diff --git a/docs/template.md b/docs/template.md index bb2ea44..bd65ee1 100644 --- a/docs/template.md +++ b/docs/template.md @@ -17,11 +17,8 @@ module load Singularity/2.6.0 ## Below are non-mandatory information on iGenomes specific configuration -A local copy of the iGenomes resource has been made available on PROFILE CLUSTER 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 PROFILE CLUSTER so have a look in the `igenomes_base` path specified in [`profile.config`](../conf/profile.config), and if your genome of interest isnt present please contact [local_contact_name_for_profile](mailto:local_contact_handle). +A local copy of the iGenomes resource has been made available on PROFILE CLUSTER 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 PROFILE CLUSTER so have a look in the `igenomes_base` path specified in [`profile.config`](../conf/profile.config). -Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://github.com/nf-core/atacseq/blob/master/docs/configuration/reference_genomes.md) for instructions). - -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 on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT. diff --git a/docs/uzh.md b/docs/uzh.md index ceb48f0..fc4fbb2 100644 --- a/docs/uzh.md +++ b/docs/uzh.md @@ -2,7 +2,7 @@ All nf-core pipelines have been successfully configured for use on the UZH cluster at the insert institution here. -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. 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.