Merge pull request #118 from vib-singlecell-nf/develop

Develop Former-commit-id: c05335e
vib-singlecell-nf · Feb 8, 2020 · 129bbc2 · 129bbc2
2 parents 7a08663 + 81214fa
commit 129bbc2
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diff --git a/README.md b/README.md
@@ -410,6 +410,24 @@ params {
 }
 ```
 
+## Parameter benchmarking
+
+The latest version only implements this feature for the following pipelines:
+
+- `single_sample`
+- `bbknn`
+
+Since `v0.9.0`, it is possible to benchmark several combinations of parameters. The current version (`v0.9.0`) of the VSN-Pipelines allows to benchmark the following parameters:
+- `params.sc.scanpy.clustering`
+  - `method`
+```
+clusteringMethods = ['louvain','leiden']
+```
+  - `resolution`
+```
+resolutions = [0.4, 0.8]
+```
+
 # Development
 
 ## Repository structure

diff --git a/examples/hungr_2019/10x_bbknn_scenic.config b/examples/hungr_2019/10x_bbknn_scenic.config
@@ -73,7 +73,7 @@ params {
          }
          clustering {
             report_ipynb = '/src/scanpy/bin/reports/sc_clustering_report.ipynb'
-            clusteringMethod = 'Louvain'
+            clusteringMethod = 'louvain'
             resolution = 2
             iff = '10x_cellranger_mex'
             off = 'h5ad'

diff --git a/src/scanpy b/src/scanpy
+39 −32		bin/cluster/sc_clustering.py
+34 −10		bin/reports/sc_bbknn_report.ipynb
+56 −13		bin/reports/sc_clustering_report.ipynb
+1 −1		conf/base.config
+4 −1		processes/batch_effect_correct.nf
+96 −0		processes/cluster.nf
+39 −12		processes/dim_reduction.nf
+51 −1		processes/marker_genes.nf
+58 −10		processes/reports.nf
+44 −12		workflows/bec_bbknn.nf
+2 −1		workflows/bec_mnn_correct.nf
+38 −10		workflows/cluster_identification.nf
+29 −12		workflows/create_report.nf
+9 −4		workflows/dim_reduction.nf
+1 −1		workflows/dim_reduction_pca.nf
+2 −1		workflows/hvg_selection.nf
+1 −2		workflows/qc_filter.nf