mirror of
https://github.com/MillironX/nf-configs.git
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commit
de9f5ab560
5 changed files with 12 additions and 16 deletions
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@ -4,17 +4,11 @@ params{
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config_profile_url = 'https://www.boehringer-ingelheim.com/'
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}
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params.globalConfig = set_global_config()
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def set_global_config() {
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def config = System.getenv('NXF_GLOBAL_CONFIG')
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if(config == null)
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{
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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."
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System.err.println(errorMessage)
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}else{
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includeConfig config
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}
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return config
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params.globalConfig = System.getenv('NXF_GLOBAL_CONFIG')
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if(params.globalConfig == null)
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{
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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."
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System.err.println(errorMessage)
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}else{
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includeConfig params.globalConfig
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}
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@ -11,7 +11,6 @@ singularity {
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}
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process {
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beforeScript = 'module load Singularity/2.6.0-foss-2016b'
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executor = 'slurm'
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}
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@ -76,7 +76,6 @@ profiles {
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bwaalnn = 0.01
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bwaalnl = 16
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run_bam_filtering = true
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bam_discard_unmapped = true
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bam_unmapped_type = 'fastq'
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run_metagenomic_screening = true
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metagenomic_tool = 'malt'
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@ -33,6 +33,10 @@ profiles {
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params {
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config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.'
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}
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// delete when CDAG will be fixed
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process {
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queue = 'long'
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}
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}
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sdag {
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params {
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@ -10,7 +10,7 @@ Before running the pipeline you will need to load Nextflow and Singularity using
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## Load Nextflow and Singularity environment modules
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module purge
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module load Nextflow/19.10.0
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module load Singularity/2.6.0-foss-2016b
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module load Singularity
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```
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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).
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