OpenPipelines release 0.11.1

openpipelines-bio · Jan 18, 2024 · 5b61b22 · 5b61b22
1 parent 59f58de
commit 5b61b22
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Showing 93 changed files with 645 additions and 800 deletions.
diff --git 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/0.12.1/./src/annotate/popv){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `leiden`
 Namespace: `cluster`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/cluster/leiden){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `compress_h5mu`
 Namespace: `compression`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/compression/compress_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_10xh5_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/convert/from_10xh5_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_10xmtx_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/convert/from_10xmtx_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_bd_to_10x_molecular_barcode_tags`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./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/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_bdrhap_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/convert/from_bdrhap_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_cellranger_multi_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/convert/from_cellranger_multi_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_h5ad_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/convert/from_h5ad_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `from_h5mu_to_h5ad`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/convert/from_h5mu_to_h5ad){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `velocyto_to_h5mu`
 Namespace: `convert`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/velocity/velocyto_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `cellbender_remove_background`
 Namespace: `correction`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/correction/cellbender_remove_background){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `cellbender_remove_background_v0_2`
 Namespace: `correction`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/correction/cellbender_remove_background_v0_2){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -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
@@ -14,7 +14,7 @@ ID: `concat`
 Namespace: `dataflow`
 
 ### Links
-[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.1/./src/dataflow/concat){.btn-action .btn-sm .btn-info .btn role="button"}
+[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.11.1/./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 0.12.1 -latest \
+  -r 0.11.1 -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 0.12.1 -latest \
+  -r 0.11.1 -latest \
   -profile docker \
   -main-script target/nextflow/dataflow/concat/main.nf \
   -params-file params.yaml