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
+                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
+                        "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
+                        "git_sha": "b1d2002587ed81dcd0f4b4ffa79fcdbda59b4e80",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     }
                 }
@@ -32,22 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "4125fb0c2152efbcec8d9ed71a756c9274b2f7f5",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "nextflowpipelineutils": {
-                        "branch": "master",
-                        "git_sha": "1405b3d5078f108f86a2c122846ed2797b4ec8bf",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "nfcore_pipeline_utils": {
-                        "branch": "master",
-                        "git_sha": "b1f3d31bbf14fe83959cc03f98db96c6b4f73b37",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "nfvalidation_plugin_utils": {
-                        "branch": "master",
-                        "git_sha": "a8223a72def6cc46f4652a348feba21845ce68c6",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     }
                 }

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