Add info about diffab

docs/index.rst

@@ -42,6 +42,9 @@ Analysis types
 :doc:`markdown/pipelines/guideseq`
    Guideseq analysis
 
+:doc:`markdown/pipelines/maxquant`
+   MaxQuant analysis
+
 
 Clusters and remotes
 --------------------
@@ -70,6 +73,7 @@ Clusters and remotes
    markdown/pipelines/scrnaseq
    markdown/pipelines/airrflow
    markdown/pipelines/guideseq
+   markdown/pipelines/maxquant
 
 .. toctree::
    :maxdepth: 3

docs/markdown/pipelines/pipeline_releases.md

@@ -6,21 +6,23 @@ These versions will be revised periodically and tested in our infrastructure bef
 
 ## Pipeline releases to be used at QBiC
 
-| Analysis type         | Pipeline                                                                  | Use version |
-| --------------------- | ------------------------------------------------------------------------- | :---------: |
-| RNAseq                | [nf-core/rnaseq](https://nf-co.re/rnaseq/1.4.2)                           |    1.4.2    |
-| 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/3.1.2)                             |    3.1.2    |
-| 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/2.1.1)                       |    2.1.1    |
-| Shotgun metagenomics  | [nf-core/mag](https://nf-co.re/mag/2.1.1)                                 |    2.1.1    |
-| BCR / TCR repseq      | [nf-core/airrflow](https://nf-co.re/airrflow/2.4.0)                       |    2.4.0    |
-| 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/2.3.1)                       |    2.3.1    |
-| ATACseq               | [nf-core/atacseq](https://nf-co.re/atacseq/1.2.2)                         |    1.2.2    |
-| 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/2.0.0)     |    2.0.0    |
-| 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    |
-| BAM/CRAM to Fastq     | [qbic-pipelines/bamtofastq](https://github.com/qbic-pipelines/bamtofastq) |    1.2.0    |
+| Analysis type         | Pipeline                                                                          | Use version |
+| --------------------- | --------------------------------------------------------------------------------- | :---------: |
+| RNAseq                | [nf-core/rnaseq](https://nf-co.re/rnaseq/1.4.2)                                   |    1.4.2    |
+| RNAseq DE analysis    | [qbic-pipelines/rnadeseq](https://github.com/qbic-pipelines/rnadeseq)             |    2.4.1    |
+| OR RNAseq DE analysis | [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance) |    1.5.0    |
+| MaxQuant proteomics   | [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance) |    1.5.0    |
+| WGS / WES             | [nf-core/sarek](https://nf-co.re/sarek/3.1.2)                                     |    3.1.2    |
+| 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/2.1.1)                               |    2.1.1    |
+| Shotgun metagenomics  | [nf-core/mag](https://nf-co.re/mag/2.1.1)                                         |    2.1.1    |
+| BCR / TCR repseq      | [nf-core/airrflow](https://nf-co.re/airrflow/2.4.0)                               |    2.4.0    |
+| 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/2.3.1)                               |    2.3.1    |
+| ATACseq               | [nf-core/atacseq](https://nf-co.re/atacseq/1.2.2)                                 |    1.2.2    |
+| 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/2.0.0)             |    2.0.0    |
+| 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    |
+| BAM/CRAM to Fastq     | [qbic-pipelines/bamtofastq](https://github.com/qbic-pipelines/bamtofastq)         |    1.2.0    |

docs/markdown/pipelines/rnaseq.md

@@ -31,23 +31,73 @@ Example command (change `cfc` for `binac` on binac cluster):
 
 ```bash
 #!/usr/bin/bash
-nextflow run qbicsoftware/rnadeseq -r 1.3.2 -profile docker \
---rawcounts 'merged_gene_counts.txt' \
---metadata 'QXXXX_sample_preparations.tsv' \
+nextflow run qbic-pipelines/rnadeseq -r 2.4.1 -profile cfc \
+--gene_counts 'merged_gene_counts.txt' \
+--input 'QXXXX_sample_preparations.tsv' \
 --model 'linear_model.txt' \
 --contrast_matrix 'contrasts.tsv' \
 --project_summary 'QXXXX_summary.tsv' \
 --multiqc 'MultiQC.zip' \
---quote 'QXXXX_signed_offer.pdf' \
---versions 'software_versions.csv' \
---report_options 'report_options.yml' \
---species Hsapiens
+--software_versions 'software_versions.csv' \
+--outdir 'results'
+```
+
+### Docker containers
+
+After the release of rnadeseq 2.1, the docker containers were moved from Docker Hub to the GitHub Container Registry (ghcr) as Docker announced a change of free subscriptions. For all rnadeseq versions >2.1, this is reflected in the pipeline, so you don't need to do anything.
+
+For version 2.1 or later, should you have trouble executing the pipeline because the container was removed from Docker Hub (this could for example lead to an error like "docker: Error response from daemon: manifest for qbicpipelines/rnadeseq:2.1 not found: manifest unknown: manifest unknown."), please save the following code to a `container.config` (change 2.1 to the version you want to use):
+
+```bash
+process {
+    withName: REPORT {
+        container = 'ghcr.io/qbic-pipelines/rnadeseq:2.1'
+    }
+}
+```
+
+If you want to run a version <2.1, the container.config has to look like this:
+
+```bash
+process.container = 'ghcr.io/qbic-pipelines/rnadeseq:1.1.0'
+```
+
+The container link has to be adjusted to the version you want to run. You should just have to change the version number, but you can double-check on https://github.com/qbic-pipelines/rnadeseq/pkgs/container/rnadeseq if you are not sure if the link is correct.
+
+Then, call this container.config when running the pipeline, like so:
+
+```bash
+qbic-pipelines/rnadeseq -r 2.4.1 -profile cfc \
+--many-many "params" \
+-c path/to/container.config
 ```
 
 ### Known issues
 
 - No known issues
 
+## Switch to nf-core/differentialabundance
+
+In the future, we want to switch to the [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance) pipeline. It was developed as a pipeline that is capable of a differential abundance analysis of different types of input data, including proteomics experiments if the upstream analysis was done with MaxQuant.
+
+### Quick start
+
+Example command on cfc:
+
+```bash
+#!/usr/bin/bash
+nextflow run nf-core/differentialabundance -r 1.5.0 -profile cfc,rnaseq \
+-params-file /sfs/9/ws/shared_files/qbic_differentialabundance_rnaseq.yml \
+--matrix 'salmon.merged.gene_counts_length_scaled.tsv' \
+--input 'sample_preparations.tsv' \
+--contrast_matrix 'contrasts.tsv' \
+--report_contributors 'Jane Doe\nDirector of Institute of Microbiology\nUniversity of Smallville;John Smith\nPhD student\nInstitute of Microbiology\nUniversity of Smallville'
+```
+
+The file `/sfs/9/ws/shared_files/qbic_differentialabundance_rnaseq.yml` contains several settings that will probably be necessary for any such analysis at QBiC and is saved in a folder on cfc which is accessible by every qbic-staff member. This includes a custom CSS and PNG file which set the style of the HTML report that is generated at the end of pipeline runs (i.e. this changes the color of highlighted text to QBiC blue and adds a combination of the QBiC rectangle and the pipeline logo to the very top of the report). If you want to run such an analysis on another machine, simply copy the relevant files from the shared_files folder over, then modify the paths in the YML file accordingly.
+
+For more information about how to run the pipeline, have a look at the [usage docs](https://nf-co.re/differentialabundance/docs/usage/).
+
 ## Reporting
 
-The reporting is taken care of as part of the [qbic-pipelines/rnadeseq](https://github.com/qbic-pipelines/rnadeseq) pipeline. Check the previous section.
+The reporting is taken care of as part of the [qbic-pipelines/rnadeseq](https://github.com/qbic-pipelines/rnadeseq) and [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance) pipelines. Check the previous sections.