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Merge pull request #306 from praveenraj2018/rnavar_munin
Added rnavar pipeline config for Munin
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praveenraj2018
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4 changed files with 105 additions and 0 deletions
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@ -190,6 +190,8 @@ Currently documentation is available for the following pipelines within specific
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* sarek
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* sarek
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* [MUNIN](docs/pipeline/sarek/munin.md)
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* [UPPMAX](docs/pipeline/sarek/uppmax.md)
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* [UPPMAX](docs/pipeline/sarek/uppmax.md)
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* rnavar
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* [MUNIN](docs/pipeline/rnavar/munin.md)
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### Pipeline-specific documentation
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### Pipeline-specific documentation
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42
conf/pipeline/rnavar/munin.config
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42
conf/pipeline/rnavar/munin.config
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// rnavar/munin specific profile config
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params {
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// Specific nf-core/configs params
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config_profile_contact = 'Praveen Raj (@praveenraj2018)'
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config_profile_description = 'nf-core/rnavar MUNIN profile provided by nf-core/configs'
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config_profile_url = 'https://ki.se/forskning/barntumorbanken'
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// Specific nf-core/rnavar params
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igenomes_ignore = true
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// Genome references
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fasta = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa'
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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'
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gtf = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_annot.gtf'
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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'
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// Known genome resources
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dbsnp = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz'
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dbsnp_tbi = '/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi'
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known_indels = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz'
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known_indels_tbi = '/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi'
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// STAR index
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star_index = '/data1/references/CTAT_GenomeLib_v37_Mar012021/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/star150bp.idx/'
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// Annotation settings
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annotation_cache = true
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cadd_cache = true
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cadd_indels = '/data1/cache/CADD/v1.4/InDels.tsv.gz'
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cadd_indels_tbi = '/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi'
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cadd_wg_snvs = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz'
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cadd_wg_snvs_tbi = '/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi'
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snpeff_cache = '/data1/cache/snpEff/'
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snpeff_db = 'GRCh38.99'
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vep_cache = '/data1/cache/VEP/'
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vep_genome = 'GRCh38'
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vep_species = 'homo_sapiens'
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vep_cache_version = '99'
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}
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48
docs/pipeline/rnavar/munin.md
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docs/pipeline/rnavar/munin.md
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# nf-core/configs: MUNIN rnavar specific configuration
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Extra specific configuration for rnavar pipeline
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## Usage
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To use, run the pipeline with `-profile munin`.
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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.
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Example: `nextflow run nf-core/rnavar -profile munin`
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## rnavar specific configurations for MUNIN
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Specific configurations for `MUNIN` has been made for rnavar.
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Genome references
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`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`
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`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`
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`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`
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`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`
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Known genome resources
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`dbsnp set to` `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz`
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`dbsnp_tbi set` to `/data1/references/annotations/GATK_bundle/dbsnp_146.hg38.vcf.gz.tbi`
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`known_indels set` to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz`
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`known_indels_tbi` set to `/data1/references/annotations/GATK_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi`
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STAR index
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`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/`
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Variant annotation configurations
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* Params `annotation_cache` and `cadd_cache` set to `true`
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* Params `snpeff_db` set to `GRCh38.99`
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* Params `vep_cache_version` set to `99`
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* Params `vep_genome` set to `GRCh38`
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* Path to `snpeff_cache`: `/data1/cache/snpEff/`
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* Path to `vep_cache`: `/data1/cache/VEP/`
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* Path to `pon`: `/data1/PON/vcfs/BTB.PON.vcf.gz`
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* Path to `pon_index`: `/data1/PON/vcfs/BTB.PON.vcf.gz.tbi`
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* Path to `cadd_indels`: `/data1/cache/CADD/v1.4/InDels.tsv.gz`
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* Path to `cadd_indels_tbi`: `/data1/cache/CADD/v1.4/InDels.tsv.gz.tbi`
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* Path to `cadd_wg_snvs`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz`
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* Path to `cadd_wg_snvs_tbi`: `/data1/cache/CADD/v1.4/whole_genome_SNVs.tsv.gz.tbi`
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13
pipeline/rnavar.config
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13
pipeline/rnavar.config
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/*
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* -------------------------------------------------
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* nfcore/rnavar custom profile Nextflow config file
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* -------------------------------------------------
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* Config options for custom environments.
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* Cluster-specific config options should be saved
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* in the conf/pipeline/rnavar folder and imported
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* under a profile name here.
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*/
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profiles {
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munin { includeConfig "${params.custom_config_base}/conf/pipeline/rnavar/munin.config" }
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}
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