Merge pull request #181 from naobservatory/harmon_change_gz

Convert gold-standard gzipped output to raw files
naobservatory · Feb 5, 2025 · 1b37a8a · 1b37a8a
2 parents e4a5bc7 + f72138b
commit 1b37a8a
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Showing 22 changed files with 430 additions and 1 deletion.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@
     - Numerous changes to column names in viral hits TSV, mainly to improve clarity
 - Updated mislabeled processes
 - Added instructions for what to do should you run out of API requests for containers
+-  Unzipped gold standard reference output in `test-data/gold-standard-results`
 
 # v2.7.0.2
 - Updated `pipeline-version.txt`

diff --git a/test-data/gold-standard-results/bracken_reports_merged.tsv b/test-data/gold-standard-results/bracken_reports_merged.tsv
@@ -0,0 +1,3 @@
+name	taxid	rank	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads	sample	ribosomal
+Viruses	10239	D	1	0	1	1.00000	gold_standard	TRUE
+Viruses	10239	D	41	0	41	1.00000	gold_standard	FALSE
diff --git a/test-data/gold-standard-results/bracken_reports_merged.tsv.gz b/test-data/gold-standard-results/bracken_reports_merged.tsv.gz
diff --git a/test-data/gold-standard-results/kraken_reports_merged.tsv b/test-data/gold-standard-results/kraken_reports_merged.tsv
@@ -0,0 +1,78 @@
+pc_reads_total	n_reads_clade	n_reads_direct	n_minimizers_total	n_minimizers_distinct	rank	taxid	name	sample	ribosomal
+95.65	22	22	0	0	U	0	unclassified	gold_standard	TRUE
+4.35	1	0	21	4	R	1	root	gold_standard	TRUE
+4.35	1	0	21	4	D	10239	  Viruses	gold_standard	TRUE
+4.35	1	0	4	3	D1	2559587	    Riboviria	gold_standard	TRUE
+4.35	1	0	4	3	K	2732396	      Orthornavirae	gold_standard	TRUE
+4.35	1	0	4	3	P	2497569	        Negarnaviricota	gold_standard	TRUE
+4.35	1	0	4	3	P1	2497571	          Polyploviricotina	gold_standard	TRUE
+4.35	1	0	4	3	C	2497576	            Ellioviricetes	gold_standard	TRUE
+4.35	1	0	4	3	O	1980410	              Bunyavirales	gold_standard	TRUE
+4.35	1	0	4	3	F	1980416	                Peribunyaviridae	gold_standard	TRUE
+4.35	1	0	4	3	G	11572	                  Orthobunyavirus	gold_standard	TRUE
+4.35	1	0	4	3	S	3052437	                    Orthobunyavirus schmallenbergense	gold_standard	TRUE
+4.35	1	1	4	3	S1	159150	                      Shamonda virus	gold_standard	TRUE
+33.87	21	21	0	0	U	0	unclassified	gold_standard	FALSE
+66.13	41	0	1001	986	R	1	root	gold_standard	FALSE
+66.13	41	0	1001	986	D	10239	  Viruses	gold_standard	FALSE
+61.29	38	0	990	977	D1	2559587	    Riboviria	gold_standard	FALSE
+61.29	38	0	989	976	K	2732396	      Orthornavirae	gold_standard	FALSE
+32.26	20	0	747	737	P	2732406	        Kitrinoviricota	gold_standard	FALSE
+20.97	13	0	616	616	C	2732461	          Alsuviricetes	gold_standard	FALSE
+20.97	13	0	616	616	O	2732544	            Martellivirales	gold_standard	FALSE
+20.97	13	0	616	616	F	675071	              Virgaviridae	gold_standard	FALSE
+20.97	13	0	616	616	G	12234	                Tobamovirus	gold_standard	FALSE
+9.68	6	6	279	279	S	12239	                  Pepper mild mottle virus	gold_standard	FALSE
+4.84	3	3	173	173	S	12235	                  Cucumber green mottle mosaic virus	gold_standard	FALSE
+3.23	2	2	79	79	S	12241	                  Tobacco mild green mosaic virus	gold_standard	FALSE
+1.61	1	1	45	45	S	12242	                  Tobacco mosaic virus	gold_standard	FALSE
+1.61	1	1	30	30	S	12253	                  Tomato mosaic virus	gold_standard	FALSE
+11.29	7	0	131	121	C	2732463	          Tolucaviricetes	gold_standard	FALSE
+11.29	7	0	131	121	O	2732548	            Tolivirales	gold_standard	FALSE
+11.29	7	0	131	121	F	39738	              Tombusviridae	gold_standard	FALSE
+11.29	7	0	131	121	F1	2560077	                Procedovirinae	gold_standard	FALSE
+11.29	7	0	131	121	G	1911601	                  Gammacarmovirus	gold_standard	FALSE
+11.29	7	0	131	121	S	3048200	                    Gammacarmovirus melonis	gold_standard	FALSE
+11.29	7	7	131	121	S1	11987	                      Melon necrotic spot virus	gold_standard	FALSE
+27.42	17	0	240	237	P	2732408	        Pisuviricota	gold_standard	FALSE
+16.13	10	0	136	136	C	2732507	          Stelpaviricetes	gold_standard	FALSE
+16.13	10	0	136	136	O	2732551	            Stellavirales	gold_standard	FALSE
+16.13	10	0	136	136	F	39733	              Astroviridae	gold_standard	FALSE
+9.68	6	0	55	55	G	249588	                Mamastrovirus	gold_standard	FALSE
+4.84	3	3	25	25	S	1239565	                  Mamastrovirus 1	gold_standard	FALSE
+3.23	2	0	24	24	S	1239570	                  Mamastrovirus 6	gold_standard	FALSE
+3.23	2	2	24	24	S1	568715	                    Astrovirus MLB1	gold_standard	FALSE
+1.61	1	0	6	6	G1	526119	                  unclassified Mamastrovirus	gold_standard	FALSE
+1.61	1	1	5	5	S	1389204	                    Feline astrovirus 2	gold_standard	FALSE
+6.45	4	0	67	67	F1	352926	                unclassified Astroviridae	gold_standard	FALSE
+6.45	4	4	66	66	S	1868658	                  Human astrovirus	gold_standard	FALSE
+11.29	7	0	103	100	C	2732506	          Pisoniviricetes	gold_standard	FALSE
+11.29	7	0	103	100	O	464095	            Picornavirales	gold_standard	FALSE
+6.45	4	0	64	64	F	12058	              Picornaviridae	gold_standard	FALSE
+4.84	3	0	56	56	F1	2946635	                Kodimesavirinae	gold_standard	FALSE
+4.84	3	0	56	56	G	194960	                  Kobuvirus	gold_standard	FALSE
+4.84	3	0	55	55	S	72149	                    Kobuvirus aichi	gold_standard	FALSE
+4.84	3	3	55	55	S1	1313215	                      aichivirus A1	gold_standard	FALSE
+1.61	1	0	4	4	F1	2946640	                Paavivirinae	gold_standard	FALSE
+1.61	1	0	4	4	G	138954	                  Parechovirus	gold_standard	FALSE
+1.61	1	0	4	4	S	1803956	                    Parechovirus A	gold_standard	FALSE
+1.61	1	1	2	2	S1	12063	                      parechovirus A1	gold_standard	FALSE
+4.84	3	0	39	36	F	232795	              Dicistroviridae	gold_standard	FALSE
+4.84	3	0	39	36	F1	336635	                unclassified Dicistroviridae	gold_standard	FALSE
+4.84	3	3	39	36	S	1776109	                  Goose dicistrovirus	gold_standard	FALSE
+1.61	1	0	2	2	P	2732405	        Duplornaviricota	gold_standard	FALSE
+1.61	1	0	2	2	C	2732459	          Resentoviricetes	gold_standard	FALSE
+1.61	1	0	2	2	O	2732541	            Reovirales	gold_standard	FALSE
+1.61	1	0	2	2	F	2946186	              Sedoreoviridae	gold_standard	FALSE
+1.61	1	0	2	2	G	10912	                Rotavirus	gold_standard	FALSE
+1.61	1	1	2	2	S	28875	                  Rotavirus A	gold_standard	FALSE
+4.84	3	0	10	8	D1	2732004	    Varidnaviria	gold_standard	FALSE
+4.84	3	0	10	8	K	2732005	      Bamfordvirae	gold_standard	FALSE
+4.84	3	0	10	8	P	2732007	        Nucleocytoviricota	gold_standard	FALSE
+4.84	3	0	10	8	C	2732525	          Pokkesviricetes	gold_standard	FALSE
+4.84	3	0	10	8	O	2732527	            Chitovirales	gold_standard	FALSE
+4.84	3	0	10	8	F	10240	              Poxviridae	gold_standard	FALSE
+4.84	3	0	10	8	F1	10241	                Chordopoxvirinae	gold_standard	FALSE
+4.84	3	0	10	8	G	2733297	                  Oryzopoxvirus	gold_standard	FALSE
+4.84	3	0	10	8	G1	2788403	                    unclassified Oryzopoxvirus	gold_standard	FALSE
+4.84	3	3	10	8	S	67082	                      BeAn 58058 virus	gold_standard	FALSE
diff --git a/test-data/gold-standard-results/kraken_reports_merged.tsv.gz b/test-data/gold-standard-results/kraken_reports_merged.tsv.gz
diff --git a/test-data/gold-standard-results/merged_blast_filtered.tsv b/test-data/gold-standard-results/merged_blast_filtered.tsv
@@ -0,0 +1,31 @@
+qseqid	sseqid	sgi	staxid	qlen	evalue	bitscore	qcovs	length	pident	mismatch	gapopen	sstrand	qstart	qend	sstart	send	bitscore_rank_dense	bitscore_fraction
+SRR12204734.102846486	gi|1799084385|gb|MN030571.1|	1799084385	2699435	141	9.47e-30	134	100	141	83.688	23	0	minus	1	141	3990	3850	1	1.0
+SRR12204734.102846486	gi|2571040051|gb|OR130732.1|	2571040051	3071813	141	9.47e-30	134	100	141	83.688	23	0	minus	1	141	3990	3850	2	1.0
+SRR12204734.132645528	gi|2510069797|gb|ON398705.1|	2510069797	3049538	128	2.89e-59	231	100	128	99.219	1	0	minus	1	128	4697	4570	1	1.0
+SRR12204734.136705306	gi|1799084385|gb|MN030571.1|	1799084385	2699435	140	1.53e-47	193	98	137	91.971	11	0	minus	4	140	1036	900	1	1.0
+SRR12204734.136705306	gi|2571040051|gb|OR130732.1|	2571040051	3071813	140	1.53e-47	193	98	137	91.971	11	0	minus	4	140	1036	900	2	1.0
+SRR12204734.146348965	gi|1799084385|gb|MN030571.1|	1799084385	2699435	142	7.38e-31	137	71	101	92.079	3	1	minus	1	101	6359	6264	1	1.0
+SRR12204734.146348965	gi|2571040051|gb|OR130732.1|	2571040051	3071813	142	7.38e-31	137	71	101	92.079	3	1	minus	1	101	6760	6665	2	1.0
+SRR12204734.146348965	gi|1430400470|gb|MF927778.1|	1430400470	2268895	142	2.69e-20	102	72	102	85.294	11	2	minus	1	102	9379	9282	2	0.7445255474452555
+SRR12204734.158389317	gi|1799084385|gb|MN030571.1|	1799084385	2699435	140	1.95e-56	222	99	138	95.652	6	0	minus	1	138	1669	1532	1	1.0
+SRR12204734.158389317	gi|2571040051|gb|OR130732.1|	2571040051	3071813	140	1.95e-56	222	99	138	95.652	6	0	minus	1	138	1669	1532	2	1.0
+SRR12204848.140127907	gi|1799084385|gb|MN030571.1|	1799084385	2699435	143	1.58e-42	176	100	143	88.811	16	0	minus	1	143	1854	1712	1	1.0
+SRR12204848.140127907	gi|2571040051|gb|OR130732.1|	2571040051	3071813	143	1.58e-42	176	100	143	88.811	16	0	minus	1	143	1854	1712	2	1.0
+SRR12204848.15085913	gi|1799084385|gb|MN030571.1|	1799084385	2699435	142	2.04e-36	156	72	103	94.175	4	2	plus	41	142	1938	2039	1	1.0
+SRR12204848.15085913	gi|2571040051|gb|OR130732.1|	2571040051	3071813	142	2.04e-36	156	72	103	94.175	4	2	plus	41	142	1938	2039	2	1.0
+SRR12204848.28156033	gi|1799084385|gb|MN030571.1|	1799084385	2699435	136	1.90e-46	189	99	135	91.852	11	0	plus	1	135	1633	1767	1	1.0
+SRR12204848.28156033	gi|2571040051|gb|OR130732.1|	2571040051	3071813	136	1.90e-46	189	99	135	91.852	11	0	plus	1	135	1633	1767	2	1.0
+SRR12204848.31434798	gi|1799084385|gb|MN030571.1|	1799084385	2699435	147	4.47e-53	211	100	147	92.517	11	0	plus	1	147	1180	1326	1	1.0
+SRR12204848.31434798	gi|2571040051|gb|OR130732.1|	2571040051	3071813	147	4.47e-53	211	100	147	92.517	11	0	plus	1	147	1180	1326	2	1.0
+SRR12204849.140297134	gi|2510069797|gb|ON398705.1|	2510069797	3049538	148	5.71e-67	257	100	148	97.973	3	0	plus	1	148	2798	2945	1	1.0
+SRR12204849.142401718	gi|2294264610|gb|MW678777.1|	2294264610	32630	144	9.31e-60	233	100	144	95.833	6	0	minus	1	144	2225	2082	1	1.0
+SRR12204849.142401718	gi|2571040051|gb|OR130732.1|	2571040051	3071813	144	4.33e-58	228	100	144	95.139	7	0	minus	1	144	5510	5367	2	0.9785407725321889
+SRR12204849.147306033	gi|2450664545|dbj|LC723624.1|	2450664545	2973485	146	4.37e-63	244	99	144	97.222	4	0	plus	3	146	499	642	1	1.0
+SRR12204849.16071359	gi|2784409127|gb|PQ072823.1|	2784409127	32630	138	1.51e-42	176	99	139	89.928	10	3	plus	1	137	63	199	1	1.0
+SRR12204850.120094795	gi|380719094|gb|JQ281544.1|	380719094	1163660	148	1.24e-63	246	100	148	96.622	5	0	minus	1	148	646	499	1	1.0
+SRR12204850.140730292	gi|1799084385|gb|MN030571.1|	1799084385	2699435	139	1.16e-53	213	100	139	94.245	8	0	plus	1	139	2108	2246	1	1.0
+SRR12204850.140730292	gi|2571040051|gb|OR130732.1|	2571040051	3071813	139	1.16e-53	213	100	139	94.245	8	0	plus	1	139	2108	2246	2	1.0
+SRR12204850.28709236	gi|380719094|gb|JQ281544.1|	380719094	1163660	148	3.51e-49	198	95	140	92.143	11	0	plus	3	142	4290	4429	1	1.0
+SRR12204850.8190301	gi|380719094|gb|JQ281544.1|	380719094	1163660	147	2.69e-50	202	99	145	91.724	12	0	minus	1	145	5481	5337	1	1.0
+SRR12204850.89255206	gi|1799084385|gb|MN030571.1|	1799084385	2699435	148	4.51e-53	211	99	147	92.517	11	0	minus	2	148	553	407	1	1.0
+SRR12204850.89255206	gi|2571040051|gb|OR130732.1|	2571040051	3071813	148	4.51e-53	211	99	147	92.517	11	0	minus	2	148	553	407	2	1.0
diff --git a/test-data/gold-standard-results/merged_blast_filtered.tsv.gz b/test-data/gold-standard-results/merged_blast_filtered.tsv.gz
diff --git a/test-data/gold-standard-results/read_counts.tsv b/test-data/gold-standard-results/read_counts.tsv
@@ -0,0 +1,2 @@
+sample	n_reads_single	n_read_pairs
+gold_standard	330	165
diff --git a/test-data/gold-standard-results/read_counts.tsv.gz b/test-data/gold-standard-results/read_counts.tsv.gz
diff --git a/test-data/gold-standard-results/subset_qc_adapter_stats.tsv b/test-data/gold-standard-results/subset_qc_adapter_stats.tsv
@@ -0,0 +1,109 @@
+position	pc_adapters	file	adapter	stage	sample
+1	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+2	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+3	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+4	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+5	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+6	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+7	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+8	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+9	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+12	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+17	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+22	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+27	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+32	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+37	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+42	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+47	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+52	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+57	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+62	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+67	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+72	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+77	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+82	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+87	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+92	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+97	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+102	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+107	0	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+112	1.1428571428571428	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+117	4.571428571428571	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+122	5.714285714285714	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+127	5.714285714285714	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+132	8.38095238095238	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+137	10.857142857142858	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+140	12.380952380952381	gold_standard_interleaved	illumina_universal_adapter	raw	gold_standard
+1	0	gold_standard_interleaved	polya	raw	gold_standard
+2	0	gold_standard_interleaved	polya	raw	gold_standard
+3	0	gold_standard_interleaved	polya	raw	gold_standard
+4	0	gold_standard_interleaved	polya	raw	gold_standard
+5	0	gold_standard_interleaved	polya	raw	gold_standard
+6	0	gold_standard_interleaved	polya	raw	gold_standard
+7	0	gold_standard_interleaved	polya	raw	gold_standard
+8	0	gold_standard_interleaved	polya	raw	gold_standard
+9	0	gold_standard_interleaved	polya	raw	gold_standard
+12	0.38095238095238093	gold_standard_interleaved	polya	raw	gold_standard
+17	0.8571428571428571	gold_standard_interleaved	polya	raw	gold_standard
+22	1.0476190476190477	gold_standard_interleaved	polya	raw	gold_standard
+27	1.4285714285714286	gold_standard_interleaved	polya	raw	gold_standard
+32	1.8095238095238095	gold_standard_interleaved	polya	raw	gold_standard
+37	1.9047619047619047	gold_standard_interleaved	polya	raw	gold_standard
+42	2.0952380952380953	gold_standard_interleaved	polya	raw	gold_standard
+47	2.380952380952381	gold_standard_interleaved	polya	raw	gold_standard
+52	2.380952380952381	gold_standard_interleaved	polya	raw	gold_standard
+57	2.380952380952381	gold_standard_interleaved	polya	raw	gold_standard
+62	2.380952380952381	gold_standard_interleaved	polya	raw	gold_standard
+67	2.380952380952381	gold_standard_interleaved	polya	raw	gold_standard
+72	2.666666666666667	gold_standard_interleaved	polya	raw	gold_standard
+77	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+82	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+87	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+92	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+97	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+102	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+107	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+112	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+117	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+122	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+127	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+132	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+137	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+140	2.857142857142857	gold_standard_interleaved	polya	raw	gold_standard
+1	1.4285714285714286	gold_standard_interleaved	polyg	raw	gold_standard
+2	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+3	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+4	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+5	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+6	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+7	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+8	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+9	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+12	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+17	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+22	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+27	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+32	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+37	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+42	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+47	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+52	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+57	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+62	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+67	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+72	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+77	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+82	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+87	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+92	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+97	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+102	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+107	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+112	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+117	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+122	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+127	1.9047619047619047	gold_standard_interleaved	polyg	raw	gold_standard
+132	2.2857142857142856	gold_standard_interleaved	polyg	raw	gold_standard
+137	2.380952380952381	gold_standard_interleaved	polyg	raw	gold_standard
+140	2.380952380952381	gold_standard_interleaved	polyg	raw	gold_standard
diff --git a/test-data/gold-standard-results/subset_qc_adapter_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_adapter_stats.tsv.gz
diff --git a/test-data/gold-standard-results/subset_qc_basic_stats.tsv b/test-data/gold-standard-results/subset_qc_basic_stats.tsv
@@ -0,0 +1,3 @@
+percent_gc	mean_seq_len	n_reads_single	n_read_pairs	percent_duplicates	n_bases_approx	per_base_sequence_quality	per_sequence_quality_scores	per_base_sequence_content	per_sequence_gc_content	per_base_n_content	sequence_length_distribution	sequence_duplication_levels	overrepresented_sequences	adapter_content	stage	sample
+46	150.24761904761905	210	105	4.285714285714278	31500	pass	pass	fail	fail	pass	warn	pass	fail	fail	raw	gold_standard
+47	145.31764705882352	170	85	7.058823529411768	24700	pass	pass	fail	fail	pass	warn	pass	fail	pass	cleaned	gold_standard
diff --git a/test-data/gold-standard-results/subset_qc_basic_stats.tsv.gz b/test-data/gold-standard-results/subset_qc_basic_stats.tsv.gz
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample n_reads_single n_read_pairs
		gold_standard 330 165