update authors (#835)

* update authors * update authors * update changelog --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
openpipelines-bio · Jul 15, 2024 · 6bcfac3 · 6bcfac3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -62,6 +62,10 @@
   One notable example of this happening is when one of the samples does not have a multimodal annotation dataframe 
   which is present in another sample; causing the values being filled with `NA` (PR #837).
 
+## DOCUMENTATION
+
+* Update authorship of components (PR #835).
+
 # openpipelines 1.0.0-rc6
 
 ## BUG FIXES

diff --git a/src/authors/elizabeth_mlynarski.yaml b/src/authors/elizabeth_mlynarski.yaml
@@ -0,0 +1,8 @@
+name: Elizabeth Mlynarski
+info:
+  role: Contributor
+  links:
+    email: [email protected]
+  organizations:
+    - name: Janssen R&D US
+      role: Principal Scientist Computational Genomics
diff --git a/src/authors/weiwei_schultz.yaml b/src/authors/weiwei_schultz.yaml
@@ -0,0 +1,8 @@
+name: Weiwei Schultz
+info:
+  role: Contributor
+  links:
+    email: [email protected]
+  organizations:
+    - name: Janssen R&D US
+      role: Associate Director Data Sciences
diff --git a/src/demux/bcl_convert/config.vsh.yaml b/src/demux/bcl_convert/config.vsh.yaml
@@ -11,6 +11,10 @@ functionality:
       roles: [ author, maintainer ]
     - __merge__: /src/authors/marijke_van_moerbeke.yaml
       roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
+    - __merge__: /src/authors/dorien_roosen.yaml
+      roles: [ author ]
   arguments:
     - name: "--input"
       alternatives: [ "-i" ]

diff --git a/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml b/src/feature_annotation/score_genes_cell_cycle_scanpy/config.vsh.yaml
@@ -3,7 +3,12 @@ functionality:
   namespace: feature_annotation
   authors:
     - __merge__: /src/authors/robrecht_cannoodt.yaml
+      roles: [ author ]
     - __merge__: /src/authors/dorien_roosen.yaml
+      roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
+
   description: |
     Calculates the score associated to S phase and G2M phase and annotates the cell cycle phase for each cell, as implemented by scanpy. 
     The score is the average expression of a set of genes subtracted with the average expression of a reference set of genes.

diff --git a/src/feature_annotation/score_genes_scanpy/config.vsh.yaml b/src/feature_annotation/score_genes_scanpy/config.vsh.yaml
@@ -3,7 +3,12 @@ functionality:
   namespace: feature_annotation
   authors:
     - __merge__: /src/authors/robrecht_cannoodt.yaml
+      roles: [ author ]
     - __merge__: /src/authors/dorien_roosen.yaml
+      roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
+
   description: |
     Calculates the score of a set of genes for each cell, as implemented by scanpy. 
     The score is the average expression of a set of genes subtracted with the average expression of a reference set of genes.

diff --git a/src/mapping/cellranger_multi/config.vsh.yaml b/src/mapping/cellranger_multi/config.vsh.yaml
@@ -9,6 +9,10 @@ functionality:
       roles: [ author, maintainer ]
     - __merge__: /src/authors/dries_de_maeyer.yaml
       roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
+    - __merge__: /src/authors/dorien_roosen.yaml
+      roles: [ author ]
   __merge__: /src/mapping/cellranger_multi/cellranger_multi.yaml
   argument_groups:
     - name: Outputs

diff --git a/src/mapping/cellranger_multi/script.py b/src/mapping/cellranger_multi/script.py
@@ -57,7 +57,7 @@
   'memory_pb': None,
   'temp_dir': '/tmp',
   'config': './target/docker/mapping/cellranger_multi/.config.vsh.yaml',
-  'resources_dir': '/Users/dorienroosen/code/openpipeline'
+  'resources_dir': './resources_test'
 }
 ## VIASH END
 

diff --git a/src/scgpt/binning/config.vsh.yaml b/src/scgpt/binning/config.vsh.yaml
@@ -6,6 +6,10 @@ functionality:
   authors:
     - __merge__: /src/authors/dorien_roosen.yaml
       roles: [ maintainer, author ]
+    - __merge__: /src/authors/elizabeth_mlynarski.yaml
+      roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
 
   argument_groups:
     - name: Inputs

diff --git a/src/scgpt/cross_check_genes/config.vsh.yaml b/src/scgpt/cross_check_genes/config.vsh.yaml
@@ -5,9 +5,14 @@ functionality:
     Cross-check genes with pre-trained scGPT model.
   authors:
     - __merge__: /src/authors/jakub_majercik.yaml
-      roles: [ maintainer, author ]
+      roles: [ author ]
     - __merge__: /src/authors/dorien_roosen.yaml
       roles: [ maintainer, author ]
+    - __merge__: /src/authors/elizabeth_mlynarski.yaml
+      roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
+
 
   argument_groups:
     - name: Inputs

diff --git a/src/scgpt/embedding/config.vsh.yaml b/src/scgpt/embedding/config.vsh.yaml
@@ -6,6 +6,10 @@ functionality:
   authors:
     - __merge__: /src/authors/dorien_roosen.yaml
       roles: [ maintainer, author ]
+    - __merge__: /src/authors/elizabeth_mlynarski.yaml
+      roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
 
   argument_groups:
     - name: Inputs

diff --git a/src/scgpt/pad_tokenize/config.vsh.yaml b/src/scgpt/pad_tokenize/config.vsh.yaml
@@ -6,6 +6,10 @@ functionality:
   authors:
     - __merge__: /src/authors/dorien_roosen.yaml
       roles: [ maintainer, author ]
+    - __merge__: /src/authors/elizabeth_mlynarski.yaml
+      roles: [ author ]
+    - __merge__: /src/authors/weiwei_schultz.yaml
+      roles: [ contributor ]
 
   argument_groups:
     - name: Inputs