From cb85acddf056dd12bc130c74f8b473133c2804cd Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Fri, 7 Aug 2020 16:29:37 +0100
Subject: [PATCH] Add docs and tests for collectmultiplemetrics

---
 .../picard/collectmultiplemetrics/meta.yml    |  70 ++++
 .../test/input/NC_010473.fa                   |   1 +
 .../test/input/test.paired_end.sorted.bam     |   1 +
 .../collectmultiplemetrics/test/main.nf       |  22 ++
 .../test/nextflow.config                      |  20 +
 ...tMultipleMetrics.alignment_summary_metrics |  12 +
 ...ipleMetrics.base_distribution_by_cycle.pdf | Bin 0 -> 9423 bytes
 ...Metrics.base_distribution_by_cycle_metrics | 209 +++++++++++
 ...tMultipleMetrics.insert_size_histogram.pdf | Bin 0 -> 9282 bytes
 ...CollectMultipleMetrics.insert_size_metrics | 343 ++++++++++++++++++
 ...ollectMultipleMetrics.quality_by_cycle.pdf | Bin 0 -> 6167 bytes
 ...ctMultipleMetrics.quality_by_cycle_metrics | 209 +++++++++++
 ...ctMultipleMetrics.quality_distribution.pdf | Bin 0 -> 4700 bytes
 ...ltipleMetrics.quality_distribution_metrics |  10 +
 14 files changed, 897 insertions(+)
 create mode 100644 software/picard/collectmultiplemetrics/meta.yml
 create mode 120000 software/picard/collectmultiplemetrics/test/input/NC_010473.fa
 create mode 120000 software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam
 create mode 100755 software/picard/collectmultiplemetrics/test/main.nf
 create mode 100644 software/picard/collectmultiplemetrics/test/nextflow.config
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
 create mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics

diff --git a/software/picard/collectmultiplemetrics/meta.yml b/software/picard/collectmultiplemetrics/meta.yml
new file mode 100644
index 00000000..02604089
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/meta.yml
@@ -0,0 +1,70 @@
+name: picard_collectmultiplemetrics
+description: Collect multiple metrics from a BAM file
+keywords:
+    - alignment
+    - metrics
+    - statistics
+    - insert
+    - quality
+    - bam
+tools:
+    - picard:
+        description: |
+            A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+            data and formats such as SAM/BAM/CRAM and VCF.
+        homepage: https://broadinstitute.github.io/picard/
+        documentation: https://broadinstitute.github.io/picard/
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam}"
+    - fasta:
+        type: file
+        description: Genome fasta file
+    - options:
+        type: map
+        description: |
+            Groovy Map containing module options for passing command-line arguments and
+            output file paths.
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - metrics:
+        type: file
+        description: Alignment metrics files generated by picard
+        pattern: "*_{metrics}"
+    - pdf:
+        type: file
+        description: PDF plots of metrics
+        pattern: "*.{pdf}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
diff --git a/software/picard/collectmultiplemetrics/test/input/NC_010473.fa b/software/picard/collectmultiplemetrics/test/input/NC_010473.fa
new file mode 120000
index 00000000..d2298ff8
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/input/NC_010473.fa
@@ -0,0 +1 @@
+../../../../../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
new file mode 120000
index 00000000..af606d91
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam
@@ -0,0 +1 @@
+../../../../../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
new file mode 100755
index 00000000..6aa30d4c
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../main.nf'
+
+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
new file mode 100644
index 00000000..44b62ed8
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/nextflow.config
@@ -0,0 +1,20 @@
+
+params {
+    outdir = "output/"
+    publish_dir_mode = "copy"
+    conda = false
+}
+
+profiles {
+    conda  {
+        params.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
new file mode 100644
index 00000000..8516e5b3
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
@@ -0,0 +1,12 @@
+## 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
new file mode 100644
index 0000000000000000000000000000000000000000..45075c6bc7a7f009d27405e98254d531127a5e66
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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
new file mode 100644
index 00000000..0a025994
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
@@ -0,0 +1,209 @@
+## 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
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+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
new file mode 100644
index 0000000000000000000000000000000000000000..038922f1565ebca82ac58da2da2008794089f5a0
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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
new file mode 100644
index 00000000..1a19682b
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics
@@ -0,0 +1,343 @@
+## 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
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+
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
new file mode 100644
index 0000000000000000000000000000000000000000..5bea51f134e2ef64e46e5c5de8dbb588e770fd5d
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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
new file mode 100644
index 00000000..f78e7066
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
@@ -0,0 +1,209 @@
+## 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
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+
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
new file mode 100644
index 0000000000000000000000000000000000000000..d51c4be34b36a2b8ba067faf96581609ef43183a
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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
new file mode 100644
index 00000000..0cba723c
--- /dev/null
+++ b/software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
@@ -0,0 +1,10 @@
+## 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
+