Removed standard profile info

cgpu · Dec 14, 2018 · 30f7f1d · 30f7f1d
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diff --git a/docs/installation.md b/docs/installation.md
@@ -12,8 +12,6 @@ To start using the nf-core/atacseq pipeline, follow the steps below:
     * [Software deps: Bioconda](#32-software-deps-bioconda)
     * [Configuration profiles](#33-configuration-profiles)
 4. [Reference genomes](#4-reference-genomes)
-5. [Appendices](#5-appendices)
-    * [Running on UPPMAX](#running-on-uppmax)
 
 ## 1) Install NextFlow
 Nextflow runs on most POSIX systems (Linux, Mac OSX etc). It can be installed by running the following commands:
@@ -60,7 +58,7 @@ export NXF_OFFLINE='TRUE'
 If you would like to make changes to the pipeline, it's best to make a fork on GitHub and then clone the files. Once cloned you can run the pipeline directly as above.
 
 ## 3) Pipeline configuration
-By default, the pipeline runs with the `standard` configuration profile. This uses a number of sensible defaults for process requirements and is suitable for running on a simple (if powerful!) basic server. You can see this configuration in [`conf/base.config`](../conf/base.config).
+By default, the pipeline loads a basic server configuration [`conf/base.config`](../conf/base.config). This uses a number of sensible defaults for process requirements and is suitable for running on a simple (if powerful!) basic server.
 
 Be warned of two important points about this default configuration:
 
@@ -72,11 +70,11 @@ Be warned of two important points about this default configuration:
 #### 3.1) Software deps: Docker
 First, install docker on your system: [Docker Installation Instructions](https://docs.docker.com/engine/installation/)
 
-Then, running the pipeline with the option `-profile standard,docker` tells Nextflow to enable Docker for this run. An image containing all of the software requirements will be automatically fetched and used from dockerhub (https://hub.docker.com/r/nfcore/atacseq).
+Then, running the pipeline with the option `-profile docker` tells Nextflow to enable Docker for this run. An image containing all of the software requirements will be automatically fetched and used from dockerhub (https://hub.docker.com/r/nfcore/atacseq).
 
 #### 3.1) Software deps: Singularity
 If you're not able to use Docker then [Singularity](http://singularity.lbl.gov/) is a great alternative.
-The process is very similar: running the pipeline with the option `-profile standard,singularity` tells Nextflow to enable singularity for this run. An image containing all of the software requirements will be automatically fetched and used from singularity hub.
+The process is very similar: running the pipeline with the option `-profile singularity` tells Nextflow to enable singularity for this run. An image containing all of the software requirements will be automatically fetched and used from singularity hub.
 
 If running offline with Singularity, you'll need to download and transfer the Singularity image first:
 
@@ -96,7 +94,7 @@ Remember to pull updated versions of the singularity image if you update the pip
 If you're not able to use Docker _or_ Singularity, you can instead use conda to manage the software requirements.
 This is slower and less reproducible than the above, but is still better than having to install all requirements yourself!
 The pipeline ships with a conda environment file and nextflow has built-in support for this.
-To use it first ensure that you have conda installed (we recommend [miniconda](https://conda.io/miniconda.html)), then follow the same pattern as above and use the flag `-profile standard,conda`
+To use it first ensure that you have conda installed (we recommend [miniconda](https://conda.io/miniconda.html)), then follow the same pattern as above and use the flag `-profile conda`
 
 #### 3.3) Configuration profiles
 
@@ -105,16 +103,3 @@ See [`docs/configuration/adding_your_own.md`](configuration/adding_your_own.md)
 ## 4) Reference genomes
 
 See [`docs/configuration/reference_genomes.md`](configuration/reference_genomes.md)
-
-## 5) Appendices
-
-#### Running on UPPMAX
-To run the pipeline on the [Swedish UPPMAX](https://www.uppmax.uu.se/) clusters (`rackham`, `irma`, `bianca` etc), use the command line flag `-profile uppmax`. This tells Nextflow to submit jobs using the SLURM job executor with Singularity for software dependencies.
-
-Note that you will need to specify your UPPMAX project ID when running a pipeline. To do this, use the command line flag `--project <project_ID>`. The pipeline will exit with an error message if you try to run it pipeline with the default UPPMAX config profile without a project.
-
-**Optional Extra:** To avoid having to specify your project every time you run Nextflow, you can add it to your personal Nextflow config file instead. Add this line to `~/.nextflow/config`:
-
-```nextflow
-params.project = 'project_ID' // eg. b2017123
-```
diff --git a/docs/usage.md b/docs/usage.md
@@ -71,7 +71,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
 ## Running the pipeline
 The typical command for running the pipeline is as follows:
 ```bash
-nextflow run nf-core/atacseq --design design.csv --genome GRCh37 -profile standard,docker
+nextflow run nf-core/atacseq --design design.csv --genome GRCh37 -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -102,7 +102,7 @@ This version number will be logged in reports when you run the pipeline, so that
 ## Main arguments
 
 ### `-profile`
-Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. Note that multiple profiles can be loaded, for example: `-profile standard,docker` - the order of arguments is important!
+Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. Note that multiple profiles can be loaded, for example: `-profile docker` - the order of arguments is important!
 
 If `-profile` is not specified at all the pipeline will be run locally and expects all software to be installed and available on the `PATH`.
 

diff --git a/main.nf b/main.nf
@@ -26,14 +26,14 @@ def helpMessage() {
 
     The typical command for running the pipeline is as follows:
 
-    nextflow run nf-core/atacseq --design design.csv --genome GRCh37 -profile standard,docker
+    nextflow run nf-core/atacseq --design design.csv --genome GRCh37 -profile docker
 
     Mandatory arguments:
       --design                      Comma-separted file containing information about the samples in the experiment (see docs/usage.md)
       --fasta                       Path to Fasta reference. Not mandatory when using reference in iGenomes config via --genome
       --gtf                         Path to GTF file in Ensembl format. Not mandatory when using reference in iGenomes config via --genome
       -profile                      Configuration profile to use. Can use multiple (comma separated)
-                                    Available: standard, conda, docker, singularity, awsbatch, test
+                                    Available: conda, docker, singularity, awsbatch, test
 
     Generic
       --genome                      Name of iGenomes reference