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Merge pull request #80 from ffmmulder/config_splitup
Config splitup and version update
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| manifest { | ||
| homePage = 'https://github.com/UMCUGenetics/RNASeq-NF' | ||
| description = 'RNASeq-NF is an NGS analysis pipeline for RNA expression quantification' | ||
| mainScript = 'main.nf' | ||
| version = '1.1' | ||
| nextflowVersion = '20.04.1' | ||
| } | ||
|
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| executor { | ||
| $sge { | ||
| queueSize = 1000 | ||
| pollInterval = '30sec' | ||
| queueStatInterval = '5min' | ||
| } | ||
| $slurm { | ||
| queueSize = 1000 | ||
| pollInterval = '30sec' | ||
| queueStatInterval = '5min' | ||
| } | ||
| } | ||
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| profiles { | ||
| sge { | ||
| process.executor = 'sge' | ||
| process.queue = 'all.q' | ||
| process.clusterOptions = '-P compgen ' | ||
| } | ||
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| slurm { | ||
| process.executor = 'slurm' | ||
| process.clusterOptions = '--gres=tmpspace:25G' | ||
| process.queue = 'cpu' | ||
| } | ||
| } | ||
|
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| report { | ||
| enabled = true | ||
| file = "$params.out_dir/log/nextflow_report.html" | ||
| } | ||
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| trace { | ||
| enabled = true | ||
| file = "$params.out_dir/log/nextflow_trace.txt" | ||
| fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt' | ||
| } | ||
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| timeline { | ||
| enabled = true | ||
| file = "$params.out_dir/log/nextflow_timeline.html" | ||
| } | ||
|
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| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| runOptions = '-B /hpc -B $TMPDIR:$TMPDIR' | ||
| cacheDir = '/hpc/local/CentOS7/cog_bioinf/singularity_cache' | ||
| } | ||
|
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| cleanup = true |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,105 @@ | ||
| params { | ||
|
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| //Default resource folder | ||
| resource_dir = "/hpc/ubec/resources/" | ||
|
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| //These are set to empty by default and can/must be overwritten per genome when required (only works with empty values?) | ||
| genome_bed = "" | ||
| genome_known_sites = [] | ||
| scatter_interval_list = "" | ||
| salmon_index = "" | ||
| transcripts_fasta = "" | ||
|
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| genomes { | ||
| "Felis_Catus_9.0" { | ||
| genome_fasta = "${params.resource_dir}/genomes/Felis_catus_9.0_ensembl/Felis_catus_9.0.dna.toplevel.fa" | ||
| genome_gtf = "${params.resource_dir}/genomes/Felis_catus_9.0_ensembl/Felis_catus_9.0.dna.toplevel.gtf" | ||
| genome_bed = "" | ||
| genome_dict = "${params.resource_dir}/genomes/Felis_catus_9.0_ensembl/Felis_catus_9.0.dna.toplevel.dict" | ||
| genome_index = "${params.resource_dir}/genomes/Felis_catus_9.0_ensembl/Felis_catus_9.0.dna.toplevel.fa.fai" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/Felis_catus_9.0" | ||
| } | ||
| "GRCh37" { | ||
| genome_fasta = "${params.resource_dir}/genomes/GRCh37/Sequence/genome.fa" | ||
| genome_gtf = "${params.resource_dir}/genomes/GRCh37/Annotation/Homo_sapiens.GRCh37.74.gtf" | ||
| genome_bed = "${params.resource_dir}/genomes/GRCh37/Annotation/Homo_sapiens.GRCh37.74.sorted.bed12" | ||
| genome_dict = "${params.resource_dir}/genomes/GRCh37/Sequence/genome.dict" | ||
| genome_index = "${params.resource_dir}/genomes/GRCh37/Sequence/genome.fa.fai" | ||
| genome_known_sites = ["${params.resource_dir}/genomes/GRCh37/Annotation/1000G_phase1.indels.b37.vcf.gz", | ||
| "${params.resource_dir}/genomes/GRCh37/Annotation/dbsnp_138.b37.vcf.gz", | ||
| "${params.resource_dir}/genomes/GRCh37/Annotation/Mills_and_1000G_gold_standard.indels.b37.vcf.gz"] | ||
| scatter_interval_list = "${params.resource_dir}/genomes/GRCh37/Sequence/genome.interval_list" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/GRCh37" | ||
| salmon_index = "${params.resource_dir}/tools/salmon/1.2.1/Homo_sapiens.GRCh37.75.cdna.all" | ||
| transcripts_fasta = "${params.resource_dir}/tools/rsem/transcripts/Homo_sapiens.GRCh37/GRCh37.transcripts.fa" | ||
| } | ||
| "GRCh38" { | ||
| genome_fasta = "${params.resource_dir}/genomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna" | ||
| genome_gtf = "${params.resource_dir}/tools/rnaseq-nf/genome_files/GRCh38/Homo_sapiens.GRCh38.104.chr.ncbi.gtf" | ||
| genome_bed = "${params.resource_dir}/tools/rnaseq-nf/genome_files/GRCh38/Homo_sapiens.GRCh38.104.chr.ncbi.sorted.bed12" | ||
| genome_dict = "${params.resource_dir}/genomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.dict" | ||
| genome_index = "${params.resource_dir}/genomes/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai" | ||
| genome_known_sites = ["${params.resource_dir}/tools/rnaseq-nf/genome_files/GRCh38/GATK_ResourceBundle/Homo_sapiens_assembly38.known_indels.vcf.gz", | ||
| "${params.resource_dir}/tools/rnaseq-nf/genome_files/GRCh38/GATK_ResourceBundle/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz", | ||
| "${params.resource_dir}/tools/rnaseq-nf/genome_files/GRCh38/GATK_ResourceBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"] | ||
| scatter_interval_list = "${params.resource_dir}/tools/rnaseq-nf/genome_files/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.interval_list" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/GRCh38" | ||
| } | ||
| "GRCm38" { | ||
| genome_fasta = "${params.resource_dir}/genomes/Mus_musculus.GRCm38/Mm_GRCm38_gatk_sorted.fasta" | ||
| genome_index = "${params.resource_dir}/genomes/Mus_musculus.GRCm38/Mm_GRCm38_gatk_sorted.fasta.fai" | ||
| genome_dict = "${params.resource_dir}/genomes/Mus_musculus.GRCm38/Mm_GRCm38_gatk_sorted.dict" | ||
| genome_gtf = "${params.resource_dir}/genomes/Mus_musculus.GRCm38/Mus_musculus.GRCm38.70.gtf" | ||
| genome_bed = "${params.resource_dir}/genomes/Mus_musculus.GRCm38/Mus_musculus.GRCm38.70.sorted.bed12" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/Mm_GRCm38_gatk_sorted/" | ||
| } | ||
| "GRCh37_GRCm38" { | ||
| genome_fasta = "${params.resource_dir}/genomes/GRCh37_MmGrcm38/Human_GRCh37_Mm_GRCm38.fasta" | ||
| genome_gtf = "${params.resource_dir}/genomes/GRCh37_MmGrcm38/GRCh37_GRCm38.gtf" | ||
| genome_bed = "" | ||
| genome_dict = "${params.resource_dir}/genomes/GRCh37_MmGrcm38/Human_GRCh37_Mm_GRCm38.dict" | ||
| genome_index = "${params.resource_dir}/genomes/GRCh37_MmGrcm38/Human_GRCh37_Mm_GRCm38.fa.fai" | ||
| genome_known_sites = ["${params.resource_dir}/genomes/GRCh37/Annotation/1000G_phase1.indels.b37.vcf.gz", | ||
| "${params.resource_dir}/genomes/GRCh37/Annotation/dbsnp_138.b37.vcf.gz", | ||
| "${params.resource_dir}/genomes/GRCh37/Annotation/Mills_and_1000G_gold_standard.indels.b37.vcf.gz"] | ||
| scatter_interval_list = "${params.resource_dir}/genomes/GRCh37_MmGrcm38/Human_GRCh37_Mm_GRCm38.interval_list" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/GRCh37_GRCm38" | ||
| } | ||
| "CanFam3.1" { | ||
| genome_fasta = "${params.resource_dir}/genomes/CanFam3.1.103/Canis_lupus_familiaris.CanFam3.1.dna.toplevel.fa" | ||
| genome_index = "${params.resource_dir}/genomes/CanFam3.1.103/Canis_lupus_familiaris.CanFam3.1.dna.toplevel.fa.fai" | ||
| genome_dict = "${params.resource_dir}/genomes/CanFam3.1.103/Canis_lupus_familiaris.CanFam3.1.dna.toplevel.dict" | ||
| genome_gtf = "${params.resource_dir}/genomes/CanFam3.1.103/Canis_lupus_familiaris.CanFam3.1.103.gtf" | ||
| genome_bed = "" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/CanFam3.1.103" | ||
| } | ||
| "ITAG4.0" { | ||
| genome_fasta = "${params.resource_dir}/genomes/Solanum_lycopersicum.ITAG4.0/S_lycopersicum_chromosomes.4.00.fa" | ||
| genome_index = "${params.resource_dir}/genomes/Solanum_lycopersicum.ITAG4.0/S_lycopersicum_chromosomes.4.00.fa.fai" | ||
| genome_dict = "${params.resource_dir}/genomes/Solanum_lycopersicum.ITAG4.0/S_lycopersicum_chromosomes.4.00.dict" | ||
| genome_gtf = "${params.resource_dir}/genomes/Solanum_lycopersicum.ITAG4.0/ITAG4.0_gene_models.gtf" | ||
| genome_bed = "" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/Solanum_lycopersicum.ITAG4.0/" | ||
| } | ||
| "UMCU_CholrocebusSabaeus_1.1" { | ||
| genome_fasta = "${params.resource_dir}/genomes/Chlorocebus_sabaeus/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa" | ||
| genome_index = "${params.resource_dir}/genomes/Chlorocebus_sabaeus/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.fa.fai" | ||
| genome_dict = "${params.resource_dir}/genomes/Chlorocebus_sabaeus/Chlorocebus_sabaeus.ChlSab1.1.dna.toplevel.dict" | ||
| genome_gtf = "${params.resource_dir}/genomes/Chlorocebus_sabaeus/Chlorocebus_sabaeus.ChlSab1.1.103.gtf" | ||
| genome_bed = "" | ||
| star_index = "${params.resource_dir}/tools/star/2.7.3a/Chlorocebus_sabaeus" | ||
| } | ||
| "LK_LSativa_v8" { | ||
| genome_fasta = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/sequence/Lactuca_sativa_lettuce.fa" | ||
| genome_dict = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/sequence/Lactuca_sativa_lettuce.dict" | ||
| genome_index = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/sequence/Lactuca_sativa_lettuce.fa.fai" | ||
| genome_gtf = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/annotation/Lactuca_sativa_lettuce_rename.gtf" | ||
| genome_bed = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/annotation/Lactuca_sativa_lettuce_rename.sorted.bed12" | ||
| transcripts_fasta = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/sequence/transcripts/RSEM_Lsv8.transcripts.fa" | ||
| star_index = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/STAR/Lactuca_sativa_lettuce" | ||
| salmon_index = "/hpc/uu_lk/GENOMES/LGR_CoGe/Lactuca_sativa_cv_Salinas_V8/Salmon/RSEM_Lsv8.transcripts" | ||
| } | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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| includeConfig 'conf/nextflow.config' | ||
| includeConfig 'conf/process.config' | ||
| includeConfig 'conf/resources.config' | ||
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| params { | ||
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| genome = 'GRCh37' | ||
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| /*==========================ƒ | ||
| workflow steps | ||
| /*==========================*/ | ||
|
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| // Pre-alignment processing. | ||
| runTrimGalore = true | ||
| runSortMeRNA = true | ||
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| // Alignment - STAR - Sambamba markdup | ||
| runMapping = true | ||
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| // Counting - SubRead / FeatureCounts | ||
| runFeatureCounts = true | ||
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| // Salmon | ||
| runSalmon = false | ||
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| // QC | ||
| runFastQC = true | ||
| runMultiQC = true | ||
| runPostQC = true | ||
| runRSeQC_TIN = true | ||
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| // GATK (v4) | ||
| runGermlineCallingGATK = false | ||
| runGATK4_BQSR = true | ||
| /*========================== | ||
| Settings | ||
| /*==========================*/ | ||
|
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| // Standard options | ||
| gencode = false | ||
| singleEnd =false | ||
| MergeFQ = true | ||
| help= false | ||
| customQC = true | ||
|
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| // Library strandedness | ||
| stranded = true | ||
| revstranded = false | ||
| unstranded = false | ||
| } |
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