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Merge pull request #13 from drpatelh/master

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Changed description for Singularity image download
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Alexander Peltzer 2019-01-11 16:04:52 +01:00 committed by GitHub
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docs/binac.md
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All nf-core pipelines have been successfully configured for use on the BinAC cluster at Baden-Württemberg HPC. All nf-core pipelines have been successfully configured for use on the BinAC cluster at Baden-Württemberg HPC.
To use, run the pipeline with `-profile binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC 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 binac`. This will download and launch the [`binac.config`](../conf/binac.config) which has been pre-configured with a setup suitable for the BINAC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on BINAC cluster. You can do this by issuing the commands below: Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on BINAC cluster. You can do this by issuing the commands below:

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docs/cfc.md
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All nf-core pipelines have been successfully configured for use on the CFC cluster at the insert institution here. All nf-core pipelines have been successfully configured for use on the CFC cluster at the insert institution here.
To use, run the pipeline with `-profile cfc`. This will download and launch the [`cfc.config`](../conf/cfc.config) which has been pre-configured with a setup suitable for the CFC 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 cfc`. This will download and launch the [`cfc.config`](../conf/cfc.config) which has been pre-configured with a setup suitable for the CFC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CFC cluster. You can do this by issuing the commands below: Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CFC cluster. You can do this by issuing the commands below:

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docs/crick.md
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All nf-core pipelines have been successfully configured for use on the CAMP HPC cluster at the [The Francis Crick Institute](https://www.crick.ac.uk/). All nf-core pipelines have been successfully configured for use on the CAMP HPC cluster at the [The Francis Crick Institute](https://www.crick.ac.uk/).
To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, Nextflow will download a temporary singularity image with all of the required software before execution of the pipeline. To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CAMP. You can do this by issuing the commands below: Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CAMP. You can do this by issuing the commands below:

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docs/munin.md
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All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron. All nf-core pipelines have been successfully configured for use on the MUNIN cluster aka big iron.
To use, run the pipeline with `-profile munin`. This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN 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 munin`. This will download and launch the [`munin.config`](../conf/munin.config) which has been pre-configured with a setup suitable for the MUNIN cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Example: `nextflow run -profile munin` Example: `nextflow run -profile munin`

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docs/shh.md
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All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG cluster at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de). All nf-core pipelines have been successfully configured for use on the Department of Archaeogenetic's SDAG cluster at the [Max Planck Institute for the Science of Human History (MPI-SHH)](http://shh.mpg.de).
To use, run the pipeline with `-profile shh`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG 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 shh`. This will download and launch the [`shh.config`](../conf/shh.config) which has been pre-configured with a setup suitable for the SDAG cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
Note that the configuration file is currently optimised for `nf-core/eager`. It Note that the configuration file is currently optimised for `nf-core/eager`. It
will submit to the medium queue but with a walltime of 48 hours. will submit to the medium queue but with a walltime of 48 hours.

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docs/template.md
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All nf-core pipelines have been successfully configured for use on the PROFILE CLUSTER at the insert institution here. All nf-core pipelines have been successfully configured for use on the PROFILE CLUSTER at the insert institution here.
To use, run the pipeline with `-profile PROFILENAME`. This will download and launch the [`profile.config`](../conf/profile.config) which has been pre-configured with a setup suitable for the PROFILE 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 PROFILENAME`. This will download and launch the [`profile.config`](../conf/profile.config) which has been pre-configured with a setup suitable for the PROFILE cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
## Below are non-mandatory information e.g. on modules to load etc. ## Below are non-mandatory information e.g. on modules to load etc.

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docs/uppmax.md
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All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters. All nf-core pipelines have been successfully configured for use on the Swedish UPPMAX clusters.
## Using the UPPMAX config profile ## Using the UPPMAX config profile
To use, run the pipeline with `-profile uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. 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 uppmax` (one hyphen). This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
In addition to this config profile, you will also need to specify an UPPMAX project id. In addition to this config profile, you will also need to specify an UPPMAX project id.
You can do this with the `--project` flag (two hyphens) when launching nextflow. For example: You can do this with the `--project` flag (two hyphens) when launching nextflow. For example:

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docs/uzh.md
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All nf-core pipelines have been successfully configured for use on the UZH cluster at the University of Zürich. All nf-core pipelines have been successfully configured for use on the UZH cluster at the University of Zürich.
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, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
>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.