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https://github.com/MillironX/nf-core_modules.git
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test(picard): Refactor collectmultiplemetrics to use pytest-workflow
This commit is contained in:
Edmund Miller
parent
234e85bdce
commit
939f5ca744
16 changed files with 45 additions and 834 deletions
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@ -17,7 +17,6 @@ jobs:
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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@ -26,5 +25,12 @@ jobs:
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: nextflow run ./software/picard/collectmultiplemetrics/test/ -profile docker
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- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
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@ -1 +0,0 @@
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../../../../../tests/data/fasta/E_coli/NC_010473.fa
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../../../../../tests/data/bam/test.paired_end.sorted.bam
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@ -1,21 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
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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("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
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PICARD_COLLECTMULTIPLEMETRICS (
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input,
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file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
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)
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}
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workflow {
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test()
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}
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@ -1,20 +0,0 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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}
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profiles {
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conda {
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params.enable_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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@ -1,12 +0,0 @@
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## htsjdk.samtools.metrics.StringHeader
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# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false 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 15:24:11 GMT 2020
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## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
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CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS PF_READS_IMPROPER_PAIRS PCT_PF_READS_IMPROPER_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP
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FIRST_OF_PAIR 10000 10000 1 0 10000 1 1000000 9367 936700 936700 0 0 0 0 100 10000 1 0 0 0 0.5078 0 0
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SECOND_OF_PAIR 10000 10000 1 0 10000 1 1000000 9366 936600 936600 0 0.000001 0.000001 0 100 10000 1 0 0 0 0.4922 0 0
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PAIR 20000 20000 1 0 20000 1 2000000 18733 1873300 1873300 0 0.000001 0.000001 0 100 20000 1 0 0 0 0.5 0 0
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Binary file not shown.
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@ -1,209 +0,0 @@
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## htsjdk.samtools.metrics.StringHeader
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# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false 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 15:24:11 GMT 2020
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## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics
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READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N
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1 1 24.74 25.02 25.61 24.63 0
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1 2 25.5 23.74 25.96 24.8 0
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1 3 24.91 25.4 24.96 24.73 0
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1 4 25.44 25.36 24.59 24.61 0
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1 5 25.33 25.28 25.04 24.35 0
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1 6 24.94 25.83 25.25 23.98 0
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1 7 24.26 25.58 26.45 23.71 0
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1 8 23.87 26.45 25.17 24.51 0
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1 9 24.03 26.08 25.7 24.19 0
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1 10 24.8 24.8 25.34 25.06 0
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1 11 25.03 25.07 24.86 25.04 0
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1 12 24.37 25.97 25.25 24.41 0
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1 13 25.16 24.85 25.59 24.4 0
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1 14 24.27 25.69 25.79 24.25 0
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1 15 24.69 25.93 25.62 23.76 0
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1 16 24.86 25.94 24.97 24.23 0
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1 17 24.38 25.68 25.18 24.76 0
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1 18 24.03 25.63 25.9 24.44 0
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1 19 24.48 24.89 25.72 24.91 0
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1 20 24.06 25.07 25.75 25.12 0
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1 21 24.76 25.39 24.4 25.45 0
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1 22 25.18 25.02 24.66 25.14 0
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1 23 24.54 25.44 25.83 24.19 0
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1 24 23.7 26.35 25.59 24.36 0
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1 25 23.81 24.86 25.83 25.5 0
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1 26 24.57 25.78 25.11 24.54 0
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1 27 24 25.53 25.8 24.67 0
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1 28 24.32 25.76 25.36 24.56 0
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1 29 24.57 25.03 26.21 24.19 0
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1 30 25.44 25.05 24.7 24.81 0
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1 31 24.16 25.28 25.86 24.7 0
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1 32 24.45 25.24 25.21 25.1 0
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1 33 24.47 26.17 24.98 24.38 0
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1 34 24.95 24.47 26.38 24.2 0
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1 35 24.46 26.59 24.82 24.13 0
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1 36 24.35 25.45 25.7 24.5 0
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1 37 24.54 25.05 25.9 24.51 0
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1 38 24.82 26.59 24.4 24.19 0
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1 39 24.37 25.48 25.59 24.56 0
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1 40 24.93 25.4 25.17 24.5 0
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1 41 24.6 25.51 24.78 25.11 0
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1 42 24.33 26.16 25.04 24.47 0
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1 43 25.01 25.57 25.51 23.91 0
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1 44 24.57 25.52 25.48 24.43 0
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1 45 24.62 25.32 25.59 24.47 0
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1 46 24.53 25.4 25.15 24.92 0
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1 47 24.59 25.66 24.94 24.81 0
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1 48 23.81 25.76 25.33 25.1 0
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1 49 25.35 25.7 23.8 25.15 0
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1 50 24.53 25.21 25.47 24.79 0
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1 51 24.03 25.69 25.92 24.36 0
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1 52 23.98 25.01 25.99 25.02 0
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1 53 24.46 25.5 25.59 24.45 0
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1 54 24.41 25.73 25.45 24.41 0
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1 55 25.18 25.19 25.45 24.18 0
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1 56 24.18 25.49 25.72 24.61 0
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1 57 24.08 25.49 25.41 25.02 0
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1 58 24.1 25.35 25.38 25.17 0
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1 59 24.58 25.58 25.39 24.45 0
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1 60 24.67 25.22 25.47 24.64 0
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1 61 24.09 25.56 25.36 24.99 0
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1 62 25.2 25.47 25.68 23.65 0
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1 63 24.47 25.4 25.28 24.85 0
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1 64 24.8 25.45 25.4 24.35 0
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1 65 25.08 26.2 24.91 23.81 0
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1 66 24.89 24.74 25.37 25 0
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1 67 25.1 25.13 25.01 24.76 0
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1 68 24.73 25.3 25.13 24.84 0
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1 69 24.94 25.18 25.2 24.68 0
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1 70 24.29 25.21 25.62 24.88 0
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1 71 24.21 26.3 25.72 23.77 0
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1 72 24.39 25.61 25.34 24.66 0
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1 73 25.29 24.55 25.67 24.49 0
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1 74 25.66 25.07 24.54 24.73 0
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1 75 24.26 26.19 24.81 24.74 0
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1 76 24.04 24.89 26.43 24.64 0
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1 77 25.01 25.04 25.04 24.91 0
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1 78 24.37 26.53 25.05 24.05 0
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1 79 24.6 25.35 25.69 24.36 0
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1 80 24.9 25.32 25.33 24.45 0
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1 81 25.1 26.14 24.64 24.12 0
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1 82 23.95 25.9 25.23 24.92 0
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1 83 24.73 25.25 25.41 24.61 0
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1 84 24.81 25.43 25.68 24.08 0
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1 85 24.73 24.72 25.57 24.98 0
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1 86 24.12 25.26 25.17 25.45 0
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1 87 24.68 25.94 25.17 24.21 0
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1 88 24.77 25.11 25.88 24.24 0
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1 89 24.09 25.62 25.34 24.95 0
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1 90 24.35 25.57 24.76 25.32 0
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1 91 25.17 25.07 25.31 24.45 0
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1 92 25.65 25.04 25 24.31 0
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1 93 25.04 25.51 25.04 24.41 0
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1 94 24.85 26.17 25.11 23.87 0
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1 95 24.81 25.37 25.5 24.32 0
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1 96 24.84 25.25 25.47 24.44 0
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1 97 24.61 25.47 25.27 24.65 0
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1 98 24.86 25 25.48 24.66 0
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1 99 23.74 25.3 25.96 25 0
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1 100 23.83 26.06 25.13 24.98 0
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2 101 24.05 25.38 26.27 24.3 0
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2 102 23.62 25.98 25.49 24.91 0
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2 103 23.93 25.62 26.32 24.13 0
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2 104 24.94 25.34 25.24 24.48 0
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2 105 24.69 25.34 25.35 24.62 0
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2 106 24.69 24.97 25.08 25.26 0
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2 107 24.1 25.17 26.68 24.05 0
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2 108 24.92 25.49 24.96 24.63 0
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2 109 24.23 25.94 24.81 25.02 0
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2 110 24.38 25.12 25.59 24.91 0
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2 111 24.42 25.6 25.75 24.23 0
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2 112 25.33 25.73 24.96 23.98 0
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2 113 25.35 24.51 26.17 23.97 0
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2 114 24.12 25.34 26.17 24.37 0
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2 115 24.77 25.23 25.13 24.87 0
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2 116 25.36 25.27 25.1 24.27 0
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2 117 24.88 24.93 25.68 24.51 0
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2 118 23.79 25.75 25.19 25.27 0
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2 119 24.43 25.82 24.93 24.82 0
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2 120 24.4 25.93 24.62 25.05 0
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2 121 25.88 24.75 25.12 24.25 0
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2 122 24.27 25.8 24.92 25.01 0
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2 123 24.61 25.95 25.28 24.16 0
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2 124 24.66 25.46 25.69 24.19 0
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2 125 24.09 25.61 25.73 24.57 0
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2 126 25.11 24.62 25.34 24.93 0
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2 127 24.51 26.23 24.74 24.52 0
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2 128 25.39 25.58 24.73 24.3 0
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2 129 24.85 25.62 24.9 24.63 0
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2 130 24.43 25.89 25.15 24.53 0
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2 131 24.7 25.53 25.58 24.19 0
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2 132 24.5 26.2 25.01 24.29 0
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2 133 23.88 25.74 25.43 24.95 0
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2 134 24.9 25.2 25.18 24.72 0
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2 135 24.16 25.63 25.75 24.46 0
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2 136 23.8 25.87 25.42 24.91 0
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2 137 24.96 25.03 26.27 23.74 0
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2 138 24.53 25.69 24.99 24.79 0
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2 139 23.96 25.89 24.7 25.45 0
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2 140 24.13 24.91 25.68 25.28 0
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2 141 24.32 25.44 25.03 25.21 0
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2 142 24.23 25.86 24.69 25.22 0
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2 143 24.44 25.74 24.6 25.22 0
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2 144 25.39 24.13 25.44 25.04 0
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2 145 24.68 25.9 25.28 24.14 0
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2 146 23.85 25.25 25.61 25.29 0
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2 147 25.2 23.57 26.09 25.14 0
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2 148 25.49 25.2 25.07 24.24 0
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2 149 25.12 25.47 25.15 24.26 0
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2 150 24.73 25.26 25.44 24.57 0
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2 151 25.43 25.54 24.96 24.07 0
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2 152 25.03 25.6 24.97 24.4 0
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2 153 25.63 25.45 24.67 24.25 0
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2 154 24.32 25.73 25.33 24.62 0
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2 155 23.73 25.22 25.57 25.48 0
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2 156 23.82 25.86 26.08 24.24 0
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2 157 24.82 24.65 25.22 25.31 0
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2 158 24.96 25.77 24.82 24.45 0
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2 159 24.16 26.01 25.42 24.41 0
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2 160 24.57 25.49 25.27 24.67 0
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2 161 24.56 25.46 25.66 24.32 0
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2 162 24.85 24.93 25.01 25.21 0
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2 163 24.54 24.82 25.87 24.77 0
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2 164 24.88 25.37 25.67 24.08 0
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2 165 24.49 25.02 26.39 24.1 0
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2 166 24.03 25.21 25.87 24.89 0
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2 167 24.37 24.94 25.79 24.9 0
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2 168 24.04 25.06 25.86 25.04 0
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2 169 24.44 25.11 25.49 24.95 0.01
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2 170 24.47 25.75 25.4 24.38 0
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2 171 24.31 25.94 25.55 24.2 0
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2 172 25.19 25.19 25.29 24.33 0
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2 173 24.78 25.82 25.31 24.09 0
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2 174 24.65 25.8 25.01 24.54 0
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2 175 24.7 25.09 25.57 24.64 0
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2 176 24.75 25 24.93 25.32 0
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2 177 24.61 25.39 25.07 24.93 0
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2 178 24.64 25.38 25.92 24.06 0
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2 179 25.21 25.97 24.86 23.96 0
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2 180 23.95 26.44 25.54 24.07 0
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2 181 25.06 25.25 26.07 23.62 0
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2 182 23.91 26.04 25.25 24.8 0
|
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2 183 25.01 25.52 25.44 24.03 0
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2 184 25.19 25.68 24.67 24.46 0
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2 185 24.81 25.27 24.82 25.1 0
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2 186 24.31 25.78 24.9 25.01 0
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2 187 24.94 24.98 25.55 24.53 0
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2 188 25.25 25.77 25.32 23.66 0
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2 189 25.07 25.91 24.94 24.08 0
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2 190 24.64 25.42 26.18 23.76 0
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2 191 24.92 25.38 25.24 24.46 0
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2 192 24.47 25.18 25.08 25.27 0
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2 193 25.02 25.58 24.58 24.82 0
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2 194 24.05 25.41 24.94 25.6 0
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2 195 24.91 25.05 25.08 24.96 0
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2 196 24.1 25.22 25.74 24.94 0
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2 197 24.56 24.56 25.68 25.2 0
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2 198 25.34 25.16 25.36 24.14 0
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2 199 24.8 25.47 25.7 24.03 0
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2 200 23.53 26.05 26.1 24.32 0
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Binary file not shown.
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## htsjdk.samtools.metrics.StringHeader
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# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false 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 15:24:11 GMT 2020
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## METRICS CLASS picard.analysis.InsertSizeMetrics
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MEDIAN_INSERT_SIZE MODE_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_95_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP
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236 117 82 69 404 234.8136 94.885497 10000 FR 35 67 99 133 165 199 231 263 295 313 329
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## HISTOGRAM java.lang.Integer
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insert_size All_Reads.fr_count
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69 36
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70 11
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71 30
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72 24
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|
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|
||||
404 1
|
||||
|
||||
Binary file not shown.
|
|
@ -1,209 +0,0 @@
|
|||
## htsjdk.samtools.metrics.StringHeader
|
||||
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false 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
|
||||
## htsjdk.samtools.metrics.StringHeader
|
||||
# Started on: Fri Aug 07 15:24:11 GMT 2020
|
||||
|
||||
|
||||
## HISTOGRAM java.lang.Integer
|
||||
CYCLE MEAN_QUALITY
|
||||
1 40
|
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|
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|
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|
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||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
Binary file not shown.
|
|
@ -1,10 +0,0 @@
|
|||
## htsjdk.samtools.metrics.StringHeader
|
||||
# CollectMultipleMetrics INPUT=test.paired_end.sorted.bam OUTPUT=test.CollectMultipleMetrics REFERENCE_SEQUENCE=NC_010473.fa ASSUME_SORTED=true STOP_AFTER=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution] INCLUDE_UNPAIRED=false 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
|
||||
## htsjdk.samtools.metrics.StringHeader
|
||||
# Started on: Fri Aug 07 15:24:11 GMT 2020
|
||||
|
||||
|
||||
## HISTOGRAM java.lang.Byte
|
||||
QUALITY COUNT_OF_Q
|
||||
40 1999999
|
||||
|
||||
|
|
@ -3,6 +3,7 @@
|
|||
nextflow.enable.dsl = 2
|
||||
|
||||
include { PICARD_MERGESAMFILES } from '../../../software/picard/mergesamfiles/main.nf' addParams( options: [:] )
|
||||
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../software/picard/collectmultiplemetrics/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_picard_mergesamfiles {
|
||||
|
||||
|
|
@ -13,3 +14,16 @@ workflow test_picard_mergesamfiles {
|
|||
|
||||
PICARD_MERGESAMFILES ( input )
|
||||
}
|
||||
|
||||
|
||||
workflow test_picard_collectmultiplemetrics {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
||||
|
||||
PICARD_COLLECTMULTIPLEMETRICS (
|
||||
input,
|
||||
file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
|
||||
)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -6,3 +6,20 @@
|
|||
files:
|
||||
- path: output/picard/test.bam
|
||||
md5sum: a9c8a28d1aac362df5973ba2d9923f86
|
||||
|
||||
- name: Run picard collectmultiplemetrics
|
||||
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
|
||||
tags:
|
||||
- picard
|
||||
- picard_collectmultiplemetrics
|
||||
files:
|
||||
# These can't be md5'd consistently
|
||||
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
|
||||
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
|
||||
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
|
||||
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
|
||||
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
|
||||
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
|
||||
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
|
||||
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
|
||||
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
|
||||
|
|
|
|||
Loading…
Reference in a new issue