Merge pull request #236 from JoseEspinosa/fixes

Update samplesheet to version 1.2
nf-core · Jan 8, 2025 · 1f8f208 · 1f8f208
2 parents 4fed074 + 3eb560f
commit 1f8f208
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Showing 17 changed files with 23 additions and 22 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,14 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Enhancements & fixes
 
-- [[#177](https://github.com/nf-core/proteinfold/issues/177)]- Fix typo in some instances of model preset `alphafold2_ptm`.
+- [[#177](https://github.com/nf-core/proteinfold/issues/177)] - Fix typo in some instances of model preset `alphafold2_ptm`.
 - [[PR #178](https://github.com/nf-core/proteinfold/pull/178)] - Enable running multiple modes in parallel.
-- [[#179](https://github.com/nf-core/proteinfold/issues/179)]- Produce an interactive html report for the predicted structures.
-- [[#180](https://github.com/nf-core/proteinfold/issues/180)]- Implement Fooldseek.
-- [[#188](https://github.com/nf-core/proteinfold/issues/188)]- Fix colabfold image to run in gpus.
+- [[#179](https://github.com/nf-core/proteinfold/issues/179)] - Produce an interactive html report for the predicted structures.
+- [[#180](https://github.com/nf-core/proteinfold/issues/180)] - Implement Fooldseek.
+- [[#188](https://github.com/nf-core/proteinfold/issues/188)] - Fix colabfold image to run in gpus.
 - [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.
-- [[PR #210](https://github.com/nf-core/proteinfold/pull/210)]- Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure.
-- [[#214](https://github.com/nf-core/proteinfold/issues/214)]- Fix colabfold image to run in cpus after [#188](https://github.com/nf-core/proteinfold/issues/188) fix.
+- [[PR #210](https://github.com/nf-core/proteinfold/pull/210)] - Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure.
+- [[#214](https://github.com/nf-core/proteinfold/issues/214)] - Fix colabfold image to run in cpus after [#188](https://github.com/nf-core/proteinfold/issues/188) fix.
+- [[#235](https://github.com/nf-core/proteinfold/issues/235)] - Update samplesheet to new version (switch from `sequence` column to `id`).
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
 

diff --git a/conf/test.config b/conf/test.config
@@ -28,7 +28,7 @@ params {
     // Input data to test alphafold2 analysis
     mode            = 'alphafold2'
     alphafold2_mode = 'standard'
-    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     alphafold2_db   = "${projectDir}/assets/dummy_db_dir"
 }
 

diff --git a/conf/test_alphafold_download.config b/conf/test_alphafold_download.config
@@ -28,7 +28,7 @@ params {
     // Input data to test alphafold2 analysis
     mode            = 'alphafold2'
     alphafold2_mode = 'standard'
-    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
 }
 
 process {

diff --git a/conf/test_alphafold_split.config b/conf/test_alphafold_split.config
@@ -28,7 +28,7 @@ params {
     // Input data to test alphafold2 splitting MSA from prediction analysis
     mode            = 'alphafold2'
     alphafold2_mode = 'split_msa_prediction'
-    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     alphafold2_db   = "${projectDir}/assets/dummy_db_dir"
 }
 

diff --git a/conf/test_colabfold_download.config b/conf/test_colabfold_download.config
@@ -28,7 +28,7 @@ params {
     // Input data to test colabfold analysis
     mode             = 'colabfold'
     colabfold_server = 'webserver'
-    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
 }
 
 process {

diff --git a/conf/test_colabfold_local.config b/conf/test_colabfold_local.config
@@ -27,7 +27,7 @@ params {
     mode             = 'colabfold'
     colabfold_server = 'local'
     colabfold_db     = "${projectDir}/assets/dummy_db_dir"
-    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
 }
 
 process {

diff --git a/conf/test_colabfold_webserver.config b/conf/test_colabfold_webserver.config
@@ -27,7 +27,7 @@ params {
     mode             = 'colabfold'
     colabfold_server = 'webserver'
     colabfold_db     = "${projectDir}/assets/dummy_db_dir"
-    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
 }
 
 process {

diff --git a/conf/test_esmfold.config b/conf/test_esmfold.config
@@ -26,7 +26,7 @@ params {
     // Input data to test esmfold
     mode             = 'esmfold'
     esmfold_db       = "${projectDir}/assets/dummy_db_dir"
-    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
 }
 
 process {

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,6 +17,6 @@ params {
     // Input data for full test of alphafold standard mode
     mode            = 'alphafold2'
     alphafold2_mode = 'standard'
-    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     alphafold2_db   = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
 }
diff --git a/conf/test_full_alphafold_multimer.config b/conf/test_full_alphafold_multimer.config
@@ -18,6 +18,6 @@ params {
     mode                    = 'alphafold2'
     alphafold2_mode         = 'standard'
     alphafold2_model_preset = 'multimer'
-    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
+    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet_multimer.csv'
     alphafold2_db           = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
 }
diff --git a/conf/test_full_alphafold_split.config b/conf/test_full_alphafold_split.config
@@ -17,6 +17,6 @@ params {
     // Input data to test colabfold with a local server analysis
     mode            = 'alphafold2'
     alphafold2_mode = 'split_msa_prediction'
-    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     alphafold2_db   = 's3://proteinfold-dataset/test-data/db/alphafold_mini'
 }
diff --git a/conf/test_full_colabfold_local.config b/conf/test_full_colabfold_local.config
@@ -19,7 +19,7 @@ params {
     mode                    = 'colabfold'
     colabfold_server        = 'local'
     colabfold_model_preset  = 'alphafold2_ptm'
-    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     colabfold_db            = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
 }
 process {

diff --git a/conf/test_full_colabfold_webserver.config b/conf/test_full_colabfold_webserver.config
@@ -18,6 +18,6 @@ params {
     mode                   = 'colabfold'
     colabfold_server       = 'webserver'
     colabfold_model_preset = 'alphafold2_ptm'
-    input                  = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input                  = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     colabfold_db            = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
 }
diff --git a/conf/test_full_colabfold_webserver_multimer.config b/conf/test_full_colabfold_webserver_multimer.config
@@ -18,6 +18,6 @@ params {
     mode                   = 'colabfold'
     colabfold_server       = 'webserver'
     colabfold_model_preset = 'alphafold2_multimer_v3'
-    input                  = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
+    input                  = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet_multimer.csv'
     colabfold_db           = 's3://proteinfold-dataset/test-data/db/colabfold_mini'
 }
diff --git a/conf/test_full_esmfold.config b/conf/test_full_esmfold.config
@@ -17,6 +17,6 @@ params {
     // Input data for full test of esmfold monomer
     mode                    = 'esmfold'
     esmfold_model_preset    = 'monomer'
-    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet.csv'
     esmfold_db              = 's3://proteinfold-dataset/db/esmfold'
 }
diff --git a/conf/test_full_esmfold_multimer.config b/conf/test_full_esmfold_multimer.config
@@ -17,6 +17,6 @@ params {
     // Input data for full test of esmfold multimer
     mode                    = 'esmfold'
     esmfold_model_preset    = 'multimer'
-    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
+    input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet_multimer.csv'
     esmfold_db              = 's3://proteinfold-dataset/test-data/db/esmfold'
 }
diff --git a/conf/test_split_fasta.config b/conf/test_split_fasta.config
@@ -28,7 +28,7 @@ params {
     colabfold_server = 'local'
     split_fasta      = true
     colabfold_db     = "${projectDir}/assets/dummy_db_dir"
-    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet_multimer.csv'
+    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.2/samplesheet_multimer.csv'
 }
 
 process {