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Get rid of examples

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Alexander Peltzer 2019-01-07 11:16:58 +01:00
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3
docs/binac.md
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@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using
module purge module purge
module load devel/java_jdk/1.8.0u112 module load devel/java_jdk/1.8.0u112
module load devel/singularity/3.0.1 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. 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.

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docs/cfc.md
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@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using
module purge module purge
module load devel/java_jdk/1.8.0u121 module load devel/java_jdk/1.8.0u121
module load qbic/singularity_slurm/3.0.1 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. 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.

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docs/crick.md
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@ -11,9 +11,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using
module purge module purge
module load Nextflow/0.32.0 module load Nextflow/0.32.0
module load Singularity/2.6.0-foss-2016b 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 <GENOME_ID>` 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). 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 <GENOME_ID>` 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).

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docs/template.md
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@ -13,9 +13,6 @@ Before running the pipeline you will need to load Nextflow and Singularity using
module purge module purge
module load Nextflow/0.32.0 module load Nextflow/0.32.0
module load Singularity/2.6.0 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 ## Below are non-mandatory information on iGenomes specific configuration

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docs/uzh.md
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@ -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. 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. 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. >NB: You will need an account to use the HPC cluster UZH in order to run the pipeline. If in doubt contact IT.