mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
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
|
|
@ -17,14 +17,20 @@ jobs:
|
|||
env:
|
||||
NXF_ANSI_LOG: false
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
|
||||
- uses: actions/checkout@v2
|
||||
- name: Install Nextflow
|
||||
run: |
|
||||
export NXF_VER="20.07.1"
|
||||
wget -qO- get.nextflow.io | bash
|
||||
sudo mv nextflow /usr/local/bin/
|
||||
|
||||
- name: Install Nextflow
|
||||
run: |
|
||||
export NXF_VER="20.07.1"
|
||||
wget -qO- get.nextflow.io | bash
|
||||
sudo mv nextflow /usr/local/bin/
|
||||
- name: Set up Python
|
||||
uses: actions/setup-python@v2
|
||||
with:
|
||||
python-version: "3.x"
|
||||
- name: Install dependencies
|
||||
run: python -m pip install --upgrade pip pytest-workflow
|
||||
|
||||
# Test the module
|
||||
- run: nextflow run ./software/picard/collectmultiplemetrics/test/ -profile docker
|
||||
# Test the module
|
||||
- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2
|
||||
|
|
|
|||
|
|
@ -1 +0,0 @@
|
|||
../../../../../tests/data/fasta/E_coli/NC_010473.fa
|
||||
|
|
@ -1 +0,0 @@
|
|||
../../../../../tests/data/bam/test.paired_end.sorted.bam
|
||||
|
|
@ -1,21 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test {
|
||||
|
||||
def input = []
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true) ]
|
||||
|
||||
PICARD_COLLECTMULTIPLEMETRICS (
|
||||
input,
|
||||
file("${baseDir}/input/NC_010473.fa", checkIfExists: true)
|
||||
)
|
||||
}
|
||||
|
||||
workflow {
|
||||
test()
|
||||
}
|
||||
|
|
@ -1,20 +0,0 @@
|
|||
|
||||
params {
|
||||
outdir = "output/"
|
||||
publish_dir_mode = "copy"
|
||||
enable_conda = false
|
||||
}
|
||||
|
||||
profiles {
|
||||
conda {
|
||||
params.enable_conda = true
|
||||
}
|
||||
docker {
|
||||
docker.enabled = true
|
||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
||||
}
|
||||
singularity {
|
||||
singularity.enabled = true
|
||||
singularity.autoMounts = true
|
||||
}
|
||||
}
|
||||
|
|
@ -1,12 +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
|
||||
|
||||
## METRICS CLASS picard.analysis.AlignmentSummaryMetrics
|
||||
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
|
||||
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
|
||||
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
|
||||
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
|
||||
|
||||
|
||||
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
|
||||
|
||||
## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics
|
||||
READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N
|
||||
1 1 24.74 25.02 25.61 24.63 0
|
||||
1 2 25.5 23.74 25.96 24.8 0
|
||||
1 3 24.91 25.4 24.96 24.73 0
|
||||
1 4 25.44 25.36 24.59 24.61 0
|
||||
1 5 25.33 25.28 25.04 24.35 0
|
||||
1 6 24.94 25.83 25.25 23.98 0
|
||||
1 7 24.26 25.58 26.45 23.71 0
|
||||
1 8 23.87 26.45 25.17 24.51 0
|
||||
1 9 24.03 26.08 25.7 24.19 0
|
||||
1 10 24.8 24.8 25.34 25.06 0
|
||||
1 11 25.03 25.07 24.86 25.04 0
|
||||
1 12 24.37 25.97 25.25 24.41 0
|
||||
1 13 25.16 24.85 25.59 24.4 0
|
||||
1 14 24.27 25.69 25.79 24.25 0
|
||||
1 15 24.69 25.93 25.62 23.76 0
|
||||
1 16 24.86 25.94 24.97 24.23 0
|
||||
1 17 24.38 25.68 25.18 24.76 0
|
||||
1 18 24.03 25.63 25.9 24.44 0
|
||||
1 19 24.48 24.89 25.72 24.91 0
|
||||
1 20 24.06 25.07 25.75 25.12 0
|
||||
1 21 24.76 25.39 24.4 25.45 0
|
||||
1 22 25.18 25.02 24.66 25.14 0
|
||||
1 23 24.54 25.44 25.83 24.19 0
|
||||
1 24 23.7 26.35 25.59 24.36 0
|
||||
1 25 23.81 24.86 25.83 25.5 0
|
||||
1 26 24.57 25.78 25.11 24.54 0
|
||||
1 27 24 25.53 25.8 24.67 0
|
||||
1 28 24.32 25.76 25.36 24.56 0
|
||||
1 29 24.57 25.03 26.21 24.19 0
|
||||
1 30 25.44 25.05 24.7 24.81 0
|
||||
1 31 24.16 25.28 25.86 24.7 0
|
||||
1 32 24.45 25.24 25.21 25.1 0
|
||||
1 33 24.47 26.17 24.98 24.38 0
|
||||
1 34 24.95 24.47 26.38 24.2 0
|
||||
1 35 24.46 26.59 24.82 24.13 0
|
||||
1 36 24.35 25.45 25.7 24.5 0
|
||||
1 37 24.54 25.05 25.9 24.51 0
|
||||
1 38 24.82 26.59 24.4 24.19 0
|
||||
1 39 24.37 25.48 25.59 24.56 0
|
||||
1 40 24.93 25.4 25.17 24.5 0
|
||||
1 41 24.6 25.51 24.78 25.11 0
|
||||
1 42 24.33 26.16 25.04 24.47 0
|
||||
1 43 25.01 25.57 25.51 23.91 0
|
||||
1 44 24.57 25.52 25.48 24.43 0
|
||||
1 45 24.62 25.32 25.59 24.47 0
|
||||
1 46 24.53 25.4 25.15 24.92 0
|
||||
1 47 24.59 25.66 24.94 24.81 0
|
||||
1 48 23.81 25.76 25.33 25.1 0
|
||||
1 49 25.35 25.7 23.8 25.15 0
|
||||
1 50 24.53 25.21 25.47 24.79 0
|
||||
1 51 24.03 25.69 25.92 24.36 0
|
||||
1 52 23.98 25.01 25.99 25.02 0
|
||||
1 53 24.46 25.5 25.59 24.45 0
|
||||
1 54 24.41 25.73 25.45 24.41 0
|
||||
1 55 25.18 25.19 25.45 24.18 0
|
||||
1 56 24.18 25.49 25.72 24.61 0
|
||||
1 57 24.08 25.49 25.41 25.02 0
|
||||
1 58 24.1 25.35 25.38 25.17 0
|
||||
1 59 24.58 25.58 25.39 24.45 0
|
||||
1 60 24.67 25.22 25.47 24.64 0
|
||||
1 61 24.09 25.56 25.36 24.99 0
|
||||
1 62 25.2 25.47 25.68 23.65 0
|
||||
1 63 24.47 25.4 25.28 24.85 0
|
||||
1 64 24.8 25.45 25.4 24.35 0
|
||||
1 65 25.08 26.2 24.91 23.81 0
|
||||
1 66 24.89 24.74 25.37 25 0
|
||||
1 67 25.1 25.13 25.01 24.76 0
|
||||
1 68 24.73 25.3 25.13 24.84 0
|
||||
1 69 24.94 25.18 25.2 24.68 0
|
||||
1 70 24.29 25.21 25.62 24.88 0
|
||||
1 71 24.21 26.3 25.72 23.77 0
|
||||
1 72 24.39 25.61 25.34 24.66 0
|
||||
1 73 25.29 24.55 25.67 24.49 0
|
||||
1 74 25.66 25.07 24.54 24.73 0
|
||||
1 75 24.26 26.19 24.81 24.74 0
|
||||
1 76 24.04 24.89 26.43 24.64 0
|
||||
1 77 25.01 25.04 25.04 24.91 0
|
||||
1 78 24.37 26.53 25.05 24.05 0
|
||||
1 79 24.6 25.35 25.69 24.36 0
|
||||
1 80 24.9 25.32 25.33 24.45 0
|
||||
1 81 25.1 26.14 24.64 24.12 0
|
||||
1 82 23.95 25.9 25.23 24.92 0
|
||||
1 83 24.73 25.25 25.41 24.61 0
|
||||
1 84 24.81 25.43 25.68 24.08 0
|
||||
1 85 24.73 24.72 25.57 24.98 0
|
||||
1 86 24.12 25.26 25.17 25.45 0
|
||||
1 87 24.68 25.94 25.17 24.21 0
|
||||
1 88 24.77 25.11 25.88 24.24 0
|
||||
1 89 24.09 25.62 25.34 24.95 0
|
||||
1 90 24.35 25.57 24.76 25.32 0
|
||||
1 91 25.17 25.07 25.31 24.45 0
|
||||
1 92 25.65 25.04 25 24.31 0
|
||||
1 93 25.04 25.51 25.04 24.41 0
|
||||
1 94 24.85 26.17 25.11 23.87 0
|
||||
1 95 24.81 25.37 25.5 24.32 0
|
||||
1 96 24.84 25.25 25.47 24.44 0
|
||||
1 97 24.61 25.47 25.27 24.65 0
|
||||
1 98 24.86 25 25.48 24.66 0
|
||||
1 99 23.74 25.3 25.96 25 0
|
||||
1 100 23.83 26.06 25.13 24.98 0
|
||||
2 101 24.05 25.38 26.27 24.3 0
|
||||
2 102 23.62 25.98 25.49 24.91 0
|
||||
2 103 23.93 25.62 26.32 24.13 0
|
||||
2 104 24.94 25.34 25.24 24.48 0
|
||||
2 105 24.69 25.34 25.35 24.62 0
|
||||
2 106 24.69 24.97 25.08 25.26 0
|
||||
2 107 24.1 25.17 26.68 24.05 0
|
||||
2 108 24.92 25.49 24.96 24.63 0
|
||||
2 109 24.23 25.94 24.81 25.02 0
|
||||
2 110 24.38 25.12 25.59 24.91 0
|
||||
2 111 24.42 25.6 25.75 24.23 0
|
||||
2 112 25.33 25.73 24.96 23.98 0
|
||||
2 113 25.35 24.51 26.17 23.97 0
|
||||
2 114 24.12 25.34 26.17 24.37 0
|
||||
2 115 24.77 25.23 25.13 24.87 0
|
||||
2 116 25.36 25.27 25.1 24.27 0
|
||||
2 117 24.88 24.93 25.68 24.51 0
|
||||
2 118 23.79 25.75 25.19 25.27 0
|
||||
2 119 24.43 25.82 24.93 24.82 0
|
||||
2 120 24.4 25.93 24.62 25.05 0
|
||||
2 121 25.88 24.75 25.12 24.25 0
|
||||
2 122 24.27 25.8 24.92 25.01 0
|
||||
2 123 24.61 25.95 25.28 24.16 0
|
||||
2 124 24.66 25.46 25.69 24.19 0
|
||||
2 125 24.09 25.61 25.73 24.57 0
|
||||
2 126 25.11 24.62 25.34 24.93 0
|
||||
2 127 24.51 26.23 24.74 24.52 0
|
||||
2 128 25.39 25.58 24.73 24.3 0
|
||||
2 129 24.85 25.62 24.9 24.63 0
|
||||
2 130 24.43 25.89 25.15 24.53 0
|
||||
2 131 24.7 25.53 25.58 24.19 0
|
||||
2 132 24.5 26.2 25.01 24.29 0
|
||||
2 133 23.88 25.74 25.43 24.95 0
|
||||
2 134 24.9 25.2 25.18 24.72 0
|
||||
2 135 24.16 25.63 25.75 24.46 0
|
||||
2 136 23.8 25.87 25.42 24.91 0
|
||||
2 137 24.96 25.03 26.27 23.74 0
|
||||
2 138 24.53 25.69 24.99 24.79 0
|
||||
2 139 23.96 25.89 24.7 25.45 0
|
||||
2 140 24.13 24.91 25.68 25.28 0
|
||||
2 141 24.32 25.44 25.03 25.21 0
|
||||
2 142 24.23 25.86 24.69 25.22 0
|
||||
2 143 24.44 25.74 24.6 25.22 0
|
||||
2 144 25.39 24.13 25.44 25.04 0
|
||||
2 145 24.68 25.9 25.28 24.14 0
|
||||
2 146 23.85 25.25 25.61 25.29 0
|
||||
2 147 25.2 23.57 26.09 25.14 0
|
||||
2 148 25.49 25.2 25.07 24.24 0
|
||||
2 149 25.12 25.47 25.15 24.26 0
|
||||
2 150 24.73 25.26 25.44 24.57 0
|
||||
2 151 25.43 25.54 24.96 24.07 0
|
||||
2 152 25.03 25.6 24.97 24.4 0
|
||||
2 153 25.63 25.45 24.67 24.25 0
|
||||
2 154 24.32 25.73 25.33 24.62 0
|
||||
2 155 23.73 25.22 25.57 25.48 0
|
||||
2 156 23.82 25.86 26.08 24.24 0
|
||||
2 157 24.82 24.65 25.22 25.31 0
|
||||
2 158 24.96 25.77 24.82 24.45 0
|
||||
2 159 24.16 26.01 25.42 24.41 0
|
||||
2 160 24.57 25.49 25.27 24.67 0
|
||||
2 161 24.56 25.46 25.66 24.32 0
|
||||
2 162 24.85 24.93 25.01 25.21 0
|
||||
2 163 24.54 24.82 25.87 24.77 0
|
||||
2 164 24.88 25.37 25.67 24.08 0
|
||||
2 165 24.49 25.02 26.39 24.1 0
|
||||
2 166 24.03 25.21 25.87 24.89 0
|
||||
2 167 24.37 24.94 25.79 24.9 0
|
||||
2 168 24.04 25.06 25.86 25.04 0
|
||||
2 169 24.44 25.11 25.49 24.95 0.01
|
||||
2 170 24.47 25.75 25.4 24.38 0
|
||||
2 171 24.31 25.94 25.55 24.2 0
|
||||
2 172 25.19 25.19 25.29 24.33 0
|
||||
2 173 24.78 25.82 25.31 24.09 0
|
||||
2 174 24.65 25.8 25.01 24.54 0
|
||||
2 175 24.7 25.09 25.57 24.64 0
|
||||
2 176 24.75 25 24.93 25.32 0
|
||||
2 177 24.61 25.39 25.07 24.93 0
|
||||
2 178 24.64 25.38 25.92 24.06 0
|
||||
2 179 25.21 25.97 24.86 23.96 0
|
||||
2 180 23.95 26.44 25.54 24.07 0
|
||||
2 181 25.06 25.25 26.07 23.62 0
|
||||
2 182 23.91 26.04 25.25 24.8 0
|
||||
2 183 25.01 25.52 25.44 24.03 0
|
||||
2 184 25.19 25.68 24.67 24.46 0
|
||||
2 185 24.81 25.27 24.82 25.1 0
|
||||
2 186 24.31 25.78 24.9 25.01 0
|
||||
2 187 24.94 24.98 25.55 24.53 0
|
||||
2 188 25.25 25.77 25.32 23.66 0
|
||||
2 189 25.07 25.91 24.94 24.08 0
|
||||
2 190 24.64 25.42 26.18 23.76 0
|
||||
2 191 24.92 25.38 25.24 24.46 0
|
||||
2 192 24.47 25.18 25.08 25.27 0
|
||||
2 193 25.02 25.58 24.58 24.82 0
|
||||
2 194 24.05 25.41 24.94 25.6 0
|
||||
2 195 24.91 25.05 25.08 24.96 0
|
||||
2 196 24.1 25.22 25.74 24.94 0
|
||||
2 197 24.56 24.56 25.68 25.2 0
|
||||
2 198 25.34 25.16 25.36 24.14 0
|
||||
2 199 24.8 25.47 25.7 24.03 0
|
||||
2 200 23.53 26.05 26.1 24.32 0
|
||||
|
||||
|
||||
Binary file not shown.
|
|
@ -1,343 +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
|
||||
|
||||
## METRICS CLASS picard.analysis.InsertSizeMetrics
|
||||
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
|
||||
236 117 82 69 404 234.8136 94.885497 10000 FR 35 67 99 133 165 199 231 263 295 313 329
|
||||
|
||||
## HISTOGRAM java.lang.Integer
|
||||
insert_size All_Reads.fr_count
|
||||
69 36
|
||||
70 11
|
||||
71 30
|
||||
72 24
|
||||
73 34
|
||||
74 25
|
||||
75 30
|
||||
76 22
|
||||
77 26
|
||||
78 24
|
||||
79 30
|
||||
80 25
|
||||
81 33
|
||||
82 33
|
||||
83 27
|
||||
84 26
|
||||
85 36
|
||||
86 26
|
||||
87 26
|
||||
88 34
|
||||
89 24
|
||||
90 33
|
||||
91 35
|
||||
92 40
|
||||
93 37
|
||||
94 20
|
||||
95 30
|
||||
96 26
|
||||
97 33
|
||||
98 29
|
||||
99 30
|
||||
100 33
|
||||
101 27
|
||||
102 29
|
||||
103 37
|
||||
104 32
|
||||
105 26
|
||||
106 38
|
||||
107 26
|
||||
108 32
|
||||
109 26
|
||||
110 29
|
||||
111 43
|
||||
112 26
|
||||
113 20
|
||||
114 34
|
||||
115 32
|
||||
116 32
|
||||
117 52
|
||||
118 30
|
||||
119 29
|
||||
120 28
|
||||
121 35
|
||||
122 25
|
||||
123 34
|
||||
124 22
|
||||
125 20
|
||||
126 38
|
||||
127 30
|
||||
128 32
|
||||
129 31
|
||||
130 33
|
||||
131 32
|
||||
132 22
|
||||
133 35
|
||||
134 30
|
||||
135 28
|
||||
136 33
|
||||
137 28
|
||||
138 29
|
||||
139 31
|
||||
140 34
|
||||
141 37
|
||||
142 30
|
||||
143 30
|
||||
144 27
|
||||
145 24
|
||||
146 26
|
||||
147 33
|
||||
148 33
|
||||
149 28
|
||||
150 25
|
||||
151 25
|
||||
152 24
|
||||
153 24
|
||||
154 33
|
||||
155 36
|
||||
156 21
|
||||
157 26
|
||||
158 26
|
||||
159 27
|
||||
160 27
|
||||
161 34
|
||||
162 28
|
||||
163 27
|
||||
164 28
|
||||
165 25
|
||||
166 34
|
||||
167 24
|
||||
168 41
|
||||
169 26
|
||||
170 34
|
||||
171 28
|
||||
172 30
|
||||
173 28
|
||||
174 26
|
||||
175 29
|
||||
176 37
|
||||
177 35
|
||||
178 28
|
||||
179 25
|
||||
180 25
|
||||
181 36
|
||||
182 31
|
||||
183 25
|
||||
184 29
|
||||
185 32
|
||||
186 24
|
||||
187 27
|
||||
188 31
|
||||
189 34
|
||||
190 45
|
||||
191 32
|
||||
192 20
|
||||
193 41
|
||||
194 30
|
||||
195 31
|
||||
196 24
|
||||
197 36
|
||||
198 27
|
||||
199 30
|
||||
200 30
|
||||
201 26
|
||||
202 40
|
||||
203 37
|
||||
204 37
|
||||
205 28
|
||||
206 33
|
||||
207 28
|
||||
208 31
|
||||
209 37
|
||||
210 28
|
||||
211 31
|
||||
212 32
|
||||
213 33
|
||||
214 33
|
||||
215 29
|
||||
216 28
|
||||
217 33
|
||||
218 27
|
||||
219 22
|
||||
220 31
|
||||
221 38
|
||||
222 29
|
||||
223 41
|
||||
224 22
|
||||
225 28
|
||||
226 29
|
||||
227 26
|
||||
228 26
|
||||
229 33
|
||||
230 21
|
||||
231 24
|
||||
232 31
|
||||
233 33
|
||||
234 23
|
||||
235 29
|
||||
236 30
|
||||
237 31
|
||||
238 33
|
||||
239 31
|
||||
240 25
|
||||
241 29
|
||||
242 40
|
||||
243 24
|
||||
244 29
|
||||
245 39
|
||||
246 32
|
||||
247 40
|
||||
248 30
|
||||
249 29
|
||||
250 32
|
||||
251 22
|
||||
252 33
|
||||
253 33
|
||||
254 27
|
||||
255 28
|
||||
256 19
|
||||
257 39
|
||||
258 27
|
||||
259 34
|
||||
260 30
|
||||
261 36
|
||||
262 34
|
||||
263 32
|
||||
264 34
|
||||
265 19
|
||||
266 45
|
||||
267 29
|
||||
268 38
|
||||
269 28
|
||||
270 27
|
||||
271 26
|
||||
272 35
|
||||
273 31
|
||||
274 31
|
||||
275 25
|
||||
276 23
|
||||
277 35
|
||||
278 31
|
||||
279 35
|
||||
280 27
|
||||
281 35
|
||||
282 28
|
||||
283 30
|
||||
284 19
|
||||
285 30
|
||||
286 31
|
||||
287 28
|
||||
288 28
|
||||
289 42
|
||||
290 34
|
||||
291 32
|
||||
292 36
|
||||
293 33
|
||||
294 34
|
||||
295 29
|
||||
296 26
|
||||
297 19
|
||||
298 37
|
||||
299 24
|
||||
300 29
|
||||
301 25
|
||||
302 26
|
||||
303 43
|
||||
304 31
|
||||
305 30
|
||||
306 28
|
||||
307 29
|
||||
308 35
|
||||
309 35
|
||||
310 29
|
||||
311 35
|
||||
312 30
|
||||
313 48
|
||||
314 17
|
||||
315 26
|
||||
316 25
|
||||
317 28
|
||||
318 31
|
||||
319 33
|
||||
320 36
|
||||
321 30
|
||||
322 34
|
||||
323 30
|
||||
324 38
|
||||
325 34
|
||||
326 23
|
||||
327 28
|
||||
328 37
|
||||
329 26
|
||||
330 30
|
||||
331 37
|
||||
332 33
|
||||
333 28
|
||||
334 28
|
||||
335 37
|
||||
336 42
|
||||
337 30
|
||||
338 33
|
||||
339 32
|
||||
340 37
|
||||
341 26
|
||||
342 37
|
||||
343 29
|
||||
344 23
|
||||
345 35
|
||||
346 25
|
||||
347 33
|
||||
348 34
|
||||
349 37
|
||||
350 30
|
||||
351 23
|
||||
352 30
|
||||
353 30
|
||||
354 35
|
||||
355 30
|
||||
356 28
|
||||
357 26
|
||||
358 31
|
||||
359 28
|
||||
360 27
|
||||
361 32
|
||||
362 30
|
||||
363 26
|
||||
364 29
|
||||
365 40
|
||||
366 33
|
||||
367 38
|
||||
368 27
|
||||
369 34
|
||||
370 43
|
||||
371 27
|
||||
372 35
|
||||
373 27
|
||||
374 24
|
||||
375 30
|
||||
376 36
|
||||
377 24
|
||||
378 30
|
||||
379 35
|
||||
380 26
|
||||
381 32
|
||||
382 34
|
||||
383 34
|
||||
384 34
|
||||
385 21
|
||||
386 34
|
||||
387 35
|
||||
388 29
|
||||
389 25
|
||||
390 24
|
||||
391 25
|
||||
392 29
|
||||
393 32
|
||||
394 33
|
||||
395 27
|
||||
396 22
|
||||
397 36
|
||||
398 28
|
||||
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
|
||||
2 40
|
||||
3 40
|
||||
4 40
|
||||
5 40
|
||||
6 40
|
||||
7 40
|
||||
8 40
|
||||
9 40
|
||||
10 40
|
||||
11 40
|
||||
12 40
|
||||
13 40
|
||||
14 40
|
||||
15 40
|
||||
16 40
|
||||
17 40
|
||||
18 40
|
||||
19 40
|
||||
20 40
|
||||
21 40
|
||||
22 40
|
||||
23 40
|
||||
24 40
|
||||
25 40
|
||||
26 40
|
||||
27 40
|
||||
28 40
|
||||
29 40
|
||||
30 40
|
||||
31 40
|
||||
32 40
|
||||
33 40
|
||||
34 40
|
||||
35 40
|
||||
36 40
|
||||
37 40
|
||||
38 40
|
||||
39 40
|
||||
40 40
|
||||
41 40
|
||||
42 40
|
||||
43 40
|
||||
44 40
|
||||
45 40
|
||||
46 40
|
||||
47 40
|
||||
48 40
|
||||
49 40
|
||||
50 40
|
||||
51 40
|
||||
52 40
|
||||
53 40
|
||||
54 40
|
||||
55 40
|
||||
56 40
|
||||
57 40
|
||||
58 40
|
||||
59 40
|
||||
60 40
|
||||
61 40
|
||||
62 40
|
||||
63 40
|
||||
64 40
|
||||
65 40
|
||||
66 40
|
||||
67 40
|
||||
68 40
|
||||
69 40
|
||||
70 40
|
||||
71 40
|
||||
72 40
|
||||
73 40
|
||||
74 40
|
||||
75 40
|
||||
76 40
|
||||
77 40
|
||||
78 40
|
||||
79 40
|
||||
80 40
|
||||
81 40
|
||||
82 40
|
||||
83 40
|
||||
84 40
|
||||
85 40
|
||||
86 40
|
||||
87 40
|
||||
88 40
|
||||
89 40
|
||||
90 40
|
||||
91 40
|
||||
92 40
|
||||
93 40
|
||||
94 40
|
||||
95 40
|
||||
96 40
|
||||
97 40
|
||||
98 40
|
||||
99 40
|
||||
100 40
|
||||
101 40
|
||||
102 40
|
||||
103 40
|
||||
104 40
|
||||
105 40
|
||||
106 40
|
||||
107 40
|
||||
108 40
|
||||
109 40
|
||||
110 40
|
||||
111 40
|
||||
112 40
|
||||
113 40
|
||||
114 40
|
||||
115 40
|
||||
116 40
|
||||
117 40
|
||||
118 40
|
||||
119 40
|
||||
120 40
|
||||
121 40
|
||||
122 40
|
||||
123 40
|
||||
124 40
|
||||
125 40
|
||||
126 40
|
||||
127 40
|
||||
128 40
|
||||
129 40
|
||||
130 40
|
||||
131 40
|
||||
132 40
|
||||
133 40
|
||||
134 40
|
||||
135 40
|
||||
136 40
|
||||
137 40
|
||||
138 40
|
||||
139 40
|
||||
140 40
|
||||
141 40
|
||||
142 40
|
||||
143 40
|
||||
144 40
|
||||
145 40
|
||||
146 40
|
||||
147 40
|
||||
148 40
|
||||
149 40
|
||||
150 40
|
||||
151 40
|
||||
152 40
|
||||
153 40
|
||||
154 40
|
||||
155 40
|
||||
156 40
|
||||
157 40
|
||||
158 40
|
||||
159 40
|
||||
160 40
|
||||
161 40
|
||||
162 40
|
||||
163 40
|
||||
164 40
|
||||
165 40
|
||||
166 40
|
||||
167 40
|
||||
168 40
|
||||
169 40
|
||||
170 40
|
||||
171 40
|
||||
172 40
|
||||
173 40
|
||||
174 40
|
||||
175 40
|
||||
176 40
|
||||
177 40
|
||||
178 40
|
||||
179 40
|
||||
180 40
|
||||
181 40
|
||||
182 40
|
||||
183 40
|
||||
184 40
|
||||
185 40
|
||||
186 40
|
||||
187 40
|
||||
188 40
|
||||
189 40
|
||||
190 40
|
||||
191 40
|
||||
192 40
|
||||
193 40
|
||||
194 40
|
||||
195 40
|
||||
196 40
|
||||
197 40
|
||||
198 40
|
||||
199 40
|
||||
200 40
|
||||
|
||||
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