update pipeline releases

Author: ggabernet

docs/markdown/pipelines/pipeline_releases.md

@@ -12,53 +12,15 @@ These versions will be revised periodically and tested in our infrastructure bef
 | RNAseq DE analysis    | [qbic-pipelines/rnadeseq](https://github.com/qbic-pipelines/rnadeseq) |    1.3.2    |
 | WGS / WES             | [nf-core/sarek](https://nf-co.re/sarek/2.7.1)                                 |    2.7.1    |
 | HLAtyping             | [nf-core/hlatyping](https://nf-co.re/hlatyping/1.2.0)                         |    1.2.0    |
-| 16S amplicon          | [nf-core/ampliseq](https://nf-co.re/ampliseq/2.1.0)                           |    2.1.0    |
+| 16S amplicon          | [nf-core/ampliseq](https://nf-co.re/ampliseq/2.1.1)                           |    2.1.1    |
 | Shotgun metagenomics  | [nf-core/mag](https://nf-co.re/mag/2.1.0)                                     |    2.1.0    |
 | BCR / TCR repseq      | [nf-core/bcellmagic](https://nf-co.re/bcellmagic/2.0.0)                       |    2.0.0    |
 | CAGEseq               | [nf-core/cageseq](https://nf-co.re/cageseq/1.0.2)                             |    1.0.2    |
 | MHC immunopeptidomics | [nf-core/mhcquant](https://nf-co.re/mhcquant/2.0.0)                           |    2.0.0    |
 | ATACseq               | [nf-core/atacseq](https://nf-co.re/atacseq/1.2.1)                             |    1.2.1    |
-| Chipseq               | [nf-core/chipseq](https://nf-co.re/chipseq/1.2.1)                             |    1.2.1    |
+| Chipseq               | [nf-core/chipseq](https://nf-co.re/chipseq/1.2.2)                             |    1.2.2    |
 | 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    |
+| scRNAseq cellranger   | [qbic-pipelines/cellranger](https://github.com/qbic-pipelines/cellranger)     |    1.0.1    |
 
-## 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 -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 -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 -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
-```