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Openpipeline release 2.1.2 #108

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6 changes: 3 additions & 3 deletions components/modules/annotate/celltypist.qmd
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Expand Up @@ -14,7 +14,7 @@ ID: `celltypist`
Namespace: `annotate`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/annotate/celltypist/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/annotate/celltypist/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/annotate/celltypist/main.nf \
--help
```
Expand Down Expand Up @@ -79,7 +79,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/annotate/celltypist/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/annotate/onclass.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `onclass`
Namespace: `annotate`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/annotate/onclass/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/annotate/onclass/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/annotate/onclass/main.nf \
--help
```
Expand Down Expand Up @@ -81,7 +81,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/annotate/onclass/main.nf \
-params-file params.yaml
Expand Down
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/2.1.1/src/annotate/popv/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/annotate/popv/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -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 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/annotate/popv/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/annotate/random_forest_annotation.qmd
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Expand Up @@ -14,7 +14,7 @@ ID: `random_forest_annotation`
Namespace: `annotate`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/annotate/random_forest_annotation/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/annotate/random_forest_annotation/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/annotate/random_forest_annotation/main.nf \
--help
```
Expand Down Expand Up @@ -78,7 +78,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/annotate/random_forest_annotation/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/annotate/scanvi.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `scanvi`
Namespace: `annotate`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/annotate/scanvi/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/annotate/scanvi/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/annotate/scanvi/main.nf \
--help
```
Expand Down Expand Up @@ -80,7 +80,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/annotate/scanvi/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/annotate/svm_annotation.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ ID: `svm_annotation`
Namespace: `annotate`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/annotate/svm_annotation/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/annotate/svm_annotation/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/annotate/svm_annotation/main.nf \
--help
```
Expand Down Expand Up @@ -77,7 +77,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/annotate/svm_annotation/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/cluster/leiden.qmd
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Expand Up @@ -14,7 +14,7 @@ ID: `leiden`
Namespace: `cluster`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/cluster/leiden/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/cluster/leiden/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -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 2.1.1 -latest \
-r 2.1.2 -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
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Expand Up @@ -14,7 +14,7 @@ ID: `compress_h5mu`
Namespace: `compression`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/compression/compress_h5mu/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/compression/compress_h5mu/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -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 2.1.1 -latest \
-r 2.1.2 -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/compression/tar_extract.qmd
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Expand Up @@ -14,7 +14,7 @@ ID: `tar_extract`
Namespace: `compression`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/compression/tar_extract/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/compression/tar_extract/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/compression/tar_extract/main.nf \
--help
```
Expand All @@ -54,7 +54,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/compression/tar_extract/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_10xh5_to_h5mu.qmd
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Expand Up @@ -14,7 +14,7 @@ ID: `from_10xh5_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/convert/from_10xh5_to_h5mu/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/convert/from_10xh5_to_h5mu/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -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 2.1.1 -latest \
-r 2.1.2 -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
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Expand Up @@ -14,7 +14,7 @@ ID: `from_10xmtx_to_h5mu`
Namespace: `convert`

### Links
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.1/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/convert/from_10xmtx_to_h5mu/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -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 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/convert/from_10xmtx_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
6 changes: 3 additions & 3 deletions components/modules/convert/from_bd_to_10x_molecular_barcode_tags.qmd
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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/2.1.1/src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -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 2.1.1 -latest \
-r 2.1.2 -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
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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/2.1.1/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/convert/from_bdrhap_to_h5mu/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
--help
```
Expand Down Expand Up @@ -58,7 +58,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -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
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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/2.1.1/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml){.btn-action .btn-sm .btn-info .btn role="button"}
[Source](https://github.com/openpipelines-bio/openpipeline/blob/2.1.2/src/convert/from_cellranger_multi_to_h5mu/config.vsh.yaml){.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 2.1.1 -latest \
-r 2.1.2 -latest \
-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
--help
```
Expand All @@ -69,7 +69,7 @@ publish_dir: # please fill in - example: "output/"

```bash
nextflow run openpipelines-bio/openpipeline \
-r 2.1.1 -latest \
-r 2.1.2 -latest \
-profile docker \
-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
-params-file params.yaml
Expand Down
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