Merge pull request #348 from Darcy220606/update_configs

change samplesheet from large testdataset to reduced
nf-core · Mar 19, 2024 · 5b0f311 · 5b0f311
2 parents ec600ff + 10dcce5
commit 5b0f311
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Showing 16 changed files with 664 additions and 21 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,4 +6,3 @@ results/
 testing/
 testing*
 *.pyc
-tests/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#348](https://github.com/nf-core/funcscan/pull/348) Updated samplesheet for pipeline tests to 'samplesheet_reduced.csv' with smaller datasets to reduce resource consumption. Updated prodigal module to fix pigz issue. (by @darcy220606)
+
 ### `Dependencies`
 
 | Tool    | Previous version | New version |

diff --git a/conf/test.config b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv'
+    input                = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv'
     amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm'
 
     annotation_tool         = 'prodigal'

diff --git a/conf/test_bgc.config b/conf/test_bgc.config
@@ -20,7 +20,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv'
+    input                = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv'
     bgc_hmmsearch_models = 'https://raw.githubusercontent.com/antismash/antismash/fd61de057e082fbf071732ac64b8b2e8883de32f/antismash/detection/hmm_detection/data/ToyB.hmm'
 
     annotation_tool      = 'prodigal'

diff --git a/conf/test_nothing.config b/conf/test_nothing.config
@@ -22,7 +22,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet.csv'
+    input                = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/samplesheet_reduced.csv'
     amp_hmmsearch_models = 'https://raw.githubusercontent.com/nf-core/test-datasets/funcscan/hmms/mybacteriocin.hmm'
 
     annotation_tool         = 'prodigal'

diff --git a/modules.json b/modules.json
@@ -143,7 +143,7 @@
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "2a196d6bfea8b6b5f49fc1885e39fae5f50bc2a0",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
@@ -153,7 +153,7 @@
                     },
                     "pyrodigal": {
                         "branch": "master",
-                        "git_sha": "0e70547d116de782ec3825f1a449a56abb894482",
+                        "git_sha": "94c4df7840d1ee5ec4d817310ff60b02e6459353",
                         "installed_by": ["modules"]
                     },
                     "rgi/main": {

diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf
diff --git a/modules/nf-core/prodigal/tests/main.nf.test b/modules/nf-core/prodigal/tests/main.nf.test
diff --git a/modules/nf-core/prodigal/tests/main.nf.test.snap b/modules/nf-core/prodigal/tests/main.nf.test.snap
diff --git a/modules/nf-core/prodigal/tests/tags.yml b/modules/nf-core/prodigal/tests/tags.yml
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,4 +6,3 @@ results/ @@
     testing/
     testing*
     *.pyc
-    tests/