From 6a12e763ea8f2c6a76c3b80ca16bb7c2f49e2974 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 7 Jan 2019 11:16:58 +0100 Subject: [PATCH] Get rid of examples --- docs/binac.md | 3 --- docs/cfc.md | 3 --- docs/crick.md | 3 --- docs/template.md | 3 --- docs/uzh.md | 4 ---- 5 files changed, 16 deletions(-) diff --git a/docs/binac.md b/docs/binac.md index aab96ad..7846383 100644 --- a/docs/binac.md +++ b/docs/binac.md @@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load devel/java_jdk/1.8.0u112 module load devel/singularity/3.0.1 - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. diff --git a/docs/cfc.md b/docs/cfc.md index a83f590..7eb893d 100644 --- a/docs/cfc.md +++ b/docs/cfc.md @@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load devel/java_jdk/1.8.0u121 module load qbic/singularity_slurm/3.0.1 - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. diff --git a/docs/crick.md b/docs/crick.md index 9fc559e..11abde2 100644 --- a/docs/crick.md +++ b/docs/crick.md @@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load Nextflow/0.32.0 module load Singularity/2.6.0-foss-2016b - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile crick --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` A local copy of the iGenomes resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome ` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk). diff --git a/docs/template.md b/docs/template.md index d927039..bb2ea44 100644 --- a/docs/template.md +++ b/docs/template.md @@ -13,9 +13,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using module purge module load Nextflow/0.32.0 module load Singularity/2.6.0 - -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk ``` ## Below are non-mandatory information on iGenomes specific configuration diff --git a/docs/uzh.md b/docs/uzh.md index 08a81d7..ceb48f0 100644 --- a/docs/uzh.md +++ b/docs/uzh.md @@ -4,10 +4,6 @@ All nf-core pipelines have been successfully configured for use on the UZH clust To use, run the pipeline with `-profile UZH`. This will download and launch the [`uzh.config`](../conf/uzh.config) which has been pre-configured with a setup suitable for the UZH cluster. Using this profile, Nextflow will download a singularity image with all of the required software before execution of the pipeline. -## Example command for nf-core/atacseq -nextflow run nf-core/atacseq -profile PROFILE --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk -``` - All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway. >NB: You will need an account to use the HPC cluster UZH in order to run the pipeline. If in doubt contact IT.