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OpenPipelines release 0.12.6 (#80)
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Co-authored-by: github-actions <[email protected]>
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DriesSchaumont and github-actions authored Feb 20, 2024
1 parent fc9c3e3 commit b29ad11
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6 changes: 3 additions & 3 deletions components/modules/annotate/popv.qmd
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Expand Up @@ -14,7 +14,7 @@ ID: `popv`
Namespace: `annotate`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/annotate/popv){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/annotate/popv){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/annotate/popv/main.nf \
--help
```
Expand Down Expand Up @@ -70,7 +70,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/annotate/popv/main.nf \
-params-file params.yaml
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6 changes: 3 additions & 3 deletions components/modules/cluster/leiden.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `leiden`
Namespace: `cluster`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/cluster/leiden){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/cluster/leiden){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/cluster/leiden/main.nf \
--help
```
Expand All @@ -66,7 +66,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/cluster/leiden/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/compression/compress_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `compress_h5mu`
Namespace: `compression`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/compression/compress_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/compression/compress_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/compression/compress_h5mu/main.nf \
--help
```
Expand All @@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/compression/compress_h5mu/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_10xh5_to_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_10xh5_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/convert/from_10xh5_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/convert/from_10xh5_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \
--help
```
Expand Down Expand Up @@ -61,7 +61,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_10xmtx_to_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_10xmtx_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/convert/from_10xmtx_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/convert/from_10xmtx_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_10xmtx_to_h5mu/main.nf \
--help
```
Expand All @@ -53,7 +53,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_10xmtx_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_bd_to_10x_molecular_barcode_tags`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./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/0.12.6/./src/convert/from_bd_to_10x_molecular_barcode_tags){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf \
--help
```
Expand All @@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_bdrhap_to_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_bdrhap_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/convert/from_bdrhap_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/convert/from_bdrhap_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
--help
```
Expand All @@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_cellranger_multi_to_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_cellranger_multi_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/convert/from_cellranger_multi_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/convert/from_cellranger_multi_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand Down Expand Up @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
--help
```
Expand All @@ -68,7 +68,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_h5ad_to_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_h5ad_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/convert/from_h5ad_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/convert/from_h5ad_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_h5ad_to_h5mu/main.nf \
--help
```
Expand All @@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_h5ad_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_h5mu_to_h5ad.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `from_h5mu_to_h5ad`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/convert/from_h5mu_to_h5ad){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/convert/from_h5mu_to_h5ad){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/from_h5mu_to_h5ad/main.nf \
--help
```
Expand All @@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/from_h5mu_to_h5ad/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/velocyto_to_h5mu.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `velocyto_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/velocity/velocyto_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/velocity/velocyto_to_h5mu){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/convert/velocyto_to_h5mu/main.nf \
--help
```
Expand Down Expand Up @@ -62,7 +62,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/convert/velocyto_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `cellbender_remove_background`
Namespace: `correction`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/correction/cellbender_remove_background){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/correction/cellbender_remove_background){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/correction/cellbender_remove_background/main.nf \
--help
```
Expand Down Expand Up @@ -101,7 +101,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/correction/cellbender_remove_background/main.nf \
-params-file params.yaml
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `cellbender_remove_background_v0_2`
Namespace: `correction`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/correction/cellbender_remove_background_v0_2){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/correction/cellbender_remove_background_v0_2){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/correction/cellbender_remove_background_v0_2/main.nf \
--help
```
Expand Down Expand Up @@ -83,7 +83,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/correction/cellbender_remove_background_v0_2/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/dataflow/concat.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `concat`
Namespace: `dataflow`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.5/./src/dataflow/concat){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/0.12.6/./src/dataflow/concat){.btn-action .btn-sm .btn-info .btn role="button"}

:::

Expand All @@ -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 0.12.5 -latest \
-r 0.12.6 -latest \
-main-script target/nextflow/dataflow/concat/main.nf \
--help
```
Expand All @@ -56,7 +56,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 0.12.5 -latest \
-r 0.12.6 -latest \
-profile docker \
-main-script target/nextflow/dataflow/concat/main.nf \
-params-file params.yaml
Expand Down
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