diff --git a/.github/workflows/software/picard_collectmultiplemetrics.yml b/.github/workflows/software/picard_collectmultiplemetrics.yml index 292d01f7..4c6576f4 100644 --- a/.github/workflows/software/picard_collectmultiplemetrics.yml +++ b/.github/workflows/software/picard_collectmultiplemetrics.yml @@ -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 diff --git a/software/picard/collectmultiplemetrics/test/input/NC_010473.fa b/software/picard/collectmultiplemetrics/test/input/NC_010473.fa deleted file mode 120000 index d2298ff8..00000000 --- a/software/picard/collectmultiplemetrics/test/input/NC_010473.fa +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/data/fasta/E_coli/NC_010473.fa \ No newline at end of file diff --git a/software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam b/software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam deleted file mode 120000 index af606d91..00000000 --- a/software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam +++ /dev/null @@ -1 +0,0 @@ -../../../../../tests/data/bam/test.paired_end.sorted.bam \ No newline at end of file diff --git a/software/picard/collectmultiplemetrics/test/main.nf b/software/picard/collectmultiplemetrics/test/main.nf deleted file mode 100755 index d52961d7..00000000 --- a/software/picard/collectmultiplemetrics/test/main.nf +++ /dev/null @@ -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() -} diff --git a/software/picard/collectmultiplemetrics/test/nextflow.config b/software/picard/collectmultiplemetrics/test/nextflow.config deleted file mode 100644 index 4149feea..00000000 --- a/software/picard/collectmultiplemetrics/test/nextflow.config +++ /dev/null @@ -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 - } -} diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics deleted file mode 100644 index 8516e5b3..00000000 --- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics +++ /dev/null @@ -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 - - diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf deleted file mode 100644 index 45075c6b..00000000 Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf and /dev/null differ diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics deleted file mode 100644 index 0a025994..00000000 --- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics +++ /dev/null @@ -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 - - diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf deleted file mode 100644 index 038922f1..00000000 Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf and /dev/null differ diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics deleted file mode 100644 index 1a19682b..00000000 --- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics +++ /dev/null @@ -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 - diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf deleted file mode 100644 index 5bea51f1..00000000 Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf and /dev/null differ diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics deleted file mode 100644 index f78e7066..00000000 --- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics +++ /dev/null @@ -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 - diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf deleted file mode 100644 index d51c4be3..00000000 Binary files a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf and /dev/null differ diff --git a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics deleted file mode 100644 index 0cba723c..00000000 --- a/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics +++ /dev/null @@ -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 - diff --git a/tests/software/picard/main.nf b/tests/software/picard/main.nf index 1835c8ba..5eae7e47 100644 --- a/tests/software/picard/main.nf +++ b/tests/software/picard/main.nf @@ -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) + ) +} diff --git a/tests/software/picard/test.yml b/tests/software/picard/test.yml index d606b7c3..77a54dd4 100644 --- a/tests/software/picard/test.yml +++ b/tests/software/picard/test.yml @@ -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