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#lohhla
#2024-02-13 12:00:00
JVMLevel=
LSID=urn:lsid:default
author=GenePattern Team + ChatGPT
commandLine=Rscript wrapper.R --bamList <bamList> --hlaList <hlaList> --outputDir <outputDir> --normalBAM <normalBAM> --hlaFastaLoc <hlaFastaLoc> --copyNumLoc <copyNumLoc> --minCoverage <minCoverage> --kmerSize <kmerSize> --numMisMatch <numMisMatch> --mappingStep <mappingStep> --fishingStep <fishingStep> --plottingStep <plottingStep> --coverageStep <coverageStep> --cleanUp <cleanUp> --novoDir <novoDir> --gatkDir <gatkDir> --hlaExonLoc <hlaExonLoc> --ignoreWarnings <ignoreWarnings> --cores <cores>
cpuType=any
description=LOHHLA (Loss Of Heterozygosity in Human Leukocyte Antigen) algorithm for evaluating HLA loss in cancer samples
documentationUrl=https://github.com/mskcc/lohhla
fileFormat=txt,pdf,png
job.cpuCount=
job.docker.image=[DOCKER IMAGE HERE]
job.memory=
job.walltime=
language=any
categories=sequence analysis
name=lohhla
os=any
p1_MODE=IN
p1_TYPE=FILE
p1_default_value=
p1_description=Text file containing paths to BAM files
p1_fileFormat=txt
p1_flag=--bamList
p1_name=BAM List File
p1_numValues=1
p1_optional=
p1_prefix=
p1_prefix_when_specified=
p1_type=java.io.File
p1_value=
p2_MODE=IN
p2_TYPE=FILE
p2_default_value=
p2_description=Text file containing paths to HLA type files
p2_fileFormat=txt
p2_flag=--hlaList
p2_name=HLA List File
p2_numValues=1
p2_optional=
p2_prefix=
p2_prefix_when_specified=
p2_type=java.io.File
p2_value=
p3_MODE=IN
p3_TYPE=
p3_default_value=current working directory
p3_description=Output directory for analysis results
p3_fileFormat=
p3_flag=--outputDir
p3_name=Output Directory
p3_numValues=1
p3_optional=on
p3_prefix=
p3_prefix_when_specified=
p3_type=java.io.File
p3_value=
p4_MODE=IN
p4_TYPE=FILE
p4_default_value=FALSE
p4_description=Normal BAM file path
p4_fileFormat=bam
p4_flag=--normalBAM
p4_name=Normal BAM File
p4_numValues=1
p4_optional=on
p4_prefix=
p4_prefix_when_specified=
p4_type=java.io.File
p4_value=
p5_MODE=IN
p5_TYPE=FILE
p5_default_value=~/lohhla/data/hla_all.fasta
p5_description=Location of HLA FASTA file
p5_fileFormat=fasta
p5_flag=--hlaFastaLoc
p5_name=HLA FASTA Location
p5_numValues=1
p5_optional=on
p5_prefix=
p5_prefix_when_specified=
p5_type=java.io.File
p5_value=
p6_MODE=IN
p6_TYPE=FILE
p6_default_value=FALSE
p6_description=Location of patient purity and ploidy output
p6_fileFormat=txt
p6_flag=--copyNumLoc
p6_name=Copy Number Location
p6_numValues=1
p6_optional=on
p6_prefix=
p6_prefix_when_specified=
p6_type=java.io.File
p6_value=
p7_MODE=
p7_TYPE=
p7_default_value=30
p7_description=Minimum coverage at mismatch site
p7_fileFormat=
p7_flag=--minCoverage
p7_name=Minimum Coverage
p7_numValues=1
p7_optional=on
p7_prefix=
p7_prefix_when_specified=
p7_type=Integer
p7_value=
p8_MODE=
p8_TYPE=
p8_default_value=50
p8_description=Size of kmers to fish with
p8_fileFormat=
p8_flag=--kmerSize
p8_name=Kmer Size
p8_numValues=1
p8_optional=on
p8_prefix=
p8_prefix_when_specified=
p8_type=Integer
p8_value=
p9_MODE=
p9_TYPE=
p9_default_value=1
p9_description=Number of mismatches allowed in read to map to HLA allele
p9_fileFormat=
p9_flag=--numMisMatch
p9_name=Number of Mismatches
p9_numValues=1
p9_optional=on
p9_prefix=
p9_prefix_when_specified=
p9_type=Integer
p9_value=
p10_MODE=
p10_TYPE=
p10_default_value=TRUE
p10_description=Perform mapping to HLA alleles
p10_fileFormat=
p10_flag=--mappingStep
p10_name=Mapping Step
p10_numValues=1
p10_optional=on
p10_prefix=
p10_prefix_when_specified=
p10_type=CHOICE
p10_value=
p11_MODE=
p11_TYPE=
p11_default_value=TRUE
p11_description=Look for fished reads matching kmers
p11_fileFormat=
p11_flag=--fishingStep
p11_name=Fishing Step
p11_numValues=1
p11_optional=on
p11_prefix=
p11_prefix_when_specified=
p11_type=CHOICE
p11_value=
p12_MODE=
p12_TYPE=
p12_default_value=TRUE
p12_description=Generate plots
p12_fileFormat=
p12_flag=--plottingStep
p12_name=Plotting Step
p12_numValues=1
p12_optional=on
p12_prefix=
p12_prefix_when_specified=
p12_type=CHOICE
p12_value=
p13_MODE=
p13_TYPE=
p13_default_value=TRUE
p13_description=Analyze coverage differences
p13_fileFormat=
p13_flag=--coverageStep
p13_name=Coverage Step
p13_numValues=1
p13_optional=on
p13_prefix=
p13_prefix_when_specified=
p13_type=CHOICE
p13_value=
p14_MODE=
p14_TYPE=
p14_default_value=TRUE
p14_description=Remove temporary files
p14_fileFormat=
p14_flag=--cleanUp
p14_name=Clean Up
p14_numValues=1
p14_optional=on
p14_prefix=
p14_prefix_when_specified=
p14_type=CHOICE
p14_value=
p15_MODE=IN
p15_TYPE=
p15_default_value=
p15_description=Path to novoalign executable
p15_fileFormat=
p15_flag=--novoDir
p15_name=Novoalign Directory
p15_numValues=1
p15_optional=on
p15_prefix=
p15_prefix_when_specified=
p15_type=java.io.File
p15_value=
p16_MODE=IN
p16_TYPE=
p16_default_value=
p16_description=Path to GATK executable
p16_fileFormat=
p16_flag=--gatkDir
p16_name=GATK Directory
p16_numValues=1
p16_optional=on
p16_prefix=
p16_prefix_when_specified=
p16_type=java.io.File
p16_value=
p17_MODE=IN
p17_TYPE=FILE
p17_default_value=~/lohhla/data/hla.dat
p17_description=HLA exon boundaries for plotting
p17_fileFormat=dat
p17_flag=--hlaExonLoc
p17_name=HLA Exon Location
p17_numValues=1
p17_optional=on
p17_prefix=
p17_prefix_when_specified=
p17_type=java.io.File
p17_value=
p18_MODE=
p18_TYPE=
p18_default_value=TRUE
p18_description=Continue running with warnings
p18_fileFormat=
p18_flag=--ignoreWarnings
p18_name=Ignore Warnings
p18_numValues=1
p18_optional=on
p18_prefix=
p18_prefix_when_specified=
p18_type=CHOICE
p18_value=
p19_MODE=
p19_TYPE=
p19_default_value=1
p19_description=Number of cores to use for parallel processing
p19_fileFormat=
p19_flag=--cores
p19_name=Number of Cores
p19_numValues=1
p19_optional=on
p19_prefix=
p19_prefix_when_specified=
p19_type=Integer
p19_value=
taskType=sequence analysis