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Merge pull request #306 from praveenraj2018/rnavar_munin

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Added rnavar pipeline config for Munin
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praveenraj2018 2021-12-14 16:10:59 +01:00 committed by GitHub
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README.md
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@ -190,6 +190,8 @@ Currently documentation is available for the following pipelines within specific
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
* [UPPMAX](docs/pipeline/sarek/uppmax.md)
* rnavar
* [MUNIN](docs/pipeline/rnavar/munin.md)
### Pipeline-specific documentation

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// rnavar/munin specific profile config
params {
// Specific nf-core/configs params
config_profile_contact = 'Praveen Raj (@praveenraj2018)'
config_profile_description = 'nf-core/rnavar MUNIN profile provided by nf-core/configs'
config_profile_url = 'https://ki.se/forskning/barntumorbanken'
// Specific nf-core/rnavar params
igenomes_ignore = true
// Genome references
fasta = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa'
fasta_fai = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai'
gtf = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf'
gene_bed = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed'
// Known genome resources
dbsnp = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz'
dbsnp_tbi = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi'
known_indels = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
known_indels_tbi = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi'
// STAR index
star_index = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/'
// Annotation settings
annotation_cache = true
cadd_cache = true
cadd_indels = '/data1/cache/CADD/v1.4/InDels.tsv.gz'
cadd_indels_tbi = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi'
cadd_wg_snvs = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz'
cadd_wg_snvs_tbi = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi'
snpeff_cache = '/data1/cache/snpEff/'
snpeff_db = 'GRCh38.99'
vep_cache = '/data1/cache/VEP/'
vep_genome = 'GRCh38'
vep_species = 'homo_sapiens'
vep_cache_version = '99'
}

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# nf-core/configs: MUNIN rnavar specific configuration
Extra specific configuration for rnavar pipeline
## Usage
To use, run the pipeline with `-profile munin`.
This will download and launch the rnavar specific [`munin.config`](../../../conf/pipeline/rnavar/munin.config) which has been pre-configured with a setup suitable for the `MUNIN` cluster.
Example: `nextflow run nf-core/rnavar -profile munin`
## rnavar specific configurations for MUNIN
Specific configurations for `MUNIN` has been made for rnavar.
Genome references
`fasta` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa`
`fasta_fai` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.fai`
`gtf` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf`
`gene_bed` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.bed`
Known genome resources
`dbsnp set to` `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz`
`dbsnp_tbi set` to `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi`
`known_indels set` to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
`known_indels_tbi` set to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
STAR index
`star_index` set to `/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/`
Variant annotation configurations
* Params `annotation_cache` and `cadd_cache` set to `true`
* Params `snpeff_db` set to `GRCh38.99`
* Params `vep_cache_version` set to `99`
* Params `vep_genome` set to `GRCh38`
* Path to `snpeff_cache`: `/data1/cache/snpEff/`
* Path to `vep_cache`: `/data1/cache/VEP/`
* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`

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/*
* -------------------------------------------------
* nfcore/rnavar custom profile Nextflow config file
* -------------------------------------------------
* Config options for custom environments.
* Cluster-specific config options should be saved
* in the conf/pipeline/rnavar folder and imported
* under a profile name here.
*/
profiles {
munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnavar/munin.config" }
}