docs: Remove mentions of conda in documentation

Signed-off-by: jvfe <[email protected]>

CITATIONS.md

@@ -112,14 +112,6 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
-
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
-
-- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
-
-  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
-
 - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
 
   > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

README.md

@@ -96,14 +96,14 @@ See our [roadmap](ROADMAP.md) for a full list of future development targets.
 
 1.  Install [`nextflow`](https://nf-co.re/usage/installation)
 
-2.  Install [`Docker`](https://www.docker.com), [`Singularity`](https://sylabs.io/guides/3.0/user-guide/installation.html), or, as a last resort, [`Conda`](https://conda.io/miniconda.html). Also ensure you have a working `curl` installed (should be present on almost all systems).
+2.  Install [`Docker`](https://www.docker.com) or [`Singularity`](https://sylabs.io/guides/3.0/user-guide/installation.html). Also ensure you have a working `curl` installed (should be present on almost all systems).
 
-    2.1. Note: this workflow should also support [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) execution for full pipeline reproducibility. We have minimized reliance on `conda` and suggest using it only as a last resort (see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles)). Configure `mail` on your system to send an email on workflow success/failure (without this you may get a small error at the end `Failed to invoke workflow.onComplete event handler` but this doesn't mean the workflow didn't finish successfully).
+    2.1. Note: this workflow should also support [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) execution for full pipeline reproducibility. Configure `mail` on your system to send an email on workflow success/failure (without this you may get a small error at the end `Failed to invoke workflow.onComplete event handler` but this doesn't mean the workflow didn't finish successfully).
 
 3.  Download the pipeline and test with a `stub-run`. The `stub-run` will ensure that the pipeline is able to download and use containers as well as execute in the proper logic.
 
     ```
-    nextflow run beiko-lab/ARETE -profile test,<docker/singularity/conda> -stub-run
+    nextflow run beiko-lab/ARETE -profile test,<docker/singularity> -stub-run
     ```
 
     3.1. Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.

docs/usage.md

@@ -295,12 +295,6 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 
       - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
 
-- `conda`
-
-      - Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud.
-      - A generic configuration profile to be used with [Conda](https://conda.io/docs/)
-      - Pulls most software from [Bioconda](https://bioconda.github.io/)
-
 - `test`
 
       - A profile with a complete configuration for automated testing