Merge pull request #89 from nf-core/refactor-sra

refactor: use nf-core modules for sratools subworkflow
nf-core · May 16, 2022 · 094f5f7 · 094f5f7
2 parents 3a795cb + 3630eb6
commit 094f5f7
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Showing 16 changed files with 370 additions and 205 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
+- [#89](https://github.com/nf-core/fetchngs/pull/89) - Improve detection and usage of the NCBI user settings by using the standardized sra-tools modules from nf-core.
+
 - [[nf-core/rnaseq#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 

diff --git a/bin/retry_with_backoff.sh b/bin/retry_with_backoff.sh
diff --git a/modules.json b/modules.json
@@ -5,6 +5,15 @@
         "nf-core/modules": {
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+            },
+            "custom/sratoolsncbisettings": {
+                "git_sha": "b2dbaa99309a2057efc32ef9d029ed91140068df"
+            },
+            "sratools/fasterqdump": {
+                "git_sha": "0cdf7767a79faf424645beeff83ecfa5528b6a7c"
+            },
+            "sratools/prefetch": {
+                "git_sha": "1b228835e9525990db99243cb4f0d07aa6e01bc3"
             }
         }
     }

diff --git a/modules/local/sratools_prefetch.nf b/modules/local/sratools_prefetch.nf
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf b/modules/nf-core/modules/custom/sratoolsncbisettings/main.nf
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/modules/custom/sratoolsncbisettings/meta.yml
diff --git a/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh b/modules/nf-core/modules/custom/sratoolsncbisettings/templates/detect_ncbi_settings.sh
diff --git a/modules/local/sratools_fasterqdump.nf → ...core/modules/sratools/fasterqdump/main.nf b/modules/local/sratools_fasterqdump.nf → ...core/modules/sratools/fasterqdump/main.nf
diff --git a/modules/nf-core/modules/sratools/fasterqdump/meta.yml b/modules/nf-core/modules/sratools/fasterqdump/meta.yml