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nextflow.config
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nextflow.config
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//export NXF_WORK="./nextflow_zwc"
params {
h =null
help =null
fastq_filelist = "/datadrive/aboddapati/Sample_Fastqlist_Test.txt"
//"/research_jude/rgs01_jude/groups/wugrp/projects/NTU/common/TCGA_AML/DIVIA_Run/DIVIA_Sample_Fastqlist.txt"
//"/research/groups/cab/projects/automapper/common/wzhang42/Downsample_AML/DIVIA_Samplesheet_Fastqlist.txt"
// "/research/groups/cab/projects/automapper/common/zhongshan/Analysis2024/NTU_RNAseq_Fastqs/DIVIA_RUN/DIVIA_TALL_New2024_ZW/TALL_new2024.list"
// "/research/groups/cab/projects/automapper/common/zhongshan/Analysis2024/NTU_RNAseq_Fastqs/DIVIA_RUN/DIVIA_TALL/DIVIA_NTU_TALL_Samplelist.txt"
//"/research/groups/cab/projects/automapper/common/wzhang42/AML_27OCT2023_n658/AML_n658_Sample_Fastqlist.txt"
// "/research/groups/cab/projects/automapper/common/wzhang42/KLCO_AML_n1034/ITD_Valid/DIVIA_ITD_Complete_Test/Sample_Fastqlist.txt"
//"/research/groups/cab/projects/automapper/common/zhongshan/test/NGS_Pipelines/arc-Apr-2022/Run_DIVIA/NTU_Samplelist.txt"
//"/research/groups/cab/projects/automapper/common/wzhang42/E1910_RNA_n35/Sample_Fastqlist.txt"
// a txt file that recording the fastq file list. Each row have three columns as samplename \t Fastq block \t and Strandness. Fastq block contain R1 block and R2 block, which are separted by space. multiple LANE's fastq separated by comma.
project = "DIVIA_Run_Test" // "DIVIA_E1910_RNA_Cluster" // "DIVIA_E1910_RNA" //"NTU_BALL_Cluster_12_25_2022"
// A project atlas for the current BALL Molecular Classfication
Lineage_Type = "BALL"
// Linage Type. BALL (Default) |TALL | AML
ChrName_withChr="Y"
// Chromosome Name can be with the prefix 'chr' such as "chr1, chr2..." and without prefix 'chr' only as numbers '1,2,...'. Y(Default)| N.
Select_Trim_Galore = "N"
// Whether select Trim_Galore for trimming reads and FastQC before STAR Mapping. Y(Default) | N
Select_Fusion_Catcher ="Y"
// Whether select Fusion_Catcher for Fusion Detection. Y(Default) | N
Select_STAR_Fusion = "Y"
// Whether select STAR_Fusion for Fusion Detection. Y(Default) | N
Select_Arriba_Fusion = "Y"
// Whether select Arriba for Fusion Detection. Y(Default) | N
Select_Pindel = "Y"
// Whether select Pindel for detecting the breakpoints of large deletions, insertions, inversions, and tandem duplications. Y(Default) | N
Select_iAdmix = "Y"
// Whether select iAdmix to estimate admixture coefficients from aligned BAM. Y(Default) | N
Select_GATK = "Y"
// Whether select GATK for rna variant calling. Y(Default) | N
Select_Haplo_PerChrom ="N"
// Whether select run HaplotypeCalle parallelly Chrom by chrom, which can speed up Haplotypecaller calling. Y (Default) |N.
Select_VarDict ="Y"
// Whether select to VarDict for Variant calling. Y (Default) |N.
Select_Variant_ANNOVAR = "Y"
// Whether select ANNOVAR for Variant Annotation. Y(Default) | N
Select_RSEM = "Y"
// Whether select RSEM for rnaseq quantification. Y(Default) | N
Select_ML_Classifier_RANK = "Y"
// Whether select the RSEM' Gene EXpression data for downstream ML_Classifier RANK . Y(Default) | N
Select_ML_Classifier_tSNE = "N"
// Whether select the RSEM' Gene EXpression data for downstream ML_Classifier tSNE. Y(Default) | N
Select_ML_Classifier_RF = "N"
// Whether select the RSEM' Gene EXpression data for downstream ML_Classifier RandomForest. Y(Default) | N
Select_RNASeqCNV = "Y"
// Whether select RNASeqCNV for RNAseq CNV calling. Y(Default) | N
Select_RNAIndel = "Y"
// Whether select RNAIndel for calling coding indels from tumor RNA-Seq data and classifying them as somatic, germline, and artifactual. Y(Default) | N
AUTO_DIR="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation"
REF_DIR= "${AUTO_DIR}/REF/Homo_sapiens/NCBI"
Fusion_Catcher {
data_dir ="/hpcf/authorized_apps/rhel7_apps/fusioncatcher/1.33/fusioncatcher-1.33/data/human_v102"
// The data directory where all the annotations files from Ensembl database are placed, This directory should be pre-built using 'fusioncatcher-build'.
ThreadN = 4
// Thread Number for Fusion_Catcher
}
STAR_Mapping {
ThreadN = 2
// Thread Number for STAR Mapping
STAR_Index="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/STAR-index/2.7.9a"
//"/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/STAR-index/2.7.9a"
//"/home/wzhang42/BALL_Classifier/nf_core/Reference/star"
// The path for STAR INDEX, which can be generated by STAR run_Mode genomeGenerate
// sjdbGTFfile="/home/wzhang42/BALL_Classifier/nf_core/Reference/ensembl/Homo_sapiens.GRCh38.102.chr.gtf"
// The path for STAR sjdbGTF file
}
STAR_Fusion {
ThreadN = 4
// Thread Number for STAR_Fusion
Ref="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/CTAT/lib_May232022"
//"/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/CTAT/lib_May232022"
//"/home/wzhang42/BALL_Classifier/nf_core/Reference/starfusion/ctat_genome_lib_build_dir"
// The path for STAR_Fusion Reference, which can be generated by STAR run_Mode genomeGenerate
}
Arriba_Fusion {
fa="/research/groups/cab/projects/automapper/common/zhongshan/test/NGS_Pipelines/arc-resource/resources/genome-resources-persistent/Homo_sapiens.GRCh38_r97.all.fa"
//"/research/rgs01/project_space/cab/automapper/common/yhui/Zhongshan/test/NGS_Pipelines/arc-Apr-2022/arc-fusion-resource-bundle/resources/genome-resources-persistent/Homo_sapiens.GRCh38_r97.all.fa"
//"/home/wzhang42/BALL_Classifier/nf_core/Reference/ensembl/Homo_sapiens.GRCh38.102.all.fa"
// The path for Arriba reference
gtf="/research/groups/cab/projects/automapper/common/zhongshan/test/NGS_Pipelines/arc-resource/resources/genome-resources-persistent/Homo_sapiens.GRCh38_r97.gtf"
//"/research/rgs01/project_space/cab/automapper/common/yhui/Zhongshan/test/NGS_Pipelines/arc-Apr-2022/arc-fusion-resource-bundle/resources/genome-resources-persistent/Homo_sapiens.GRCh38_r97.gtf"
//"/home/wzhang42/BALL_Classifier/nf_core/Reference/ensembl/Homo_sapiens.GRCh38.102.gtf"
// The path for Arriba' gtf
blacklist="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Arriba_ref/blacklist_hg38_GRCh38_v2.3.0.tsv.gz"
// /research/rgs01/project_space/cab/automapper/common/yhui/Zhongshan/test/NGS_Pipelines/arc-Apr-2022/arc-fusion-resource-bundle/resources/genome-resources-persistent/arriba/blacklist_hg38_GRCh38_2018-11-04.tsv
// blacklist="/usr/local/var/lib/arriba/blacklist_hg38_GRCh38_v2.3.0.tsv.gz"
known_fusion_k="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Arriba_ref/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"
// "/home/wzhang42/BALL_Classifier/Arriba_ref/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"
// known_fusion_k="/usr/local/var/lib/arriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"
known_fusion_t="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Arriba_ref/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"
// known_fusion_t="/usr/local/var/lib/arriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz"
protein_domains="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Arriba_ref/protein_domains_hg38_GRCh38_v2.3.0.gff3"
// protein_domains="/usr/local/var/lib/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3"
}
RSEM {
ThreadN = 4
// Thread Number for RSEM
Ref="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/RSEM-index/v1.3.3/GRCh38.primary_assembly.genome"
//"/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/RSEM-index/v1.3.1/GRCh38.primary_assembly.genome"
//"/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/RSEM-index/v1.3.3/GRCh38.primary_assembly.genome"
// "/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode/r31/RSEM-index/v1.3.3/GRCh38.primary_assembly.genome"
// The path for RSEM Reference
}
ML_Classifier {
RScript_Path="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/ML_Classifier"
//"/home/wzhang42/Nextflow_DIVIA/ML_Classifier"
BALL {
RANK_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/ML_Classifier/RANK_model.rds"
//"/home/wzhang42/Nextflow_DIVIA/ML_Classifier/SJBALL1425_TPS_allSample_trainclassifier_codingGene.rds"
RF_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/ML_Classifier/RF_model.rds"
}
TALL {
RANK_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/TALL/SJTALL_937_TPS_trainclassifier_linc_codingGene_bc0_1000.rds"
//RANK_Training_RDS=" /research/groups/cab/projects/automapper/common/DIVIA/ref_data/TALL/SJTLL783_SJonly_TPS_trainclassifier_linc_codingGene_1000.rds"
RF_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/ML_Classifier/RF_model.rds"
}
AML {
RANK_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/AML/SJAML_658_TPS_trainclassifier_linc_codingGene_bc1_500.rds"
//RANK_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/AML/SJAML668_SJonly_TPS_trainclassifier_linc_codingGene_1000.rds"
RF_Training_RDS="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/ML_Classifier/RF_model.rds"
}
tSNE {
LibraryType="Stranded_total_RNA_PE100bp"
// Stranded_total_RNA_PE100bp|Stranded_total_RNA_PE125bp |Stranded_total_RNA_PE75bp |
// Stranded_total_RNA_PE75bp-TARGET |Unstranded_mRNA_PE100bp |Unstranded_mRNA_PE75bp
Metadata="${fastq_filelist}"
ReferenceMetaData="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/BALL/1452_TPM_COUNT/SJBALL1452_meta_simplified.txt"
ReferenceCountsFile="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/BALL/1452_TPM_COUNT/SJBALL1452_count.txt"
Top1kGenesFile="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/BALL/1452_TPM_COUNT/STD-BALL-top1kMadGenesGRch38v31.txt"
//stdFile="/rgs01/project_space/cab/automapper/common/DIVIA/ref_data/BALL/1452_TPM_COUNT/input.STD-BALL-1452S-tSNE-plot_GRch38v31.txt"
// id2geFile="/rgs01/project_space/cab/automapper/common/DIVIA/ref_data/BALL/etc/geneID2symbol_GRCh38_31.txt"
// codingGenesFile="/rgs01/project_space/cab/automapper/common/DIVIA/ref_data/BALL/etc/ENSGgenesGRch38v31_coding12.txt"
}
}
GATK {
Ref="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/bwa-index/0.7.17-r1188/GRCh38.primary_assembly.genome.fa"
// "${REF_DIR}/GRCh38_no_alt/bwa-index/0.7.17-r1188/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa"
KNOWN_SITE1="/research/groups/cab/projects/automapper/common/yhui/Ti-Cheng/snv/GATK_known_sites/hg38/Homo_sapiens_assembly38.known_indels.vcf.gz"
KNOWN_SITE2="/research/groups/cab/projects/automapper/common/yhui/Ti-Cheng/snv/GATK_known_sites/hg38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf"
KNOWN_SITE3="/research/groups/cab/projects/automapper/common/yhui/Ti-Cheng/snv/GATK_known_sites/hg38/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf"
}
VarDict {
CALLBED ="/research/groups/cab/projects/Control/common/scripts/VariantCalling/beta/SV/bed/ITD.hg38.bed"
REFERENCE ="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/NCBI/GRCh38_no_alt/bwa-index/0.7.17-r1188/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa"
ThreadN=4
}
ANNOVAR
{
ANNOVAR_PATH="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/Variant_ANNOVAR"
//"/hpcf/apps/annovar/install/030717"
// The path for perl script table_annovar.pl
ANNOVAR_DB="/research/groups/cab/projects/Control/common/scripts/VariantCalling/beta/REF/Homo_sapiens/Annovar/humandb"
// Database for ANNOVAR
REF_BUILD="hg38"
// Reference Build for ANNOVAR , hg38|h18|hg19
CONFIG_ANNOVAR="-F ANNOVAR_DATE -F Func.refGene -F Gene.refGene -F GeneDetail.refGene -F ExonicFunc.refGene -F AAChange.refGene -F 1000g2015aug_all -F ExAC_ALL -F ExAC_AFR -F ExAC_AMR -F ExAC_EAS -F ExAC_FIN -F ExAC_NFE -F ExAC_OTH -F ExAC_SAS -F ExAC_nontcga_ALL -F ExAC_nontcga_AFR -F ExAC_nontcga_AMR -F ExAC_nontcga_EAS -F ExAC_nontcga_FIN -F ExAC_nontcga_NFE -F ExAC_nontcga_OTH -F ExAC_nontcga_SAS -F esp6500siv2_all -F gnomAD_exome_ALL -F gnomAD_exome_AFR -F gnomAD_exome_AMR -F gnomAD_exome_ASJ -F gnomAD_exome_EAS -F gnomAD_exome_FIN -F gnomAD_exome_NFE -F gnomAD_exome_OTH -F gnomAD_exome_SAS -F gnomAD_genome_ALL -F gnomAD_genome_AFR -F gnomAD_genome_AMR -F gnomAD_genome_ASJ -F gnomAD_genome_EAS -F gnomAD_genome_FIN -F gnomAD_genome_NFE -F gnomAD_genome_OTH -F SIFT_score -F SIFT_converted_rankscore -F SIFT_pred -F Polyphen2_HDIV_score -F Polyphen2_HDIV_rankscore -F Polyphen2_HDIV_pred -F Polyphen2_HVAR_score -F Polyphen2_HVAR_rankscore -F Polyphen2_HVAR_pred -F LRT_score -F LRT_converted_rankscore -F LRT_pred -F MutationTaster_score -F MutationTaster_converted_rankscore -F MutationTaster_pred -F MutationAssessor_score -F MutationAssessor_score_rankscore -F MutationAssessor_pred -F FATHMM_score -F FATHMM_converted_rankscore -F FATHMM_pred -F PROVEAN_score -F PROVEAN_converted_rankscore -F PROVEAN_pred -F VEST3_score -F VEST3_rankscore -F MetaSVM_score -F MetaSVM_rankscore -F MetaSVM_pred -F MetaLR_score -F MetaLR_rankscore -F MetaLR_pred -F M-CAP_score -F M-CAP_rankscore -F M-CAP_pred -F REVEL_score -F REVEL_rankscore -F MutPred_score -F MutPred_rankscore -F CADD_raw -F CADD_raw_rankscore -F CADD_phred -F DANN_score -F DANN_rankscore -F fathmm-MKL_coding_score -F fathmm-MKL_coding_rankscore -F fathmm-MKL_coding_pred -F Eigen_coding_or_noncoding -F Eigen-raw -F Eigen-PC-raw -F GenoCanyon_score -F GenoCanyon_score_rankscore -F integrated_fitCons_score -F integrated_fitCons_score_rankscore -F integrated_confidence_value -F GERP++_RS -F GERP++_RS_rankscore -F phyloP100way_vertebrate -F phyloP100way_vertebrate_rankscore -F phyloP20way_mammalian -F phyloP20way_mammalian_rankscore -F phastCons100way_vertebrate -F phastCons100way_vertebrate_rankscore -F phastCons20way_mammalian -F phastCons20way_mammalian_rankscore -F SiPhy_29way_logOdds -F SiPhy_29way_logOdds_rankscore -F Interpro_domain -F GTEx_V6p_gene -F GTEx_V6p_tissue -F REVEL -F dbscSNV_ADA_SCORE -F dbscSNV_RF_SCORE -F cosmic70 -F nci60 -F CLNALLELEID -F CLNDN -F CLNDISDB -F CLNREVSTAT -F ALLELE_END -F InterVar_automated -F PVS1 -F PS1 -F PS2 -F PS3 -F PS4 -F PM1 -F PM2 -F PM3 -F PM4 -F PM5 -F PM6 -F PP1 -F PP2 -F PP3 -F PP4 -F PP5 -F BA1 -F BS1 -F BS2 -F BS3 -F BS4 -F BP1 -F BP2 -F BP3 -F BP4 -F BP5 -F BP6 -F BP7 -F dbscSNV_ADA_SCORE -F dbscSNV_RF_SCORE -F cosmic70 -F nci60 -F CLNALLELEID -F CLNDN -F CLNDISDB -F CLNREVSTAT -F CLNSIG -F ALLELE_END"
CONFIG_STANDARD="-F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER"
CONFIG_INFO="-F DP -F SOMATIC -F SS -F SSC -F GPV -F SPV"
CONFIG_FORMAT="-GF GT -GF GQ -GF DP -GF RD -GF AD -GF FREQ -GF DP4"
}
RNASeq_CNV
{
RScript_Path="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia/Module_Scripts/RNASeq_CNV"
}
RNAIndel
{
Ref_Fa="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/STAR-index/2.7.9a/GRCh38.primary_assembly.genome.fa"
// Reference required in RNAIndel, must corresponds to the reference used in STAR-Mapping.
//"/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/NCBI/GRCh38_no_alt/bwa-index/0.7.17-r1188/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa"
// "/research/rgs01/reference/public/genomes/Homo_sapiens/GRCh38_no_alt/FASTA/chromosomes/chr10.fa"
Database_model="/research/groups/cab/projects/automapper/common/DIVIA/ref_data/rnaindel/data_dir_grch38"
// Database_model="/research/rgs01/home/clusterHome/wzhang42/Misc_Database/RNAIndel_Database_Model/data_dir_grch38"
ThreadN = 4
CONFIG_STANDARD="-F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER"
CONFIG_INFO="-F predicted_class -F probabilities -F annotation -F cosmic_cnt -F maximum_population_frequency -F COMMON -F repeat -F lc -F local_lc -F gc -F local_gc -F strength -F local_strength -F dissimilarity -F indel_complexity -F indel_size -F INS -F AT_INS -F AT_DEL -F GC_INS -F GC_DEL -F ref_count -F alt_count -F BIDIRECTIONAL -F UNIQ_MAPPED -F NEAR_EXON_BOUNDARY -F EQUIVALENCE_EXISTS -F MULTIALLELIC -F INFRAME -F SPLICE -F TRUNCATING -F CONSERVED_DOMAIN -F indel_location -F NMD_INSENSITIVE -F indel_per_gene -F coding_sequence_length -F GERMLINE_DB -F RECLASSIFIED -F OUTLYING -F CALLER"
CONFIG_FORMAT="-GF AD"
}
Pindel
{
ThreadN = 8
Ref="/research/rgs01/applications/hpcf/authorized_apps/cab/Automation/REF/Homo_sapiens/Gencode_ERCC92/r31/bwa-index/0.7.17-r1188/GRCh38.primary_assembly.genome.fa"
ITD_BED="/research/groups/cab/projects/Control/common/scripts/VariantCalling/beta/SV/bed/ITD.hg38.bed"
REF_BUILD="hg38"
REF_Date="20200328"
InsertSize=450
Min_Coverage=1
Het_Cutoff=0.01
Hom_Cutoff=0.99
}
iAdmix
{
AFFILE="/research_jude/rgs01_jude/groups/cab/projects/automapper/common/DIVIA/ref_data/popuFreq/thou.omni.hg38.ref.chr.txt"
// Allele frequency file that can used in iAdMix
iAdmix_PATH="/hpcf/authorized_apps/rhel7_apps/iadmix/vendor/iAdmix"
}
containerPath="/research/groups/cab/projects/automapper/common/DIVIA/Nextflow_Divia"
///containerPath="/home/wzhang42/Nextflow_DIVIA"
//"/home/wzhang42/Nextflow_DIVIA"
// "./DIVIA_Container"
// The path for contianer
TMP_DIR="/datadrive/aboddapati/tmp" ///scratch_space/wzhang42/tmp_DIVIA_TALL // "/lustre_scratch/user_scratch/wzhang42/tmp"
// Tempoary Directory that used to store the intermediate files.
R_4_2_LIBS= "/home/wzhang42/R/tmp/x86_64-pc-linux-gnu-library/rhel8_4.2" //"/home/wzhang42/R/tmp/x86_64-pc-linux-gnu-library/4.2"
R_4_1_LIBS= "/home/wzhang42/R/tmp/x86_64-pc-linux-gnu-library/rhel8_4.1" //"/home/wzhang42/R/tmp/x86_64-pc-linux-gnu-library/4.1"
outdir= "./"
//"/research/dept/cab/common/Wenchao_share" // "./"
//"/research/groups/cab/projects/automapper/common/wzhang42/E1910_RNA" //./DIVIA_Result"
// Output dir for storing the intermediate publishedDir
}
'export TMPDIR=/datadrive/aboddapati/tmp'
'rm -rf $TMPDIR'
profiles {
local {
process.executor = 'local'
process {
withName: Zcat_MergeFastq {
memory = '8GB'
}
}
process {
withName: Trim_Galore {
module = ['trimgalore/0.6.6', 'cutadapt/4.4']
// module = ['trimgalore/0.6.6', 'fastqc/0.11.8', 'python/3.5.2', 'cutadapt/4.4']
memory = '8GB'
}
}
process {
withName: Trim_Galore_Adaptor_STARMapping {
memory = '2GB'
}
}
process {
withName: Fusion_Catcher {
module = 'fusioncatcher/1.33'
cpus= "${params.Fusion_Catcher.ThreadN}"
memory = '64GB'
}
}
process {
withName: STAR_Mapping {
module = 'star/2.7.9a'
// module = 'star/2.7.9a'
// module = 'star/2.7.10a'
// module = 'star/2.7.0f'
cpus= "${params.STAR_Mapping.ThreadN}"
memory = '32GB'
}
}
process {
withName: STARMapping_Adaptor_STAR_Fusion {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_Arriba_Fusion {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_RNAseq_RSEM {
memory = '4GB'
}
}
process {
withName: STARMapping_MarkDuplicate {
module = ['samtools/1.17', 'gatk/4.1.8.0']
memory = '64GB'
}
}
process {
withName: STARMapping_Adaptor_RNAvar_GATK {
// module = 'samtools/1.17'
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_Pindel {
module = 'samtools/1.17'
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_iAdmix {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_RNAIndel {
memory = '2GB'
}
}
process {
withName: STAR_Fusion {
module = 'star-fusion/1.6.0'
memory = '32GB'
}
}
process {
withName: Arriba_Fusion {
module = 'arriba/2.4.0'
memory = '80GB'
}
}
process {
withName: RNAseq_RSEM {
module = 'rsem/1.3.1'
memory = '80GB'
}
}
process {
withName: Get_ExpectedCount_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: Get_ModifiedCount_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: Get_TPM_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: Get_FPKM_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: ML_Classifier_RANK {
module = 'R/4.2.0-rhel8'
memory = '16GB'
}
}
process {
withName: ML_Classifier_RF {
module = 'R/4.2.0-rhel8'
memory = '32GB'
}
}
process {
withName: ML_Classifier_tSNE {
module = 'R/4.2.0-rhel8'
memory = '16GB'
}
}
/*
process {
withName: RNAvar_GATK {
module = 'gatk/4.1.8.0'
memory = '80GB'
}
}
*/
process {
withName: GATK_SplitNCigarReads {
module = 'gatk/4.1.8.0'
memory = '64GB'
}
}
process {
withName: GATK_BaseRecalibrator {
module = 'gatk/4.1.8.0'
memory = '32GB'
}
}
process {
withName: GATK_ApplyBQSR {
module = 'gatk/4.1.8.0'
memory = '32GB'
}
}
process {
withName: VarDict {
module = ['vardict/1.8.3', 'tabix/0.2.6'] // must not include 'R/4.1.2-rhel8'
memory = '32GB'
}
}
process {
withName: GATK_HaplotypeCaller {
module = 'gatk/4.1.8.0'
memory = '64GB'
}
}
process {
withName: GATK_HaplotypeCaller_perChrom {
module = 'gatk/4.1.8.0'
memory = '16GB'
}
}
process {
withName: MergeVCF {
module = 'gatk/4.1.8.0'
memory = '16GB'
}
}
process {
withName: GATK_VariantFiltration {
module = 'gatk/4.1.8.0'
memory = '32GB'
}
}
process {
withName: Variant_ANNOVAR {
module = ['perl/5.28.1', 'tabix/0.2.6', 'gatk/4.1.8.0']
memory = '32GB'
}
}
process {
withName: RNASeqCNV {
module = 'R/4.1.0'
memory = '32GB'
}
}
process {
withName: RNAIndel {
module = ['rnaindel/3.3.5', 'tabix/0.2.6', 'gatk/4.1.8.0'] // 'python/3.11.0'
memory = '32GB'
cpus= "${params.RNAIndel.ThreadN}"
}
}
process {
withName: Pindel {
module = 'pindel/0.2.4'
memory = '32GB'
cpus= "${params.Pindel.ThreadN}"
}
}
process {
withName: Pindel2VCF {
module = ['pindel/0.2.4', 'tabix/0.2.6', 'bcftools/1.14' ]
memory = '32GB'
}
}
process {
withName: iAdmix {
module = 'iadmix/c188a70-rhel7'
memory = '32GB'
}
}
}
cluster {
process.executor = 'lsf'
executor.queueSize = 500
process.queue = 'rhel8_heavy_io' //'rhel8_standard' // 'priority'
process.scratch=true
process.scratch='/scratch_space/wzhang42/tmp'
process.clusterOptions = '-P Test'
executor.jobName = { "$task.name - $task.hash" }
process {
withName: Zcat_MergeFastq {
memory = '8GB'
}
}
process {
withName: Trim_Galore {
module = ['trimgalore/0.6.6', 'cutadapt/4.4']
// module = ['trimgalore/0.6.6', 'fastqc/0.11.8', 'python/3.5.2', 'cutadapt/4.4']
memory = '8GB'
}
}
process {
withName: Trim_Galore_Adaptor_STARMapping {
memory = '2GB'
}
}
process {
withName: Fusion_Catcher {
module = 'fusioncatcher/1.33'
cpus= "${params.Fusion_Catcher.ThreadN}"
memory = '64GB'
}
}
process {
withName: STAR_Mapping {
module = 'star/2.7.9a'
// module = 'star/2.7.9a'
// module = 'star/2.7.10a'
// module = 'star/2.7.0f'
cpus= "${params.STAR_Mapping.ThreadN}"
memory = '32GB'
}
}
process {
withName: STARMapping_Adaptor_STAR_Fusion {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_Arriba_Fusion {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_RNAseq_RSEM {
memory = '4GB'
}
}
process {
withName: STARMapping_MarkDuplicate {
module = ['samtools/1.17', 'gatk/4.1.8.0']
memory = '64GB'
}
}
process {
withName: STARMapping_Adaptor_RNAvar_GATK {
// module = 'samtools/1.17'
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_Pindel {
module = 'samtools/1.17'
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_iAdmix {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_RNAIndel {
memory = '2GB'
}
}
process {
withName: STAR_Fusion {
module = 'star-fusion/1.6.0'
// module = ['star-fusion/1.6.0', 'gcc/8.3.0', 'perl/5.28.1']
// 'star-fusion/1.2.0'
cpus = "${params.STAR_Fusion.ThreadN}"
memory = '32GB'
}
}
process {
withName: Arriba_Fusion {
module = 'arriba/2.4.0'
memory = '100GB'
}
}
process {
withName: RNAseq_RSEM {
module = 'rsem/1.3.1'
memory = '100GB'
}
}
process {
withName: Get_ExpectedCount_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: Get_ModifiedCount_Matrix {
module = 'rsem/1.3.1'
memory = '32GB'
}
}
process {
withName: Get_TPM_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: Get_FPKM_Matrix {
module = 'rsem/1.3.1'
memory = '8GB'
}
}
process {
withName: ML_Classifier_RANK {
module = 'R/4.2.0-rhel8' //'R/4.2.0'
memory = '16GB'
}
}
process {
withName: ML_Classifier_RF {
module = 'R/4.2.0-rhel8' //'R/4.2.0'
memory = '32GB'
}
}
process {
withName: ML_Classifier_tSNE {
module = 'R/4.2.0-rhel8' //'R/4.2.0'
memory = '16GB'
}
}
process {
withName: GATK_SplitNCigarReads {
module = 'gatk/4.1.8.0'
memory = '64GB'
}
}
process {
withName: GATK_BaseRecalibrator {
module = 'gatk/4.1.8.0'
memory = '64GB'
}
}
process {
withName: GATK_ApplyBQSR {
module = 'gatk/4.1.8.0'
memory = '64GB'
}
}
process {
withName: VarDict {
module = ['vardict/1.8.3', 'tabix/0.2.6'] // must not include 'R/4.1.2-rhel8', vardict have contianed it already
memory = '64GB'
}
}
process {
withName: GATK_HaplotypeCaller {
module = 'gatk/4.1.8.0'
memory = '64GB'
}
}
process {
withName: GATK_HaplotypeCaller_perChrom {
module = 'gatk/4.1.8.0'
memory = '16GB'
}
}
process {
withName: MergeVCF {
module = 'gatk/4.1.8.0'
memory = '16GB'
}
}
process {
withName: GATK_VariantFiltration {
module = 'gatk/4.1.8.0'
memory = '32GB'
}
}
process {
withName: Variant_ANNOVAR {
module = ['perl/5.28.1', 'tabix/0.2.6', 'gatk/4.1.8.0']
memory = '32GB'
}
}
process {
withName: RNASeqCNV {
module = 'R/4.1.0-rhel8' //'R/4.1.0'
memory = '32GB'
//env.R_LIBS="~/R/tmp/x86_64-pc-linux-gnu-library/4.1"
}
}
process {
withName: RNAIndel {
module = ['rnaindel/3.3.5', 'tabix/0.2.6', 'gatk/4.1.8.0'] // 'python/3.11.0'
memory = '64GB'
cpus= "${params.RNAIndel.ThreadN}"
}
}
process {
withName: Pindel {
module = 'pindel/0.2.4'
memory = '32GB'
cpus= "${params.Pindel.ThreadN}"
}
}
process {
withName: Pindel2VCF {
module = ['pindel/0.2.4', 'tabix/0.2.6', 'bcftools/1.14' ]
memory = '32GB'
}
}
process {
withName: iAdmix {
module = 'iadmix/c188a70-rhel7'
memory = '32GB'
// iAdmix_PATH="/hpcf/authorized_apps/rhel7_apps/iadmix/vendor/iAdmix"
// can be got by "1.) module load iadmix/c188a70-rhel7, 2.) which ANCESTRY|sed -e 's/\/ANCESTRY//g'"
}
}
}
singularity {
process.executor = 'local'
process.scratch=true
process.clusterOptions = '-P Test'
executor.jobName = { "$task.name - $task.hash" }
singularity.enabled = true
singularity.autoMounts = true
//containerOptions = "--env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/RSEM:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
process {
withName: Zcat_MergeFastq {
memory = '8GB'
}
}
process {
withName: Trim_Galore {
memory = '8GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: Trim_Galore_Adaptor_STARMapping {
memory = '2GB'
}
}
process {
withName: STAR_Mapping {
memory = '64GB'
container= "file:///${params.containerPath}/DIVIA.sif"
//container= "file:///${params.containerPath}/docker.io-trinityctat-starfusion-1.10.1.img"
}
}
process {
withName: STARMapping_Adaptor_STAR_Fusion {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_Arriba_Fusion {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_RNAseq_RSEM {
memory = '4GB'
}
}
process {
withName: STARMapping_Adaptor_RNAvar_GATK {
memory = '4GB'
}
}
process {
withName: STAR_Fusion {
memory = '64GB'
container= "file:///${params.containerPath}/DIVIA.sif"
//container= "file:///${params.containerPath}/docker.io-trinityctat-starfusion-1.10.1.img"
//containerOptions = "--cleanenv --env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion-v1.6.0/ctat-genome-lib-builder:/usr/local/STAR-Fusion-v1.6.0:/usr/local/RSEM:$PATH --env LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib:$LD_LIBRARY_PATH"
//containerOptions = "--env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/RSEM:$PATH"
//env.SINGULARITYENV_APPEND_PATH="/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/RSEM"
}
}
process {
withName: Arriba_Fusion {
memory = '64GB'
container= "file:///${params.containerPath}/DIVIA.sif"
//container= "file:///${params.containerPath}/depot.galaxyproject.org-singularity-arriba-2.1.0--h3198e80_1.img"
//container= "file:///${params.containerPath}/depot.galaxyproject.org-singularity-arriba-2.3.0--haa8aa89_0.img"
//env.SINGULARITYENV_APPEND_PATH="/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/RSEM"
//containerOptions = "--env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion-v1.6.0/ctat-genome-lib-builder:/usr/local/STAR-Fusion-v1.6.0:/usr/local/RSEM:$PATH"
//containerOptions = "--env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/RSEM:$PATH"
}
}
process {
withName: RNAseq_RSEM {
memory = '80GB'
container= "file:///${params.containerPath}/DIVIA.sif"
//containerOptions = "--env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion-v1.6.0/ctat-genome-lib-builder:/usr/local/STAR-Fusion-v1.6.0:/usr/local/RSEM:$PATH"
//containerOptions = "--env PATH=/usr/local/arriba_v2.3.0:/usr/local/STAR-Fusion/ctat-genome-lib-builder:/usr/local/STAR-Fusion:/usr/local/RSEM:$PATH"
}
}
process {
withName: Get_ExpectedCount_Matrix {
memory = '8GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: Get_ModifiedCount_Matrix {
memory = '8GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: Get_TPM_Matrix {
memory = '8GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: Get_FPKM_Matrix {
memory = '8GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: ML_Classifier_RANK {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
containerOptions="--app Rscript"
// containerOptions = "--env R_LIBS=/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library"
}
}
process {
withName: ML_Classifier_RF {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
containerOptions="--app Rscript"
//containerOptions = "--env R_LIBS=/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library"
}
}
process {
withName: ML_Classifier_tSNE {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
containerOptions="--app Rscript"
//containerOptions = "--env R_LIBS=/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library"
}
}
process {
withName: GATK_SplitNCigarReads {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: GATK_BaseRecalibrator {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: GATK_ApplyBQSR {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: GATK_HaplotypeCaller {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: GATK_VariantFiltration {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"
}
}
process {
withName: Variant_ANNOVAR {
memory = '32GB'
container= "file:///${params.containerPath}/DIVIA.sif"