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Merge pull request #11 from nf-core/master

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James A. Fellows Yates 2020-08-11 09:10:13 +02:00 committed by GitHub
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5 changed files with 12 additions and 16 deletions
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12
conf/bi.config
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@ -4,17 +4,11 @@ params{
config_profile_url = 'https://www.boehringer-ingelheim.com/' config_profile_url = 'https://www.boehringer-ingelheim.com/'
} }
params.globalConfig = set_global_config() params.globalConfig = System.getenv('NXF_GLOBAL_CONFIG')
if(params.globalConfig == null)
def set_global_config() {
def config = System.getenv('NXF_GLOBAL_CONFIG')
if(config == null)
{ {
def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile." def errorMessage = "WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile."
System.err.println(errorMessage) System.err.println(errorMessage)
}else{ }else{
includeConfig config includeConfig params.globalConfig
}
return config
} }

1
conf/crick.config
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@ -11,7 +11,6 @@ singularity {
} }
process { process {
beforeScript = 'module load Singularity/2.6.0-foss-2016b'
executor = 'slurm' executor = 'slurm'
} }

1
conf/pipeline/eager/shh.config
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@ -76,7 +76,6 @@ profiles {
bwaalnn = 0.01 bwaalnn = 0.01
bwaalnl = 16 bwaalnl = 16
run_bam_filtering = true run_bam_filtering = true
bam_discard_unmapped = true
bam_unmapped_type = 'fastq' bam_unmapped_type = 'fastq'
run_metagenomic_screening = true run_metagenomic_screening = true
metagenomic_tool = 'malt' metagenomic_tool = 'malt'

4
conf/shh.config
View file

@ -33,6 +33,10 @@ profiles {
params { params {
config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.' config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.'
} }
// delete when CDAG will be fixed
process {
queue = 'long'
}
} }
sdag { sdag {
params { params {

2
docs/crick.md
View file

@ -10,7 +10,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using
## Load Nextflow and Singularity environment modules ## Load Nextflow and Singularity environment modules
module purge module purge
module load Nextflow/19.10.0 module load Nextflow/19.10.0
module load Singularity/2.6.0-foss-2016b module load Singularity
``` ```
A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-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 [AWS-iGenomes](https://github.com/ewels/AWS-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).