Update docs for hasta config
commit
c59149d64c
@ -0,0 +1,29 @@
|
||||
params {
|
||||
// Specific nf-core/configs params
|
||||
config_profile_contact = 'James Fellows Yates (@jfy133)'
|
||||
config_profile_description = 'nf-core/taxprofiler EVA profile provided by nf-core/configs'
|
||||
}
|
||||
|
||||
process {
|
||||
|
||||
withName: BBMAP_BBDUK {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: MALT_RUN {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: METAPHLAN3 {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
withName: MEGAN_RMA2INFO {
|
||||
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
|
||||
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
|
||||
}
|
||||
|
||||
}
|
@ -0,0 +1,19 @@
|
||||
# nf-core/configs: eva taxprofiler specific configuration
|
||||
|
||||
Extra specific configuration for taxprofiler pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run the pipeline with `-profile hasta`.
|
||||
|
||||
This will download and launch the taxprofiler specific [`hasta.config`](../../../conf/pipeline/taxprofiler/hasta.config) which has been pre-configured with a setup suitable for the hasta cluster.
|
||||
|
||||
Example: `nextflow run nf-core/taxprofiler -profile hasta`
|
||||
|
||||
## taxprofiler specific configurations for hasta
|
||||
|
||||
Specific configurations for hasta has been made for taxprofiler.
|
||||
|
||||
### General profiles
|
||||
|
||||
- The general hasta profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues with: BBDUK and MALT.
|
@ -0,0 +1,19 @@
|
||||
# nf-core/configs: eva taxprofiler specific configuration
|
||||
|
||||
Extra specific configuration for taxprofiler pipeline
|
||||
|
||||
## Usage
|
||||
|
||||
To use, run the pipeline with `-profile eva`.
|
||||
|
||||
This will download and launch the taxprofiler specific [`eva.config`](../../../conf/pipeline/taxprofiler/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
|
||||
|
||||
Example: `nextflow run nf-core/taxprofiler -profile eva`
|
||||
|
||||
## taxprofiler specific configurations for eva
|
||||
|
||||
Specific configurations for eva has been made for taxprofiler.
|
||||
|
||||
### General profiles
|
||||
|
||||
- The general MPI-EVA profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues SGE have with Java and python tools, nameling: BBDUK, MALT, MetaPhlAn3, and MEGAN
|
Loading…
Reference in New Issue