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Add docs and tests for markduplicates
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software/picard/markduplicates/meta.yml
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software/picard/markduplicates/meta.yml
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name: picard_markduplicates
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description: Locate and tag duplicate reads in a BAM file
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keywords:
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- markduplicates
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- pcr
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- duplicates
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- bam
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- sam
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- cram
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tools:
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- picard:
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description: |
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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
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data and formats such as SAM/BAM/CRAM and VCF.
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homepage: https://broadinstitute.github.io/picard/
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documentation: https://broadinstitute.github.io/picard/
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params:
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- outdir:
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type: string
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description: |
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The pipeline's output directory. By default, the module will
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output files into `$params.outdir/<SOFTWARE>`
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- publish_dir_mode:
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type: string
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description: |
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Value for the Nextflow `publishDir` mode parameter.
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Available: symlink, rellink, link, copy, copyNoFollow, move.
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- conda:
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type: boolean
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description: |
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Run the module with Conda using the software specified
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via the `conda` directive
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM file
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pattern: "*.{bam}"
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- options:
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type: map
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description: |
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Groovy Map containing module options for passing command-line arguments and
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output file paths.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM file with duplicate reads marked/removed
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pattern: "*.{bam}"
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- metrics:
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type: file
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description: Duplicate metrics file generated by picard
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pattern: "*.{metrics.txt}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@drpatelh"
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../../../../../tests/data/bam/test.paired_end.sorted.bam
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software/picard/markduplicates/test/main.nf
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software/picard/markduplicates/test/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_MARKDUPLICATES } from '../main.nf'
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workflow test {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
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PICARD_MARKDUPLICATES ( input, [:] )
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}
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workflow {
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test()
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}
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software/picard/markduplicates/test/nextflow.config
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software/picard/markduplicates/test/nextflow.config
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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conda = false
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}
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profiles {
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conda {
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params.conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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## htsjdk.samtools.metrics.StringHeader
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# MarkDuplicates INPUT=[test.paired_end.sorted.bam] OUTPUT=test.bam METRICS_FILE=test.MarkDuplicates.metrics.txt MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
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## htsjdk.samtools.metrics.StringHeader
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# Started on: Fri Aug 07 15:11:32 GMT 2020
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## METRICS CLASS picard.sam.DuplicationMetrics
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LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
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Unknown Library 0 10000 0 0 0 0 0 0
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## HISTOGRAM java.lang.Double
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set_size all_sets non_optical_sets
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1.0 10000 10000
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BIN
software/picard/markduplicates/test/output/picard/test.bam
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BIN
software/picard/markduplicates/test/output/picard/test.bam
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