Merge pull request #45 from ggabernet/dev

Update pipeline releases

Author: ggabernet

docs/markdown/pipelines/pipeline_releases.md

@@ -22,43 +22,4 @@ These versions will be revised periodically and tested in our infrastructure bef
 | Epitope prediction    | [nf-core/epitopeprediction](https://nf-co.re/epitopeprediction/1.1.0)         |    1.1.0    |
 | Bacterial assembly    | [nf-core/bacass](https://nf-co.re/bacass/2.0.0)                               |    2.0.0    |
 | RNA fusion            | [nf-core/rnafusion](https://nf-co.re/rnafusion/1.2.0)                         |    1.2.0    |
-
-## Routine params to trigger most common pipelines
-
-For our Slurm cluster, we use the profile `cfc` that is stored under [nf-core/configs](https://github.com/nf-core/configs/blob/master/conf/cfc.config).
-
-If you want to test the pipelines in your system, you can use `-profile test,docker` or `-profile test,singularity` if you have docker or singularity installed. Note that the params files will need to be edited to your input data.
-
-### Sarek variant calling
-
-To run pipeline tests use the following command:
-
-```bash
-nextflow run nf-core/sarek -r 2.7.1 -profile test,cfc
-```
-
-To launch sarek for germline WGS using the [example params](https://github.com/qbic-pipelines/pipeline-docs/blob/master/docs/params/sarek_WGS_germline.json) use the following command:
-
-```bash
-nextflow run nf-core/sarek -r 2.7.1 -profile cfc -params-file sarek_WGS_germline.json
-```
-
-To launch sarek for somatic WES / WXS using the [example params](https://github.com/qbic-pipelines/pipeline-docs/blob/master/docs/params/sarek_WXS_somatic.json) use the following command:
-
-```bash
-nextflow run nf-core/sarek -r 2.7.1 -profile cfc -params-file sarek_WXS_somatic.json
-```
-
-### RNAseq analysis
-
-To run pipeline tests we use the following command:
-
-```bash
-nextflow run nf-core/rnaseq -r 1.4.2 -profile test,cfc
-```
-
-To launch rnaseq for RNAseq using our [example params](https://github.com/qbic-pipelines/pipeline-docs/blob/master/docs/params/rnaseq.json) use the following command:
-
-```bash
-nextflow run nf-core/rnaseq -r 1.4.2 -profile cfc -params-file rnaseq.json
-```
+| scRNAseq cellranger   | [qbic-pipelines/cellranger](https://github.com/qbic-pipelines/cellranger)     |    1.0.1    |