millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-12-22 10:38:16 +00:00
Code Issues Releases Packages Activity

Get rid of template / iGenomes stuff

Browse source
This commit is contained in:
Alexander Peltzer 2019-01-07 11:21:17 +01:00
parent 6a12e763ea
commit 02e97811c6
2 changed files with 2 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

5
docs/template.md
View file

@ -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 <GENOME_ID>` 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 <GENOME_ID>` 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.

2
docs/uzh.md
View file

@ -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.