From d6b868972cd72eb22a63b7398c16208667c6fe74 Mon Sep 17 00:00:00 2001
From: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Tue, 20 Feb 2024 15:41:29 +0100
Subject: [PATCH] OpenPipelines release 0.10.1 (#74)

Co-authored-by: github-actions <github-actions@github.com>
---
 components/modules/annotate/popv.qmd          |   6 +-
 components/modules/cluster/leiden.qmd         |   6 +-
 .../modules/compression/compress_h5mu.qmd     |   6 +-
 .../modules/convert/from_10xh5_to_h5mu.qmd    |   6 +-
 .../modules/convert/from_10xmtx_to_h5mu.qmd   |   6 +-
 .../from_bd_to_10x_molecular_barcode_tags.qmd |   6 +-
 .../modules/convert/from_bdrhap_to_h5mu.qmd   |   6 +-
 .../convert/from_cellranger_multi_to_h5mu.qmd |   6 +-
 .../modules/convert/from_h5ad_to_h5mu.qmd     |   6 +-
 .../modules/convert/from_h5mu_to_h5ad.qmd     |   6 +-
 .../modules/convert/velocyto_to_h5mu.qmd      |   6 +-
 .../cellbender_remove_background.qmd          |   6 +-
 .../cellbender_remove_background_v0_2.qmd     |   6 +-
 components/modules/dataflow/concat.qmd        |   6 +-
 components/modules/dataflow/merge.qmd         |   6 +-
 .../modules/dataflow/split_modalities.qmd     |   6 +-
 components/modules/demux/bcl2fastq.qmd        |   6 +-
 components/modules/demux/bcl_convert.qmd      |   6 +-
 .../modules/demux/cellranger_mkfastq.qmd      |   6 +-
 components/modules/dimred/pca.qmd             |   6 +-
 components/modules/dimred/umap.qmd            |   6 +-
 components/modules/download/download_file.qmd |   6 +-
 .../modules/download/sync_test_resources.qmd  |   6 +-
 components/modules/files/make_params.qmd      |   6 +-
 components/modules/filter/do_filter.qmd       |   6 +-
 .../modules/filter/filter_with_counts.qmd     |   6 +-
 components/modules/filter/filter_with_hvg.qmd |   6 +-
 .../modules/filter/filter_with_scrublet.qmd   |   6 +-
 components/modules/filter/remove_modality.qmd |   6 +-
 components/modules/filter/subset_h5mu.qmd     |   6 +-
 components/modules/integrate/harmonypy.qmd    |   6 +-
 components/modules/integrate/scanorama.qmd    |   6 +-
 components/modules/integrate/scarches.qmd     |   6 +-
 components/modules/integrate/scvi.qmd         |   6 +-
 components/modules/integrate/totalvi.qmd      |   6 +-
 components/modules/interpret/lianapy.qmd      |   6 +-
 components/modules/labels_transfer/knn.qmd    |   6 +-
 .../modules/labels_transfer/xgboost.qmd       |   6 +-
 components/modules/mapping/bd_rhapsody.qmd    |   6 +-
 .../modules/mapping/cellranger_count.qmd      |   6 +-
 .../mapping/cellranger_count_split.qmd        |   6 +-
 .../modules/mapping/cellranger_multi.qmd      |   6 +-
 components/modules/mapping/htseq_count.qmd    |   6 +-
 .../modules/mapping/htseq_count_to_h5mu.qmd   |   6 +-
 components/modules/mapping/multi_star.qmd     |   6 +-
 .../modules/mapping/multi_star_to_h5mu.qmd    |   6 +-
 components/modules/mapping/samtools_sort.qmd  |   6 +-
 components/modules/mapping/star_align.qmd     |   6 +-
 .../modules/mapping/star_align_v273a.qmd      |   6 +-
 .../modules/mapping/star_build_reference.qmd  |   6 +-
 components/modules/metadata/add_id.qmd        |   6 +-
 components/modules/metadata/join_csv.qmd      |   6 +-
 .../modules/metadata/join_uns_to_obs.qmd      |   6 +-
 .../modules/metadata/move_obsm_to_obs.qmd     |   6 +-
 components/modules/neighbors/bbknn.qmd        |   6 +-
 .../modules/neighbors/find_neighbors.qmd      |   6 +-
 .../modules/process_10xh5/filter_10xh5.qmd    |   6 +-
 .../modules/qc/calculate_qc_metrics.qmd       |   6 +-
 components/modules/qc/fastqc.qmd              |   6 +-
 components/modules/qc/multiqc.qmd             |   6 +-
 components/modules/query/cellxgene_census.qmd |   6 +-
 .../reference/build_bdrhap_reference.qmd      |   6 +-
 .../reference/build_cellranger_reference.qmd  |   6 +-
 .../modules/reference/make_reference.qmd      |   6 +-
 components/modules/report/mermaid.qmd         |   6 +-
 components/modules/transfer/publish.qmd       |   6 +-
 components/modules/transform/clr.qmd          |   6 +-
 components/modules/transform/delete_layer.qmd |   6 +-
 components/modules/transform/log1p.qmd        |   6 +-
 .../modules/transform/normalize_total.qmd     |   6 +-
 components/modules/transform/regress_out.qmd  |   6 +-
 components/modules/transform/scale.qmd        |   6 +-
 components/modules/velocity/scvelo.qmd        |   6 +-
 components/modules/velocity/velocyto.qmd      |   6 +-
 .../workflows/ingestion/bd_rhapsody.qmd       |   6 +-
 .../ingestion/cellranger_mapping.qmd          |   6 +-
 .../workflows/ingestion/cellranger_multi.qmd  |   6 +-
 .../ingestion/cellranger_postprocessing.qmd   |   6 +-
 components/workflows/ingestion/conversion.qmd |   6 +-
 components/workflows/ingestion/demux.qmd      |   6 +-
 .../workflows/ingestion/make_reference.qmd    |   6 +-
 .../workflows/multiomics/full_pipeline.qmd    |   6 +-
 .../multiomics/integration/bbknn_leiden.qmd   |  16 +-
 .../multiomics/integration/harmony_leiden.qmd |   6 +-
 .../integration/initialize_integration.qmd    |   6 +-
 .../integration/scanorama_leiden.qmd          |   6 +-
 .../multiomics/integration/scvi_leiden.qmd    | 199 ++++++++++++++++++
 .../multiomics/integration/totalvi_leiden.qmd |   6 +-
 .../workflows/multiomics/multisample.qmd      |   6 +-
 .../workflows/multiomics/prot_multisample.qmd |   6 +-
 .../multiomics/prot_singlesample.qmd          |   6 +-
 .../workflows/multiomics/rna_multisample.qmd  |   6 +-
 .../workflows/multiomics/rna_singlesample.qmd |   6 +-
 93 files changed, 480 insertions(+), 281 deletions(-)
 create mode 100644 components/workflows/multiomics/integration/scvi_leiden.qmd

diff --git a/components/modules/annotate/popv.qmd b/components/modules/annotate/popv.qmd
index 341c6d24..e4bf852d 100644
--- a/components/modules/annotate/popv.qmd
+++ b/components/modules/annotate/popv.qmd
@@ -14,7 +14,7 @@ ID: `popv`
 Namespace: `annotate`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/annotate/popv){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/annotate/popv){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/annotate/popv/main.nf \
   --help
 ```
@@ -70,7 +70,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/annotate/popv/main.nf \
   -params-file params.yaml
diff --git a/components/modules/cluster/leiden.qmd b/components/modules/cluster/leiden.qmd
index 361f7aaf..e96a2113 100644
--- a/components/modules/cluster/leiden.qmd
+++ b/components/modules/cluster/leiden.qmd
@@ -14,7 +14,7 @@ ID: `leiden`
 Namespace: `cluster`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/cluster/leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/cluster/leiden){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -39,7 +39,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/cluster/leiden/main.nf \
   --help
 ```
@@ -66,7 +66,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/cluster/leiden/main.nf \
   -params-file params.yaml
diff --git a/components/modules/compression/compress_h5mu.qmd b/components/modules/compression/compress_h5mu.qmd
index 36706795..3a6e8fa0 100644
--- a/components/modules/compression/compress_h5mu.qmd
+++ b/components/modules/compression/compress_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `compress_h5mu`
 Namespace: `compression`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/compression/compress_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/compression/compress_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -31,7 +31,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/compression/compress_h5mu/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/compression/compress_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_10xh5_to_h5mu.qmd b/components/modules/convert/from_10xh5_to_h5mu.qmd
index fd22f246..d440a219 100644
--- a/components/modules/convert/from_10xh5_to_h5mu.qmd
+++ b/components/modules/convert/from_10xh5_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `from_10xh5_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_10xh5_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_10xh5_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \
   --help
 ```
@@ -61,7 +61,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_10xmtx_to_h5mu.qmd b/components/modules/convert/from_10xmtx_to_h5mu.qmd
index 883ee892..58e35735 100644
--- a/components/modules/convert/from_10xmtx_to_h5mu.qmd
+++ b/components/modules/convert/from_10xmtx_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `from_10xmtx_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_10xmtx_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_10xmtx_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_10xmtx_to_h5mu/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_10xmtx_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_bd_to_10x_molecular_barcode_tags.qmd b/components/modules/convert/from_bd_to_10x_molecular_barcode_tags.qmd
index 00c90cd0..7114f0d5 100644
--- a/components/modules/convert/from_bd_to_10x_molecular_barcode_tags.qmd
+++ b/components/modules/convert/from_bd_to_10x_molecular_barcode_tags.qmd
@@ -14,7 +14,7 @@ ID: `from_bd_to_10x_molecular_barcode_tags`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_bd_to_10x_molecular_barcode_tags){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_bd_to_10x_molecular_barcode_tags){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_bdrhap_to_h5mu.qmd b/components/modules/convert/from_bdrhap_to_h5mu.qmd
index 79a7f130..5444c7c7 100644
--- a/components/modules/convert/from_bdrhap_to_h5mu.qmd
+++ b/components/modules/convert/from_bdrhap_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `from_bdrhap_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_bdrhap_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_bdrhap_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_cellranger_multi_to_h5mu.qmd b/components/modules/convert/from_cellranger_multi_to_h5mu.qmd
index 5d5b5133..fe72fcb1 100644
--- a/components/modules/convert/from_cellranger_multi_to_h5mu.qmd
+++ b/components/modules/convert/from_cellranger_multi_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `from_cellranger_multi_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_cellranger_multi_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_cellranger_multi_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -44,7 +44,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
   --help
 ```
@@ -68,7 +68,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_h5ad_to_h5mu.qmd b/components/modules/convert/from_h5ad_to_h5mu.qmd
index ea6b4e9d..018b5582 100644
--- a/components/modules/convert/from_h5ad_to_h5mu.qmd
+++ b/components/modules/convert/from_h5ad_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `from_h5ad_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_h5ad_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_h5ad_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_h5ad_to_h5mu/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_h5ad_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/from_h5mu_to_h5ad.qmd b/components/modules/convert/from_h5mu_to_h5ad.qmd
index f3d698e8..dcc12810 100644
--- a/components/modules/convert/from_h5mu_to_h5ad.qmd
+++ b/components/modules/convert/from_h5mu_to_h5ad.qmd
@@ -14,7 +14,7 @@ ID: `from_h5mu_to_h5ad`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/convert/from_h5mu_to_h5ad){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/convert/from_h5mu_to_h5ad){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/from_h5mu_to_h5ad/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/from_h5mu_to_h5ad/main.nf \
   -params-file params.yaml
diff --git a/components/modules/convert/velocyto_to_h5mu.qmd b/components/modules/convert/velocyto_to_h5mu.qmd
index 873d1ed6..81464380 100644
--- a/components/modules/convert/velocyto_to_h5mu.qmd
+++ b/components/modules/convert/velocyto_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `velocyto_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/velocity/velocyto_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/velocity/velocyto_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -32,7 +32,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/convert/velocyto_to_h5mu/main.nf \
   --help
 ```
@@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/convert/velocyto_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/correction/cellbender_remove_background.qmd b/components/modules/correction/cellbender_remove_background.qmd
index 0b452614..be86bbe8 100644
--- a/components/modules/correction/cellbender_remove_background.qmd
+++ b/components/modules/correction/cellbender_remove_background.qmd
@@ -14,7 +14,7 @@ ID: `cellbender_remove_background`
 Namespace: `correction`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/correction/cellbender_remove_background){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/correction/cellbender_remove_background){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -35,7 +35,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/correction/cellbender_remove_background/main.nf \
   --help
 ```
@@ -101,7 +101,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/correction/cellbender_remove_background/main.nf \
   -params-file params.yaml
diff --git a/components/modules/correction/cellbender_remove_background_v0_2.qmd b/components/modules/correction/cellbender_remove_background_v0_2.qmd
index 1d117f4f..6121d203 100644
--- a/components/modules/correction/cellbender_remove_background_v0_2.qmd
+++ b/components/modules/correction/cellbender_remove_background_v0_2.qmd
@@ -14,7 +14,7 @@ ID: `cellbender_remove_background_v0_2`
 Namespace: `correction`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/correction/cellbender_remove_background_v0_2){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/correction/cellbender_remove_background_v0_2){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -35,7 +35,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/correction/cellbender_remove_background_v0_2/main.nf \
   --help
 ```
@@ -83,7 +83,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/correction/cellbender_remove_background_v0_2/main.nf \
   -params-file params.yaml
diff --git a/components/modules/dataflow/concat.qmd b/components/modules/dataflow/concat.qmd
index 77890716..f2e14625 100644
--- a/components/modules/dataflow/concat.qmd
+++ b/components/modules/dataflow/concat.qmd
@@ -14,7 +14,7 @@ ID: `concat`
 Namespace: `dataflow`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dataflow/concat){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/dataflow/concat){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/dataflow/concat/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/dataflow/concat/main.nf \
   -params-file params.yaml
diff --git a/components/modules/dataflow/merge.qmd b/components/modules/dataflow/merge.qmd
index 9dd5c31b..46429a4b 100644
--- a/components/modules/dataflow/merge.qmd
+++ b/components/modules/dataflow/merge.qmd
@@ -14,7 +14,7 @@ ID: `merge`
 Namespace: `dataflow`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dataflow/merge){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/dataflow/merge){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/dataflow/merge/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/dataflow/merge/main.nf \
   -params-file params.yaml
diff --git a/components/modules/dataflow/split_modalities.qmd b/components/modules/dataflow/split_modalities.qmd
index a33ff5c8..cdf33427 100644
--- a/components/modules/dataflow/split_modalities.qmd
+++ b/components/modules/dataflow/split_modalities.qmd
@@ -14,7 +14,7 @@ ID: `split_modalities`
 Namespace: `dataflow`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dataflow/split_modalities){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/dataflow/split_modalities){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -31,7 +31,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/dataflow/split_modalities/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/dataflow/split_modalities/main.nf \
   -params-file params.yaml
diff --git a/components/modules/demux/bcl2fastq.qmd b/components/modules/demux/bcl2fastq.qmd
index 0cebf7e3..c86a16f3 100644
--- a/components/modules/demux/bcl2fastq.qmd
+++ b/components/modules/demux/bcl2fastq.qmd
@@ -14,7 +14,7 @@ ID: `bcl2fastq`
 Namespace: `demux`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/demux/bcl2fastq){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/demux/bcl2fastq){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/demux/bcl2fastq/main.nf \
   --help
 ```
@@ -55,7 +55,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/demux/bcl2fastq/main.nf \
   -params-file params.yaml
diff --git a/components/modules/demux/bcl_convert.qmd b/components/modules/demux/bcl_convert.qmd
index c42b2801..578a0af6 100644
--- a/components/modules/demux/bcl_convert.qmd
+++ b/components/modules/demux/bcl_convert.qmd
@@ -14,7 +14,7 @@ ID: `bcl_convert`
 Namespace: `demux`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/demux/bcl_convert){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/demux/bcl_convert){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -33,7 +33,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/demux/bcl_convert/main.nf \
   --help
 ```
@@ -58,7 +58,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/demux/bcl_convert/main.nf \
   -params-file params.yaml
diff --git a/components/modules/demux/cellranger_mkfastq.qmd b/components/modules/demux/cellranger_mkfastq.qmd
index f0a19cc2..141991cb 100644
--- a/components/modules/demux/cellranger_mkfastq.qmd
+++ b/components/modules/demux/cellranger_mkfastq.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_mkfastq`
 Namespace: `demux`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/demux/cellranger_mkfastq){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/demux/cellranger_mkfastq){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/demux/cellranger_mkfastq/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/demux/cellranger_mkfastq/main.nf \
   -params-file params.yaml
diff --git a/components/modules/dimred/pca.qmd b/components/modules/dimred/pca.qmd
index 340dfbf5..39034bd3 100644
--- a/components/modules/dimred/pca.qmd
+++ b/components/modules/dimred/pca.qmd
@@ -14,7 +14,7 @@ ID: `pca`
 Namespace: `dimred`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dimred/pca){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/dimred/pca){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/dimred/pca/main.nf \
   --help
 ```
@@ -61,7 +61,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/dimred/pca/main.nf \
   -params-file params.yaml
diff --git a/components/modules/dimred/umap.qmd b/components/modules/dimred/umap.qmd
index b59899e9..957162d4 100644
--- a/components/modules/dimred/umap.qmd
+++ b/components/modules/dimred/umap.qmd
@@ -14,7 +14,7 @@ ID: `umap`
 Namespace: `dimred`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/dimred/umap){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/dimred/umap){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/dimred/umap/main.nf \
   --help
 ```
@@ -68,7 +68,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/dimred/umap/main.nf \
   -params-file params.yaml
diff --git a/components/modules/download/download_file.qmd b/components/modules/download/download_file.qmd
index 8f930361..aa022dcf 100644
--- a/components/modules/download/download_file.qmd
+++ b/components/modules/download/download_file.qmd
@@ -14,7 +14,7 @@ ID: `download_file`
 Namespace: `download`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/download/download_file){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/download/download_file){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/download/download_file/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/download/download_file/main.nf \
   -params-file params.yaml
diff --git a/components/modules/download/sync_test_resources.qmd b/components/modules/download/sync_test_resources.qmd
index 38eb7a7a..7fd1ee66 100644
--- a/components/modules/download/sync_test_resources.qmd
+++ b/components/modules/download/sync_test_resources.qmd
@@ -14,7 +14,7 @@ ID: `sync_test_resources`
 Namespace: `download`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/download/sync_test_resources){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/download/sync_test_resources){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/download/sync_test_resources/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/download/sync_test_resources/main.nf \
   -params-file params.yaml
diff --git a/components/modules/files/make_params.qmd b/components/modules/files/make_params.qmd
index e0083b5c..a0f8e45d 100644
--- a/components/modules/files/make_params.qmd
+++ b/components/modules/files/make_params.qmd
@@ -14,7 +14,7 @@ ID: `make_params`
 Namespace: `files`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/files/make_params){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/files/make_params){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/files/make_params/main.nf \
   --help
 ```
@@ -58,7 +58,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/files/make_params/main.nf \
   -params-file params.yaml
diff --git a/components/modules/filter/do_filter.qmd b/components/modules/filter/do_filter.qmd
index 779b4e8f..0097a7e8 100644
--- a/components/modules/filter/do_filter.qmd
+++ b/components/modules/filter/do_filter.qmd
@@ -14,7 +14,7 @@ ID: `do_filter`
 Namespace: `filter`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/do_filter){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/filter/do_filter){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/filter/do_filter/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/filter/do_filter/main.nf \
   -params-file params.yaml
diff --git a/components/modules/filter/filter_with_counts.qmd b/components/modules/filter/filter_with_counts.qmd
index b07593ae..fd10cebc 100644
--- a/components/modules/filter/filter_with_counts.qmd
+++ b/components/modules/filter/filter_with_counts.qmd
@@ -14,7 +14,7 @@ ID: `filter_with_counts`
 Namespace: `filter`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/filter_with_counts){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/filter/filter_with_counts){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -32,7 +32,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/filter/filter_with_counts/main.nf \
   --help
 ```
@@ -74,7 +74,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/filter/filter_with_counts/main.nf \
   -params-file params.yaml
diff --git a/components/modules/filter/filter_with_hvg.qmd b/components/modules/filter/filter_with_hvg.qmd
index 6bc7d8dc..64561509 100644
--- a/components/modules/filter/filter_with_hvg.qmd
+++ b/components/modules/filter/filter_with_hvg.qmd
@@ -14,7 +14,7 @@ ID: `filter_with_hvg`
 Namespace: `filter`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/filter_with_hvg){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/filter/filter_with_hvg){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -37,7 +37,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/filter/filter_with_hvg/main.nf \
   --help
 ```
@@ -74,7 +74,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/filter/filter_with_hvg/main.nf \
   -params-file params.yaml
diff --git a/components/modules/filter/filter_with_scrublet.qmd b/components/modules/filter/filter_with_scrublet.qmd
index 66e48508..b36ae73b 100644
--- a/components/modules/filter/filter_with_scrublet.qmd
+++ b/components/modules/filter/filter_with_scrublet.qmd
@@ -14,7 +14,7 @@ ID: `filter_with_scrublet`
 Namespace: `filter`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/filter_with_scrublet){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/filter/filter_with_scrublet){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -49,7 +49,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/filter/filter_with_scrublet/main.nf \
   --help
 ```
@@ -82,7 +82,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/filter/filter_with_scrublet/main.nf \
   -params-file params.yaml
diff --git a/components/modules/filter/remove_modality.qmd b/components/modules/filter/remove_modality.qmd
index aaccac30..6d8d843a 100644
--- a/components/modules/filter/remove_modality.qmd
+++ b/components/modules/filter/remove_modality.qmd
@@ -14,7 +14,7 @@ ID: `remove_modality`
 Namespace: `filter`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/remove_modality){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/filter/remove_modality){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/filter/remove_modality/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/filter/remove_modality/main.nf \
   -params-file params.yaml
diff --git a/components/modules/filter/subset_h5mu.qmd b/components/modules/filter/subset_h5mu.qmd
index d69e10ff..a57b80e4 100644
--- a/components/modules/filter/subset_h5mu.qmd
+++ b/components/modules/filter/subset_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `subset_h5mu`
 Namespace: `filter`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/filter/subset_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/filter/subset_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/filter/subset_h5mu/main.nf \
   --help
 ```
@@ -55,7 +55,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/filter/subset_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/integrate/harmonypy.qmd b/components/modules/integrate/harmonypy.qmd
index 2a164381..cb0afe2e 100644
--- a/components/modules/integrate/harmonypy.qmd
+++ b/components/modules/integrate/harmonypy.qmd
@@ -14,7 +14,7 @@ ID: `harmonypy`
 Namespace: `integrate`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/integrate/harmonypy){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/integrate/harmonypy){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/integrate/harmonypy/main.nf \
   --help
 ```
@@ -58,7 +58,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/integrate/harmonypy/main.nf \
   -params-file params.yaml
diff --git a/components/modules/integrate/scanorama.qmd b/components/modules/integrate/scanorama.qmd
index 14d37bd7..572b877e 100644
--- a/components/modules/integrate/scanorama.qmd
+++ b/components/modules/integrate/scanorama.qmd
@@ -14,7 +14,7 @@ ID: `scanorama`
 Namespace: `integrate`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/integrate/scanorama){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/integrate/scanorama){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/integrate/scanorama/main.nf \
   --help
 ```
@@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/integrate/scanorama/main.nf \
   -params-file params.yaml
diff --git a/components/modules/integrate/scarches.qmd b/components/modules/integrate/scarches.qmd
index 7c984f78..b6a86b21 100644
--- a/components/modules/integrate/scarches.qmd
+++ b/components/modules/integrate/scarches.qmd
@@ -14,7 +14,7 @@ ID: `scarches`
 Namespace: `integrate`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/integrate/scarches){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/integrate/scarches){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/integrate/scarches/main.nf \
   --help
 ```
@@ -72,7 +72,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/integrate/scarches/main.nf \
   -params-file params.yaml
diff --git a/components/modules/integrate/scvi.qmd b/components/modules/integrate/scvi.qmd
index 575c47e7..9fee7056 100644
--- a/components/modules/integrate/scvi.qmd
+++ b/components/modules/integrate/scvi.qmd
@@ -14,7 +14,7 @@ ID: `scvi`
 Namespace: `integrate`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/integrate/scvi){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/integrate/scvi){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/integrate/scvi/main.nf \
   --help
 ```
@@ -96,7 +96,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/integrate/scvi/main.nf \
   -params-file params.yaml
diff --git a/components/modules/integrate/totalvi.qmd b/components/modules/integrate/totalvi.qmd
index 5b228fb8..9ab4faba 100644
--- a/components/modules/integrate/totalvi.qmd
+++ b/components/modules/integrate/totalvi.qmd
@@ -14,7 +14,7 @@ ID: `totalvi`
 Namespace: `integrate`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/integrate/totalvi){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/integrate/totalvi){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/integrate/totalvi/main.nf \
   --help
 ```
@@ -73,7 +73,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/integrate/totalvi/main.nf \
   -params-file params.yaml
diff --git a/components/modules/interpret/lianapy.qmd b/components/modules/interpret/lianapy.qmd
index 51cb3f39..c5899600 100644
--- a/components/modules/interpret/lianapy.qmd
+++ b/components/modules/interpret/lianapy.qmd
@@ -14,7 +14,7 @@ ID: `lianapy`
 Namespace: `interpret`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/interpret/lianapy){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/interpret/lianapy){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/interpret/lianapy/main.nf \
   --help
 ```
@@ -63,7 +63,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/interpret/lianapy/main.nf \
   -params-file params.yaml
diff --git a/components/modules/labels_transfer/knn.qmd b/components/modules/labels_transfer/knn.qmd
index bc54b45d..ca464c76 100644
--- a/components/modules/labels_transfer/knn.qmd
+++ b/components/modules/labels_transfer/knn.qmd
@@ -14,7 +14,7 @@ ID: `knn`
 Namespace: `labels_transfer`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/labels_transfer/knn){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/labels_transfer/knn){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/labels_transfer/knn/main.nf \
   --help
 ```
@@ -51,7 +51,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/labels_transfer/knn/main.nf \
   -params-file params.yaml
diff --git a/components/modules/labels_transfer/xgboost.qmd b/components/modules/labels_transfer/xgboost.qmd
index 0d9cf99b..285a1526 100644
--- a/components/modules/labels_transfer/xgboost.qmd
+++ b/components/modules/labels_transfer/xgboost.qmd
@@ -14,7 +14,7 @@ ID: `xgboost`
 Namespace: `labels_transfer`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/labels_transfer/xgboost){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/labels_transfer/xgboost){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/labels_transfer/xgboost/main.nf \
   --help
 ```
@@ -69,7 +69,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/labels_transfer/xgboost/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/bd_rhapsody.qmd b/components/modules/mapping/bd_rhapsody.qmd
index cd527309..cd252f12 100644
--- a/components/modules/mapping/bd_rhapsody.qmd
+++ b/components/modules/mapping/bd_rhapsody.qmd
@@ -14,7 +14,7 @@ ID: `bd_rhapsody`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/bd_rhapsody){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/bd_rhapsody){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -44,7 +44,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/bd_rhapsody/main.nf \
   --help
 ```
@@ -95,7 +95,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/bd_rhapsody/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/cellranger_count.qmd b/components/modules/mapping/cellranger_count.qmd
index 1b7f81b3..29e3f647 100644
--- a/components/modules/mapping/cellranger_count.qmd
+++ b/components/modules/mapping/cellranger_count.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_count`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/cellranger_count){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/cellranger_count){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/cellranger_count/main.nf \
   --help
 ```
@@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/cellranger_count/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/cellranger_count_split.qmd b/components/modules/mapping/cellranger_count_split.qmd
index de90c164..86390425 100644
--- a/components/modules/mapping/cellranger_count_split.qmd
+++ b/components/modules/mapping/cellranger_count_split.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_count_split`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/cellranger_count_split){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/cellranger_count_split){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/cellranger_count_split/main.nf \
   --help
 ```
@@ -57,7 +57,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/cellranger_count_split/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/cellranger_multi.qmd b/components/modules/mapping/cellranger_multi.qmd
index 504b54ae..2cf57a03 100644
--- a/components/modules/mapping/cellranger_multi.qmd
+++ b/components/modules/mapping/cellranger_multi.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_multi`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/cellranger_multi){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/cellranger_multi){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/cellranger_multi/main.nf \
   --help
 ```
@@ -79,7 +79,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/cellranger_multi/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/htseq_count.qmd b/components/modules/mapping/htseq_count.qmd
index 58a7f2bc..0e56ecbf 100644
--- a/components/modules/mapping/htseq_count.qmd
+++ b/components/modules/mapping/htseq_count.qmd
@@ -14,7 +14,7 @@ ID: `htseq_count`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/htseq_count){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/htseq_count){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -33,7 +33,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/htseq_count/main.nf \
   --help
 ```
@@ -75,7 +75,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/htseq_count/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/htseq_count_to_h5mu.qmd b/components/modules/mapping/htseq_count_to_h5mu.qmd
index adea5ae5..b9174378 100644
--- a/components/modules/mapping/htseq_count_to_h5mu.qmd
+++ b/components/modules/mapping/htseq_count_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `htseq_count_to_h5mu`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/htseq_count_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/htseq_count_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/htseq_count_to_h5mu/main.nf \
   --help
 ```
@@ -57,7 +57,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/htseq_count_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/multi_star.qmd b/components/modules/mapping/multi_star.qmd
index 0f601dfa..05976260 100644
--- a/components/modules/mapping/multi_star.qmd
+++ b/components/modules/mapping/multi_star.qmd
@@ -14,7 +14,7 @@ ID: `multi_star`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/multi_star){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/multi_star){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/multi_star/main.nf \
   --help
 ```
@@ -61,7 +61,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/multi_star/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/multi_star_to_h5mu.qmd b/components/modules/mapping/multi_star_to_h5mu.qmd
index a6075fe1..0c64fda4 100644
--- a/components/modules/mapping/multi_star_to_h5mu.qmd
+++ b/components/modules/mapping/multi_star_to_h5mu.qmd
@@ -14,7 +14,7 @@ ID: `multi_star_to_h5mu`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/multi_star_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/multi_star_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/multi_star_to_h5mu/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/multi_star_to_h5mu/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/samtools_sort.qmd b/components/modules/mapping/samtools_sort.qmd
index 654f8b3f..dd93a0bb 100644
--- a/components/modules/mapping/samtools_sort.qmd
+++ b/components/modules/mapping/samtools_sort.qmd
@@ -14,7 +14,7 @@ ID: `samtools_sort`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/samtools_sort){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/samtools_sort){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -36,7 +36,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/samtools_sort/main.nf \
   --help
 ```
@@ -70,7 +70,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/samtools_sort/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/star_align.qmd b/components/modules/mapping/star_align.qmd
index ebb69f8a..0400ba06 100644
--- a/components/modules/mapping/star_align.qmd
+++ b/components/modules/mapping/star_align.qmd
@@ -14,7 +14,7 @@ ID: `star_align`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/star_align){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/star_align){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/star_align/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/star_align/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/star_align_v273a.qmd b/components/modules/mapping/star_align_v273a.qmd
index 841908fb..7603268b 100644
--- a/components/modules/mapping/star_align_v273a.qmd
+++ b/components/modules/mapping/star_align_v273a.qmd
@@ -14,7 +14,7 @@ ID: `star_align_v273a`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/star_align_v273a){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/star_align_v273a){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/star_align_v273a/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/star_align_v273a/main.nf \
   -params-file params.yaml
diff --git a/components/modules/mapping/star_build_reference.qmd b/components/modules/mapping/star_build_reference.qmd
index 4ebdc30d..709b0b1c 100644
--- a/components/modules/mapping/star_build_reference.qmd
+++ b/components/modules/mapping/star_build_reference.qmd
@@ -14,7 +14,7 @@ ID: `star_build_reference`
 Namespace: `mapping`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/mapping/star_build_reference){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/mapping/star_build_reference){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/mapping/star_build_reference/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/mapping/star_build_reference/main.nf \
   -params-file params.yaml
diff --git a/components/modules/metadata/add_id.qmd b/components/modules/metadata/add_id.qmd
index 4a1020f8..8afdafb4 100644
--- a/components/modules/metadata/add_id.qmd
+++ b/components/modules/metadata/add_id.qmd
@@ -14,7 +14,7 @@ ID: `add_id`
 Namespace: `metadata`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/metadata/add_id){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/metadata/add_id){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -31,7 +31,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/metadata/add_id/main.nf \
   --help
 ```
@@ -57,7 +57,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/metadata/add_id/main.nf \
   -params-file params.yaml
diff --git a/components/modules/metadata/join_csv.qmd b/components/modules/metadata/join_csv.qmd
index aa8e4821..63003246 100644
--- a/components/modules/metadata/join_csv.qmd
+++ b/components/modules/metadata/join_csv.qmd
@@ -14,7 +14,7 @@ ID: `join_csv`
 Namespace: `metadata`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/metadata/join_csv){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/metadata/join_csv){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/metadata/join_csv/main.nf \
   --help
 ```
@@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/metadata/join_csv/main.nf \
   -params-file params.yaml
diff --git a/components/modules/metadata/join_uns_to_obs.qmd b/components/modules/metadata/join_uns_to_obs.qmd
index a32b71b9..168c325b 100644
--- a/components/modules/metadata/join_uns_to_obs.qmd
+++ b/components/modules/metadata/join_uns_to_obs.qmd
@@ -14,7 +14,7 @@ ID: `join_uns_to_obs`
 Namespace: `metadata`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/metadata/join_uns_to_obs){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/metadata/join_uns_to_obs){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/metadata/join_uns_to_obs/main.nf \
   --help
 ```
@@ -55,7 +55,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/metadata/join_uns_to_obs/main.nf \
   -params-file params.yaml
diff --git a/components/modules/metadata/move_obsm_to_obs.qmd b/components/modules/metadata/move_obsm_to_obs.qmd
index 770bb63b..46c0690a 100644
--- a/components/modules/metadata/move_obsm_to_obs.qmd
+++ b/components/modules/metadata/move_obsm_to_obs.qmd
@@ -14,7 +14,7 @@ ID: `move_obsm_to_obs`
 Namespace: `metadata`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/metadata/move_obsm_to_obs){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/metadata/move_obsm_to_obs){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -32,7 +32,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/metadata/move_obsm_to_obs/main.nf \
   --help
 ```
@@ -59,7 +59,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/metadata/move_obsm_to_obs/main.nf \
   -params-file params.yaml
diff --git a/components/modules/neighbors/bbknn.qmd b/components/modules/neighbors/bbknn.qmd
index 4d7ff785..efadfe5e 100644
--- a/components/modules/neighbors/bbknn.qmd
+++ b/components/modules/neighbors/bbknn.qmd
@@ -14,7 +14,7 @@ ID: `bbknn`
 Namespace: `neighbors`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/neighbors/bbknn){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/neighbors/bbknn){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/neighbors/bbknn/main.nf \
   --help
 ```
@@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/neighbors/bbknn/main.nf \
   -params-file params.yaml
diff --git a/components/modules/neighbors/find_neighbors.qmd b/components/modules/neighbors/find_neighbors.qmd
index c22aabc6..5253cefc 100644
--- a/components/modules/neighbors/find_neighbors.qmd
+++ b/components/modules/neighbors/find_neighbors.qmd
@@ -14,7 +14,7 @@ ID: `find_neighbors`
 Namespace: `neighbors`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/neighbors/find_neighbors){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/neighbors/find_neighbors){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -31,7 +31,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/neighbors/find_neighbors/main.nf \
   --help
 ```
@@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/neighbors/find_neighbors/main.nf \
   -params-file params.yaml
diff --git a/components/modules/process_10xh5/filter_10xh5.qmd b/components/modules/process_10xh5/filter_10xh5.qmd
index 9bd8a116..4305fc2e 100644
--- a/components/modules/process_10xh5/filter_10xh5.qmd
+++ b/components/modules/process_10xh5/filter_10xh5.qmd
@@ -14,7 +14,7 @@ ID: `filter_10xh5`
 Namespace: `process_10xh5`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/process_10xh5/filter_10xh5){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/process_10xh5/filter_10xh5){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/process_10xh5/filter_10xh5/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/process_10xh5/filter_10xh5/main.nf \
   -params-file params.yaml
diff --git a/components/modules/qc/calculate_qc_metrics.qmd b/components/modules/qc/calculate_qc_metrics.qmd
index 7fb7ccaf..aac8f03a 100644
--- a/components/modules/qc/calculate_qc_metrics.qmd
+++ b/components/modules/qc/calculate_qc_metrics.qmd
@@ -14,7 +14,7 @@ ID: `calculate_qc_metrics`
 Namespace: `qc`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/qc/calculate_qc_metrics){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/qc/calculate_qc_metrics){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -46,7 +46,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/qc/calculate_qc_metrics/main.nf \
   --help
 ```
@@ -76,7 +76,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/qc/calculate_qc_metrics/main.nf \
   -params-file params.yaml
diff --git a/components/modules/qc/fastqc.qmd b/components/modules/qc/fastqc.qmd
index e8a18370..e725fe06 100644
--- a/components/modules/qc/fastqc.qmd
+++ b/components/modules/qc/fastqc.qmd
@@ -14,7 +14,7 @@ ID: `fastqc`
 Namespace: `qc`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/qc/fastqc){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/qc/fastqc){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/qc/fastqc/main.nf \
   --help
 ```
@@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/qc/fastqc/main.nf \
   -params-file params.yaml
diff --git a/components/modules/qc/multiqc.qmd b/components/modules/qc/multiqc.qmd
index a11971e3..96d004bb 100644
--- a/components/modules/qc/multiqc.qmd
+++ b/components/modules/qc/multiqc.qmd
@@ -14,7 +14,7 @@ ID: `multiqc`
 Namespace: `qc`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/qc/multiqc){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/qc/multiqc){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/qc/multiqc/main.nf \
   --help
 ```
@@ -52,7 +52,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/qc/multiqc/main.nf \
   -params-file params.yaml
diff --git a/components/modules/query/cellxgene_census.qmd b/components/modules/query/cellxgene_census.qmd
index 1e6c350d..1ea1199e 100644
--- a/components/modules/query/cellxgene_census.qmd
+++ b/components/modules/query/cellxgene_census.qmd
@@ -14,7 +14,7 @@ ID: `cellxgene_census`
 Namespace: `query`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/query/cellxgene_census){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/query/cellxgene_census){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/query/cellxgene_census/main.nf \
   --help
 ```
@@ -63,7 +63,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/query/cellxgene_census/main.nf \
   -params-file params.yaml
diff --git a/components/modules/reference/build_bdrhap_reference.qmd b/components/modules/reference/build_bdrhap_reference.qmd
index c9727beb..e6e85744 100644
--- a/components/modules/reference/build_bdrhap_reference.qmd
+++ b/components/modules/reference/build_bdrhap_reference.qmd
@@ -14,7 +14,7 @@ ID: `build_bdrhap_reference`
 Namespace: `reference`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/reference/build_bdrhap_reference){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/reference/build_bdrhap_reference){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/reference/build_bdrhap_reference/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/reference/build_bdrhap_reference/main.nf \
   -params-file params.yaml
diff --git a/components/modules/reference/build_cellranger_reference.qmd b/components/modules/reference/build_cellranger_reference.qmd
index 6b5b9a8e..221ecf09 100644
--- a/components/modules/reference/build_cellranger_reference.qmd
+++ b/components/modules/reference/build_cellranger_reference.qmd
@@ -14,7 +14,7 @@ ID: `build_cellranger_reference`
 Namespace: `reference`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/reference/build_cellranger_reference){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/reference/build_cellranger_reference){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/reference/build_cellranger_reference/main.nf \
   --help
 ```
@@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/reference/build_cellranger_reference/main.nf \
   -params-file params.yaml
diff --git a/components/modules/reference/make_reference.qmd b/components/modules/reference/make_reference.qmd
index 234a9df4..e4d7c5b2 100644
--- a/components/modules/reference/make_reference.qmd
+++ b/components/modules/reference/make_reference.qmd
@@ -14,7 +14,7 @@ ID: `make_reference`
 Namespace: `reference`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/reference/make_reference){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/reference/make_reference){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -34,7 +34,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/reference/make_reference/main.nf \
   --help
 ```
@@ -60,7 +60,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/reference/make_reference/main.nf \
   -params-file params.yaml
diff --git a/components/modules/report/mermaid.qmd b/components/modules/report/mermaid.qmd
index 95157707..5be31910 100644
--- a/components/modules/report/mermaid.qmd
+++ b/components/modules/report/mermaid.qmd
@@ -14,7 +14,7 @@ ID: `mermaid`
 Namespace: `report`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/report/mermaid){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/report/mermaid){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/report/mermaid/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/report/mermaid/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transfer/publish.qmd b/components/modules/transfer/publish.qmd
index 96ef4816..57edc502 100644
--- a/components/modules/transfer/publish.qmd
+++ b/components/modules/transfer/publish.qmd
@@ -14,7 +14,7 @@ ID: `publish`
 Namespace: `transfer`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transfer/publish){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transfer/publish){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transfer/publish/main.nf \
   --help
 ```
@@ -52,7 +52,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transfer/publish/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transform/clr.qmd b/components/modules/transform/clr.qmd
index 4938fb7d..0e4f68c4 100644
--- a/components/modules/transform/clr.qmd
+++ b/components/modules/transform/clr.qmd
@@ -14,7 +14,7 @@ ID: `clr`
 Namespace: `transform`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transform/clr){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transform/clr){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transform/clr/main.nf \
   --help
 ```
@@ -55,7 +55,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transform/clr/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transform/delete_layer.qmd b/components/modules/transform/delete_layer.qmd
index 302c567e..82395cd4 100644
--- a/components/modules/transform/delete_layer.qmd
+++ b/components/modules/transform/delete_layer.qmd
@@ -14,7 +14,7 @@ ID: `delete_layer`
 Namespace: `transform`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transform/delete_layer){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transform/delete_layer){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transform/delete_layer/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transform/delete_layer/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transform/log1p.qmd b/components/modules/transform/log1p.qmd
index 056d2b82..99bd6f78 100644
--- a/components/modules/transform/log1p.qmd
+++ b/components/modules/transform/log1p.qmd
@@ -14,7 +14,7 @@ ID: `log1p`
 Namespace: `transform`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transform/log1p){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transform/log1p){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transform/log1p/main.nf \
   --help
 ```
@@ -57,7 +57,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transform/log1p/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transform/normalize_total.qmd b/components/modules/transform/normalize_total.qmd
index 35113b47..3720084b 100644
--- a/components/modules/transform/normalize_total.qmd
+++ b/components/modules/transform/normalize_total.qmd
@@ -14,7 +14,7 @@ ID: `normalize_total`
 Namespace: `transform`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transform/normalize_total){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transform/normalize_total){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -33,7 +33,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transform/normalize_total/main.nf \
   --help
 ```
@@ -61,7 +61,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transform/normalize_total/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transform/regress_out.qmd b/components/modules/transform/regress_out.qmd
index 33c5b68e..a261516d 100644
--- a/components/modules/transform/regress_out.qmd
+++ b/components/modules/transform/regress_out.qmd
@@ -14,7 +14,7 @@ ID: `regress_out`
 Namespace: `transform`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transform/regress_out){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transform/regress_out){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -31,7 +31,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transform/regress_out/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transform/regress_out/main.nf \
   -params-file params.yaml
diff --git a/components/modules/transform/scale.qmd b/components/modules/transform/scale.qmd
index e1722711..16845b4c 100644
--- a/components/modules/transform/scale.qmd
+++ b/components/modules/transform/scale.qmd
@@ -14,7 +14,7 @@ ID: `scale`
 Namespace: `transform`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/transform/scaling){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/transform/scaling){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/transform/scale/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/transform/scale/main.nf \
   -params-file params.yaml
diff --git a/components/modules/velocity/scvelo.qmd b/components/modules/velocity/scvelo.qmd
index 17f9d374..17bac24c 100644
--- a/components/modules/velocity/scvelo.qmd
+++ b/components/modules/velocity/scvelo.qmd
@@ -14,7 +14,7 @@ ID: `scvelo`
 Namespace: `velocity`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/velocity/scvelo){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/velocity/scvelo){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/velocity/scvelo/main.nf \
   --help
 ```
@@ -69,7 +69,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/velocity/scvelo/main.nf \
   -params-file params.yaml
diff --git a/components/modules/velocity/velocyto.qmd b/components/modules/velocity/velocyto.qmd
index ef1c92e1..e28ec28d 100644
--- a/components/modules/velocity/velocyto.qmd
+++ b/components/modules/velocity/velocyto.qmd
@@ -14,7 +14,7 @@ ID: `velocyto`
 Namespace: `velocity`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/src/velocity/velocyto){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./src/velocity/velocyto){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script target/nextflow/velocity/velocyto/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script target/nextflow/velocity/velocyto/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/bd_rhapsody.qmd b/components/workflows/ingestion/bd_rhapsody.qmd
index ece09d44..74f6b8ee 100644
--- a/components/workflows/ingestion/bd_rhapsody.qmd
+++ b/components/workflows/ingestion/bd_rhapsody.qmd
@@ -14,7 +14,7 @@ ID: `bd_rhapsody`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/bd_rhapsody){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/bd_rhapsody){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -42,7 +42,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/bd_rhapsody/main.nf \
   --help
 ```
@@ -95,7 +95,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/bd_rhapsody/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/cellranger_mapping.qmd b/components/workflows/ingestion/cellranger_mapping.qmd
index 1a8d607b..d5b524ac 100644
--- a/components/workflows/ingestion/cellranger_mapping.qmd
+++ b/components/workflows/ingestion/cellranger_mapping.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_mapping`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/cellranger_mapping){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/cellranger_mapping){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/cellranger_mapping/main.nf \
   --help
 ```
@@ -66,7 +66,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/cellranger_mapping/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/cellranger_multi.qmd b/components/workflows/ingestion/cellranger_multi.qmd
index 86a6cf48..61b6b7ac 100644
--- a/components/workflows/ingestion/cellranger_multi.qmd
+++ b/components/workflows/ingestion/cellranger_multi.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_multi`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/cellranger_multi){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/cellranger_multi){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/cellranger_multi/main.nf \
   --help
 ```
@@ -79,7 +79,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/cellranger_multi/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/cellranger_postprocessing.qmd b/components/workflows/ingestion/cellranger_postprocessing.qmd
index 898e6bf6..7ef3eafe 100644
--- a/components/workflows/ingestion/cellranger_postprocessing.qmd
+++ b/components/workflows/ingestion/cellranger_postprocessing.qmd
@@ -14,7 +14,7 @@ ID: `cellranger_postprocessing`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/cellranger_postprocessing){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/cellranger_postprocessing){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/cellranger_postprocessing/main.nf \
   --help
 ```
@@ -63,7 +63,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/cellranger_postprocessing/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/conversion.qmd b/components/workflows/ingestion/conversion.qmd
index e0c767a1..db752082 100644
--- a/components/workflows/ingestion/conversion.qmd
+++ b/components/workflows/ingestion/conversion.qmd
@@ -14,7 +14,7 @@ ID: `conversion`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/conversion){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/conversion){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/conversion/main.nf \
   --help
 ```
@@ -59,7 +59,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/conversion/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/demux.qmd b/components/workflows/ingestion/demux.qmd
index 8618c4e4..8499f535 100644
--- a/components/workflows/ingestion/demux.qmd
+++ b/components/workflows/ingestion/demux.qmd
@@ -14,7 +14,7 @@ ID: `demux`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/demux){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/demux){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -31,7 +31,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/demux/main.nf \
   --help
 ```
@@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/demux/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/ingestion/make_reference.qmd b/components/workflows/ingestion/make_reference.qmd
index 25773d23..61cb0948 100644
--- a/components/workflows/ingestion/make_reference.qmd
+++ b/components/workflows/ingestion/make_reference.qmd
@@ -14,7 +14,7 @@ ID: `make_reference`
 Namespace: `ingestion`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/ingestion/make_reference){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/ingestion/make_reference){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/ingestion/make_reference/main.nf \
   --help
 ```
@@ -65,7 +65,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/ingestion/make_reference/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/full_pipeline.qmd b/components/workflows/multiomics/full_pipeline.qmd
index c7f52941..8b4d9bda 100644
--- a/components/workflows/multiomics/full_pipeline.qmd
+++ b/components/workflows/multiomics/full_pipeline.qmd
@@ -14,7 +14,7 @@ ID: `full_pipeline`
 Namespace: `multiomics`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/full_pipeline){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/full_pipeline){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/full_pipeline/main.nf \
   --help
 ```
@@ -92,7 +92,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/full_pipeline/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/integration/bbknn_leiden.qmd b/components/workflows/multiomics/integration/bbknn_leiden.qmd
index 7c921fdc..d11dedbf 100644
--- a/components/workflows/multiomics/integration/bbknn_leiden.qmd
+++ b/components/workflows/multiomics/integration/bbknn_leiden.qmd
@@ -14,7 +14,7 @@ ID: `bbknn_leiden`
 Namespace: `multiomics/integration`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/integration/bbknn_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/integration/bbknn_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/integration/bbknn_leiden/main.nf \
   --help
 ```
@@ -61,7 +61,7 @@ n_pcs: 50
 
 # Clustering options
 obs_cluster: "bbknn_integration_leiden"
-leiden_resolution: 1
+leiden_resolution: [1]
 
 # UMAP options
 obsm_umap: "X_leiden_bbknn_umap"
@@ -74,7 +74,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/integration/bbknn_leiden/main.nf \
   -params-file params.yaml
@@ -119,10 +119,10 @@ Replace `-profile docker` with `-profile podman` or `-profile singularity` depen
 
 ### Clustering options
 
-|Name                  |Description                                                                                                                                                                                                                                                        |Attributes                                      |
-|:---------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------|
-|`--obs_cluster`       |Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will  be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions resolutions specified in '--leiden_resolution'. |`string`, default: `"bbknn_integration_leiden"` |
-|`--leiden_resolution` |Control the coarseness of the clustering. Higher values lead to more clusters.                                                                                                                                                                                     |`double`, default: `1`                          |
+|Name                  |Description                                                                                                                                                                                                                                                        |Attributes                                          |
+|:---------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------|
+|`--obs_cluster`       |Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will  be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions resolutions specified in '--leiden_resolution'. |`string`, default: `"bbknn_integration_leiden"`     |
+|`--leiden_resolution` |Control the coarseness of the clustering. Higher values lead to more clusters.                                                                                                                                                                                     |List of `double`, default: `1`, multiple_sep: `":"` |
 
 
 ### UMAP options
diff --git a/components/workflows/multiomics/integration/harmony_leiden.qmd b/components/workflows/multiomics/integration/harmony_leiden.qmd
index 7583cc50..2b6598db 100644
--- a/components/workflows/multiomics/integration/harmony_leiden.qmd
+++ b/components/workflows/multiomics/integration/harmony_leiden.qmd
@@ -14,7 +14,7 @@ ID: `harmony_leiden`
 Namespace: `multiomics/integration`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/integration/harmony_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/integration/harmony_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/integration/harmony_leiden/main.nf \
   --help
 ```
@@ -75,7 +75,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/integration/harmony_leiden/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/integration/initialize_integration.qmd b/components/workflows/multiomics/integration/initialize_integration.qmd
index 717411b9..97dc543b 100644
--- a/components/workflows/multiomics/integration/initialize_integration.qmd
+++ b/components/workflows/multiomics/integration/initialize_integration.qmd
@@ -14,7 +14,7 @@ ID: `initialize_integration`
 Namespace: `multiomics/integration`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/integration/initialize_integration){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/integration/initialize_integration){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/integration/initialize_integration/main.nf \
   --help
 ```
@@ -70,7 +70,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/integration/initialize_integration/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/integration/scanorama_leiden.qmd b/components/workflows/multiomics/integration/scanorama_leiden.qmd
index c29be001..208f2d1e 100644
--- a/components/workflows/multiomics/integration/scanorama_leiden.qmd
+++ b/components/workflows/multiomics/integration/scanorama_leiden.qmd
@@ -14,7 +14,7 @@ ID: `scanorama_leiden`
 Namespace: `multiomics/integration`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/integration/scanorama_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/integration/scanorama_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/integration/scanorama_leiden/main.nf \
   --help
 ```
@@ -79,7 +79,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/integration/scanorama_leiden/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/integration/scvi_leiden.qmd b/components/workflows/multiomics/integration/scvi_leiden.qmd
new file mode 100644
index 00000000..560748bf
--- /dev/null
+++ b/components/workflows/multiomics/integration/scvi_leiden.qmd
@@ -0,0 +1,199 @@
+---
+title: "Scvi leiden"
+namespace: "Multiomics/integration"
+description: "Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result."
+type: "workflow"
+toc: false
+---
+
+::: {.column-margin}
+
+### Info
+
+ID: `scvi_leiden`  
+Namespace: `multiomics/integration`
+
+### Links
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/integration/scvi_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+
+:::
+
+
+
+## Example commands
+
+You can run the pipeline using `nextflow run`.
+
+### View help
+
+You can use `--help` as a parameter to get an overview of the possible parameters.
+
+```bash
+nextflow run openpipelines-bio/openpipeline \
+  -r 0.10.1 -latest \
+  -main-script ./workflows/multiomics/integration/scvi_leiden/main.nf \
+  --help
+```
+
+### Run command
+
+<details>
+<summary>Example of `params.yaml`</summary>
+```yaml
+# Inputs
+id: # please fill in - example: "foo"
+input: # please fill in - example: "dataset.h5mu"
+layer: "log_normalized"
+modality: "rna"
+
+# Outputs
+# output: "$id.$key.output.h5mu"
+# output_model: "$id.$key.output_model.output_model"
+
+# Neighbour calculation
+uns_neighbors: "scvi_integration_neighbors"
+obsp_neighbor_distances: "scvi_integration_distances"
+obsp_neighbor_connectivities: "scvi_integration_connectivities"
+
+# Scvi integration options
+obs_batch: # please fill in - example: "foo"
+obsm_output: "X_scvi_integrated"
+# var_input: "foo"
+# early_stopping: true
+early_stopping_monitor: "elbo_validation"
+early_stopping_patience: 45
+early_stopping_min_delta: 0.0
+# max_epochs: 123
+reduce_lr_on_plateau: true
+lr_factor: 0.6
+lr_patience: 30
+
+# Clustering options
+obs_cluster: "scvi_integration_leiden"
+leiden_resolution: [1]
+
+# Umap options
+obsm_umap: "X_scvi_umap"
+
+# Nextflow input-output arguments
+publish_dir: # please fill in - example: "output/"
+# param_list: "my_params.yaml"
+```
+</details>
+
+```bash
+nextflow run openpipelines-bio/openpipeline \
+  -r 0.10.1 -latest \
+  -profile docker \
+  -main-script ./workflows/multiomics/integration/scvi_leiden/main.nf \
+  -params-file params.yaml
+```
+
+:::{.callout-note}
+Replace `-profile docker` with `-profile podman` or `-profile singularity` depending on the desired backend.
+:::
+
+## Argument groups
+
+### Inputs
+
+|Name         |Description                                                                           |Attributes                                  |
+|:------------|:-------------------------------------------------------------------------------------|:-------------------------------------------|
+|`--id`       |ID of the sample.                                                                     |`string`, required, example: `"foo"`        |
+|`--input`    |Path to the sample.                                                                   |`file`, required, example: `"dataset.h5mu"` |
+|`--layer`    |use specified layer for expression values instead of the .X object from the modality. |`string`, default: `"log_normalized"`       |
+|`--modality` |Which modality to process.                                                            |`string`, default: `"rna"`                  |
+
+
+### Outputs
+
+|Name             |Description                                                   |Attributes                                 |
+|:----------------|:-------------------------------------------------------------|:------------------------------------------|
+|`--output`       |Destination path to the output.                               |`file`, required, example: `"output.h5mu"` |
+|`--output_model` |Folder where the state of the trained model will be saved to. |`file`, required, example: `"output_dir"`  |
+
+
+### Neighbour calculation
+
+|Name                             |Description                                                                             |Attributes                                             |
+|:--------------------------------|:---------------------------------------------------------------------------------------|:------------------------------------------------------|
+|`--uns_neighbors`                |In which .uns slot to store various neighbor output objects.                            |`string`, default: `"scvi_integration_neighbors"`      |
+|`--obsp_neighbor_distances`      |In which .obsp slot to store the distance matrix between the resulting neighbors.       |`string`, default: `"scvi_integration_distances"`      |
+|`--obsp_neighbor_connectivities` |In which .obsp slot to store the connectivities matrix between the resulting neighbors. |`string`, default: `"scvi_integration_connectivities"` |
+
+
+### Scvi integration options
+
+|Name                         |Description                                                                                                                                          |Attributes                               |
+|:----------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------|
+|`--obs_batch`                |Column name discriminating between your batches.                                                                                                     |`string`, required                       |
+|`--obsm_output`              |In which .obsm slot to store the resulting integrated embedding.                                                                                     |`string`, default: `"X_scvi_integrated"` |
+|`--var_input`                |.var column containing highly variable genes. By default, do not subset genes.                                                                       |`string`                                 |
+|`--early_stopping`           |Whether to perform early stopping with respect to the validation set.                                                                                |`boolean`                                |
+|`--early_stopping_monitor`   |Metric logged during validation set epoch.                                                                                                           |`string`, default: `"elbo_validation"`   |
+|`--early_stopping_patience`  |Number of validation epochs with no improvement after which training will be stopped.                                                                |`integer`, default: `45`                 |
+|`--early_stopping_min_delta` |Minimum change in the monitored quantity to qualify as an improvement, i.e. an absolute change of less than min_delta, will count as no improvement. |`double`, default: `0`                   |
+|`--max_epochs`               |Number of passes through the dataset, defaults to (20000 / number of cells) * 400 or 400; whichever is smallest.                                     |`integer`                                |
+|`--reduce_lr_on_plateau`     |Whether to monitor validation loss and reduce learning rate when validation set `lr_scheduler_metric` plateaus.                                      |`boolean`, default: `TRUE`               |
+|`--lr_factor`                |Factor to reduce learning rate.                                                                                                                      |`double`, default: `0.6`                 |
+|`--lr_patience`              |Number of epochs with no improvement after which learning rate will be reduced.                                                                      |`double`, default: `30`                  |
+
+
+### Clustering options
+
+|Name                  |Description                                                                                                                                                                                                                                                        |Attributes                                          |
+|:---------------------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------|
+|`--obs_cluster`       |Prefix for the .obs keys under which to add the cluster labels. Newly created columns in .obs will  be created from the specified value for '--obs_cluster' suffixed with an underscore and one of the resolutions resolutions specified in '--leiden_resolution'. |`string`, default: `"scvi_integration_leiden"`      |
+|`--leiden_resolution` |Control the coarseness of the clustering. Higher values lead to more clusters.                                                                                                                                                                                     |List of `double`, default: `1`, multiple_sep: `":"` |
+
+
+### Umap options
+
+|Name          |Description                                                |Attributes                         |
+|:-------------|:----------------------------------------------------------|:----------------------------------|
+|`--obsm_umap` |In which .obsm slot to store the resulting UMAP embedding. |`string`, default: `"X_scvi_umap"` |
+
+## Authors
+
+
+  * Dries Schaumont [{{< fa brands github >}}](https://github.com/DriesSchaumont) [{{< fa brands orcid >}}](https://orcid.org/0000-0002-4389-0440) [{{< fa brands linkedin >}}](https://linkedin.com/in/dries-schaumont) (author)
+
+## Visualisation
+
+```{mermaid}
+%%| column: screen-inset-shaded
+flowchart LR
+    p0(Input)
+    p3(toSortedList)
+    p5(flatMap)
+    p12(scvi)
+    p14(join)
+    p23(find_neighbors)
+    p25(join)
+    p33(leiden)
+    p35(join)
+    p43(umap)
+    p45(join)
+    p53(move_obsm_to_obs)
+    p55(join)
+    p62(Output)
+    p0-->p3
+    p3-->p5
+    p5-->p14
+    p5-->p12
+    p12-->p14
+    p14-->p25
+    p14-->p23
+    p23-->p25
+    p25-->p35
+    p25-->p33
+    p33-->p35
+    p35-->p45
+    p35-->p43
+    p43-->p45
+    p45-->p55
+    p45-->p53
+    p53-->p55
+    p55-->p62
+
+```
diff --git a/components/workflows/multiomics/integration/totalvi_leiden.qmd b/components/workflows/multiomics/integration/totalvi_leiden.qmd
index 5f0decfb..24400112 100644
--- a/components/workflows/multiomics/integration/totalvi_leiden.qmd
+++ b/components/workflows/multiomics/integration/totalvi_leiden.qmd
@@ -14,7 +14,7 @@ ID: `totalvi_leiden`
 Namespace: `multiomics/integration`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/integration/totalvi_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/integration/totalvi_leiden){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/integration/totalvi_leiden/main.nf \
   --help
 ```
@@ -98,7 +98,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/integration/totalvi_leiden/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/multisample.qmd b/components/workflows/multiomics/multisample.qmd
index 4385ff88..17f3698f 100644
--- a/components/workflows/multiomics/multisample.qmd
+++ b/components/workflows/multiomics/multisample.qmd
@@ -14,7 +14,7 @@ ID: `multisample`
 Namespace: `multiomics`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/multisample){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/multisample){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -34,7 +34,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/multisample/main.nf \
   --help
 ```
@@ -70,7 +70,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/multisample/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/prot_multisample.qmd b/components/workflows/multiomics/prot_multisample.qmd
index 9477589e..83fbe390 100644
--- a/components/workflows/multiomics/prot_multisample.qmd
+++ b/components/workflows/multiomics/prot_multisample.qmd
@@ -14,7 +14,7 @@ ID: `prot_multisample`
 Namespace: `multiomics`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/prot_multisample){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/prot_multisample){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/prot_multisample/main.nf \
   --help
 ```
@@ -58,7 +58,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/prot_multisample/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/prot_singlesample.qmd b/components/workflows/multiomics/prot_singlesample.qmd
index 521a9171..fa624921 100644
--- a/components/workflows/multiomics/prot_singlesample.qmd
+++ b/components/workflows/multiomics/prot_singlesample.qmd
@@ -14,7 +14,7 @@ ID: `prot_singlesample`
 Namespace: `multiomics`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/prot_singlesample){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/prot_singlesample){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/prot_singlesample/main.nf \
   --help
 ```
@@ -64,7 +64,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/prot_singlesample/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/rna_multisample.qmd b/components/workflows/multiomics/rna_multisample.qmd
index ec373feb..9497d16a 100644
--- a/components/workflows/multiomics/rna_multisample.qmd
+++ b/components/workflows/multiomics/rna_multisample.qmd
@@ -14,7 +14,7 @@ ID: `rna_multisample`
 Namespace: `multiomics`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/rna_multisample){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/rna_multisample){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/rna_multisample/main.nf \
   --help
 ```
@@ -65,7 +65,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/rna_multisample/main.nf \
   -params-file params.yaml
diff --git a/components/workflows/multiomics/rna_singlesample.qmd b/components/workflows/multiomics/rna_singlesample.qmd
index 3c79cc33..79cf3dbf 100644
--- a/components/workflows/multiomics/rna_singlesample.qmd
+++ b/components/workflows/multiomics/rna_singlesample.qmd
@@ -14,7 +14,7 @@ ID: `rna_singlesample`
 Namespace: `multiomics`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.0/workflows/multiomics/rna_singlesample){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.10.1/./workflows/multiomics/rna_singlesample){.btn-action .btn-sm .btn-info .btn role="button"}
 
 :::
 
@@ -30,7 +30,7 @@ You can use `--help` as a parameter to get an overview of the possible parameter
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -main-script ./workflows/multiomics/rna_singlesample/main.nf \
   --help
 ```
@@ -69,7 +69,7 @@ publish_dir: # please fill in - example: "output/"
 
 ```bash
 nextflow run openpipelines-bio/openpipeline \
-  -r 0.10.0 -latest \
+  -r 0.10.1 -latest \
   -profile docker \
   -main-script ./workflows/multiomics/rna_singlesample/main.nf \
   -params-file params.yaml