test(picard): Refactor collectmultiplemetrics to use pytest-workflow

This commit is contained in:
Edmund Miller 2020-11-24 18:48:59 -06:00
parent 234e85bdce
commit 939f5ca744
No known key found for this signature in database
GPG key ID: BD387FF7BC10AA9D
16 changed files with 45 additions and 834 deletions

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@ -17,7 +17,6 @@ jobs:
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
@ -26,5 +25,12 @@ jobs:
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
- run: pytest --tag picard_collectmultiplemetrics --symlink --wt 2

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@ -1 +0,0 @@
../../../../../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 @@
#!/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()
}

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@ -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
}
}

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@ -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

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@ -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
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1 2 25.5 23.74 25.96 24.8 0
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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
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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
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1 65 25.08 26.2 24.91 23.81 0
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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
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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
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2 112 25.33 25.73 24.96 23.98 0
2 113 25.35 24.51 26.17 23.97 0
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@ -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
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83 27
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85 36
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397 36
398 28
404 1

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@ -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
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@ -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

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@ -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)
)
}

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@ -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