Commit 3c67f259 authored by Hanna  JULIENNE's avatar Hanna JULIENNE

add test_data

parent 3e65e282
GRP1;z_GIANT_HEIGHT z_GIANT_BMI
filename internalDataLink Consortium Outcome FullName Type Reference ReferenceLink dataLink Nsample Ncase Ncontrol Nsnp snpid a1 a2 freq pval n z OR se code imp ncas ncont altNcas altNcont Unnamed: 28
GIANT_HEIGHT_Wood_et_al_2014_publicrelease_HapMapCeuFreq.txt GIANT HEIGHT Height Anthropometry Wood et al. 2014 http://www.ncbi.nlm.nih.gov/pubmed/25282103 https://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files 253288 2550858.0 MarkerName Allele1 Allele2 Freq.Allele1.HapMapCEU p N b SE
SNP_gwas_mc_merge_nogc.tbl.uniq GIANT BMI Body Mass Index Anthropometry Locke et al. 2015 http://www.ncbi.nlm.nih.gov/pubmed/25673413 https://www.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files 339224 2554637.0 SNP A1 A2 Freq1.Hapmap p N b se
......@@ -25,7 +25,7 @@ process{
maxRetries=3
maxForks=400
queueSize=500
errorStrategy='retry'
errorStrategy='finish'
cache='deep'
......
dag {
enabled = true
file = 'dag.dot'
}
report {
enabled = true
file = 'nextflow_logs/report.html'
}
trace {
enabled = true
file = 'nextflow_logs/trace.txt'
}
singularity {
enabled = true
autoMounts = true
runOptions = '--home $HOME:/home/$USER'
}
process{
executor='local'
maxErrors=10
maxRetries=3
maxForks=400
queueSize=500
errorStrategy='retry'
cache='deep'
withName: 'Compute_MAF' {
container='docker://quay.io/biocontainers/plink_1.90b5--heea4ae3_0'
cpus=1
}
withName: 'create_WG_reference_panel' {
container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
cpus=1
}
withName: 'meta_data_GWAS' {
cpus=1
}
withName: 'Clean_GWAS' {
container='docker://quay.io/biocontainers/jass_preprocessing:2.0.1--py_0'
cpus=1
}
withName: 'Impute_GWAS' {
container="docker://quay.io/biocontainers/raiss_2.0--py_0"
cpus=1
}
withName: 'Munge_LDSC_data' {
container='docker://quay.io/biocontainers/ldsc_1.0.1--py_0'
cpus=1
}
withName: 'Generate_trait_pair' {
container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
cpus=1
}
withName: 'Correlation_LDSC_data' {
container="docker://quay.io/biocontainers/ldsc_1.0.1--py_0.sif"
cpus=1
}
withName: 'Correlation_matrices' {
container='docker://quay.io/biocontainers/jass_preprocessing_2.0.1--py_0'
cpus=1
}
withName: 'Create_inittable_LDSC' {
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
cpus=1
}
withName: 'Create_inittable' {
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
cpus=1
}
withName: 'get_pheno_group' {
cpus=1
}
withName: 'Create_project_data' {
container='docker://quay.io/biocontainers/jass_2.0--pyh5ca1d4c_0'
cpus=1
}
}
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