From 939f5ca7441c35c0fa2292b60661a06459709115 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Tue, 24 Nov 2020 18:48:59 -0600
Subject: [PATCH] test(picard): Refactor collectmultiplemetrics to use
 pytest-workflow

---
 .../picard_collectmultiplemetrics.yml         |  22 +-
 .../test/input/NC_010473.fa                   |   1 -
 .../test/input/test.paired_end.sorted.bam     |   1 -
 .../collectmultiplemetrics/test/main.nf       |  21 --
 .../test/nextflow.config                      |  20 -
 ...tMultipleMetrics.alignment_summary_metrics |  12 -
 ...ipleMetrics.base_distribution_by_cycle.pdf | Bin 9423 -> 0 bytes
 ...Metrics.base_distribution_by_cycle_metrics | 209 -----------
 ...tMultipleMetrics.insert_size_histogram.pdf | Bin 9282 -> 0 bytes
 ...CollectMultipleMetrics.insert_size_metrics | 343 ------------------
 ...ollectMultipleMetrics.quality_by_cycle.pdf | Bin 6167 -> 0 bytes
 ...ctMultipleMetrics.quality_by_cycle_metrics | 209 -----------
 ...ctMultipleMetrics.quality_distribution.pdf | Bin 4700 -> 0 bytes
 ...ltipleMetrics.quality_distribution_metrics |  10 -
 tests/software/picard/main.nf                 |  14 +
 tests/software/picard/test.yml                |  17 +
 16 files changed, 45 insertions(+), 834 deletions(-)
 delete mode 120000 software/picard/collectmultiplemetrics/test/input/NC_010473.fa
 delete mode 120000 software/picard/collectmultiplemetrics/test/input/test.paired_end.sorted.bam
 delete mode 100755 software/picard/collectmultiplemetrics/test/main.nf
 delete mode 100644 software/picard/collectmultiplemetrics/test/nextflow.config
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.insert_size_metrics
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
 delete mode 100644 software/picard/collectmultiplemetrics/test/output/picard/test.CollectMultipleMetrics.quality_distribution_metrics

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 45075c6bc7a7f009d27405e98254d531127a5e66..0000000000000000000000000000000000000000
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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
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
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-
-
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
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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
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
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-73	34
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-112	26
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-115	32
-116	32
-117	52
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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
deleted file mode 100644
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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
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
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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
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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
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