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Release/12.0.1 #2054

Merged
merged 14 commits into from
Oct 9, 2023
Merged

Release/12.0.1 #2054

merged 14 commits into from
Oct 9, 2023

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jemten
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@jemten jemten commented Oct 5, 2023

This PR adds | fixes:

How to test:

  • Automatic and continuous test suite

Expected outcome:

  • Installation, unit and integration test suite pass

Review:

  • Code review
  • Tests pass

This version is a:

  • MAJOR - when you make incompatible API changes. If applicable record manual test results in PR header
  • MINOR - when you add functionality in a backwards compatible manner. If applicable record manual test results in PR header
  • PATCH - when you make backwards compatible bug fixes or documentation/instructions

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@henrikstranneheim henrikstranneheim left a comment

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Well done 👍

@jemten
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jemten commented Oct 9, 2023

Tested on justhusky without error.

#jobid	jobname	account	partition	alloccpus	TotalCPU	elapsed	start	end	state	exitcode
5257926	fastqc_ar_earlycasualcaiman	developme+	core	2	01:20:51	00:40:58	2023-10-05T15:40:09	2023-10-05T16:21:07	COMPLETED	0:0
5257927	fastqc_ar_hugelymodelbat	developme+	core	2	01:20:42	00:40:57	2023-10-05T15:40:09	2023-10-05T16:21:06	COMPLETED	0:0
5257928	fastqc_ar_slowlycivilbuck	developme+	core	2	01:23:53	00:48:33	2023-10-05T15:40:09	2023-10-05T16:28:42	COMPLETED	0:0
5257929	bwa_mem2_earlycasualcaiman	developme+	core	36	1-18:44:43	02:01:28	2023-10-05T15:45:58	2023-10-05T17:47:26	COMPLETED	0:0
5257930	bwa_mem2_hugelymodelbat	developme+	core	36	1-21:51:20	02:06:17	2023-10-05T15:49:22	2023-10-05T17:55:39	COMPLETED	0:0
5257931	bwa_mem2_slowlycivilbuck	developme+	core	36	1-12:26:04	01:52:30	2023-10-05T15:53:07	2023-10-05T17:45:37	COMPLETED	0:0
5257932	samtools_merge_earlycasualcaiman	developme+	core	13	01:04:07	00:05:47	2023-10-05T17:54:51	2023-10-05T18:00:38	COMPLETED	0:0
5257933	samtools_merge_hugelymodelbat	developme+	core	13	01:28:22	00:07:50	2023-10-05T17:56:48	2023-10-05T18:04:38	COMPLETED	0:0
5257934	samtools_merge_slowlycivilbuck	developme+	core	13	01:04:28	00:06:15	2023-10-05T17:46:24	2023-10-05T17:52:39	COMPLETED	0:0
5257935	markduplicates_earlycasualcaiman	developme+	core	32	10:08:08	00:39:13	2023-10-05T19:58:24	2023-10-05T20:37:37	COMPLETED	0:0
5257936	markduplicates_hugelymodelbat	developme+	core	32	10:39:30	00:41:36	2023-10-05T19:58:35	2023-10-05T20:40:11	COMPLETED	0:0
5257937	markduplicates_slowlycivilbuck	developme+	core	32	10:26:13	00:42:46	2023-10-05T20:00:56	2023-10-05T20:43:42	COMPLETED	0:0
5257938	chanjo_sexcheck_earlycasualcaiman	developme+	core	1	01:14.005	00:01:19	2023-10-06T02:08:38	2023-10-06T02:09:57	COMPLETED	0:0
5257939	chanjo_sexcheck_hugelymodelbat	developme+	core	1	01:13.312	00:01:18	2023-10-06T02:08:38	2023-10-06T02:09:56	COMPLETED	0:0
5257940	chanjo_sexcheck_slowlycivilbuck	developme+	core	1	01:09.884	00:01:16	2023-10-06T02:08:38	2023-10-06T02:09:54	COMPLETED	0:0
5257941	samtools_subsample_mt_earlycasualcaiman	developme+	core	1	00:17.468	00:00:21	2023-10-06T02:08:38	2023-10-06T02:08:59	COMPLETED	0:0
5257942	samtools_subsample_mt_hugelymodelbat	developme+	core	1	00:15.256	00:00:19	2023-10-06T02:08:38	2023-10-06T02:08:57	COMPLETED	0:0
5257943	samtools_subsample_mt_slowlycivilbuck	developme+	core	1	00:15.182	00:00:19	2023-10-06T02:08:38	2023-10-06T02:08:57	COMPLETED	0:0
5257944	tiddit_coverage_earlycasualcaiman	developme+	core	1	28:57.761	00:31:38	2023-10-06T02:08:38	2023-10-06T02:40:16	COMPLETED	0:0
5257945	tiddit_coverage_hugelymodelbat	developme+	core	1	29:00.572	00:31:40	2023-10-06T02:08:38	2023-10-06T02:40:18	COMPLETED	0:0
5257946	tiddit_coverage_slowlycivilbuck	developme+	core	1	17:10.187	00:19:49	2023-10-06T02:08:38	2023-10-06T02:28:27	COMPLETED	0:0
5257947	chromograph_cov_earlycasualcaiman	developme+	core	1	00:21.066	00:00:22	2023-10-06T02:40:56	2023-10-06T02:41:18	COMPLETED	0:0
5257948	chromograph_cov_hugelymodelbat	developme+	core	1	00:21.715	00:00:23	2023-10-06T02:40:56	2023-10-06T02:41:19	COMPLETED	0:0
5257949	chromograph_cov_slowlycivilbuck	developme+	core	1	00:22.109	00:00:25	2023-10-06T02:29:51	2023-10-06T02:30:16	COMPLETED	0:0
5257950	mitodel_earlycasualcaiman	developme+	core	1	00:07.476	00:00:12	2023-10-06T02:08:38	2023-10-06T02:08:50	COMPLETED	0:0
5257951	mitodel_hugelymodelbat	developme+	core	1	00:05.272	00:00:10	2023-10-06T02:08:38	2023-10-06T02:08:48	COMPLETED	0:0
5257952	mitodel_slowlycivilbuck	developme+	core	1	00:05.012	00:00:10	2023-10-06T02:08:38	2023-10-06T02:08:48	COMPLETED	0:0
5257953	sambamba_depth_earlycasualcaiman	developme+	core	2	05:12.029	00:07:53	2023-10-06T02:12:59	2023-10-06T02:20:52	COMPLETED	0:0
5257954	sambamba_depth_hugelymodelbat	developme+	core	2	05:10.427	00:08:04	2023-10-06T02:12:59	2023-10-06T02:21:03	COMPLETED	0:0
5257955	sambamba_depth_slowlycivilbuck	developme+	core	2	06:17.483	00:06:54	2023-10-06T03:17:41	2023-10-06T03:24:35	COMPLETED	0:0
5257956	smncopynumbercaller_justhusky	developme+	core	4	00:23.104	00:01:31	2023-10-06T02:13:47	2023-10-06T02:15:18	COMPLETED	0:0
5257957	picardtools_collectmultiplemetrics_earlycasualcai+	developme+	core	2	01:15:35	01:16:29	2023-10-06T03:17:41	2023-10-06T04:34:10	COMPLETED	0:0
5257958	picardtools_collectmultiplemetrics_hugelymodelbat	developme+	core	2	01:18:35	01:20:37	2023-10-06T03:31:34	2023-10-06T04:52:11	COMPLETED	0:0
5257959	picardtools_collectmultiplemetrics_slowlycivilbuck	developme+	core	2	01:16:47	01:18:46	2023-10-06T03:31:34	2023-10-06T04:50:20	COMPLETED	0:0
5257960	picardtools_collecthsmetrics_earlycasualcaiman	developme+	core	2	44:25.207	00:44:29	2023-10-06T03:31:34	2023-10-06T04:16:03	COMPLETED	0:0
5257961	picardtools_collecthsmetrics_hugelymodelbat	developme+	core	2	43:38.154	00:43:33	2023-10-06T03:33:07	2023-10-06T04:16:40	COMPLETED	0:0
5257962	picardtools_collecthsmetrics_slowlycivilbuck	developme+	core	2	43:55.938	00:43:48	2023-10-06T03:33:07	2023-10-06T04:16:55	COMPLETED	0:0
5257963	cnvnator_ar_earlycasualcaiman	developme+	core	13	43:49.711	00:03:46	2023-10-06T02:08:37	2023-10-06T02:12:23	COMPLETED	0:0
5257964	cnvnator_ar_hugelymodelbat	developme+	core	13	52:44.858	00:04:33	2023-10-06T02:40:53	2023-10-06T02:45:26	COMPLETED	0:0
5257965	cnvnator_ar_slowlycivilbuck	developme+	core	13	43:34.873	00:03:55	2023-10-06T02:44:57	2023-10-06T02:48:52	COMPLETED	0:0
5257966	expansionhunter_justhusky	developme+	core	3	15:14.977	00:05:45	2023-10-06T02:13:48	2023-10-06T02:19:33	COMPLETED	0:0
5257967	manta_justhusky	developme+	core	36	3-02:08:05	02:19:48	2023-10-06T05:05:31	2023-10-06T07:25:19	COMPLETED	0:0
5257968	tiddit_justhusky	developme+	core	12	09:43:06	01:58:22	2023-10-06T04:37:42	2023-10-06T06:36:04	COMPLETED	0:0
5257969	sv_combinevariantcallsets_justhusky	developme+	core	1	00:58.284	00:01:04	2023-10-06T07:27:05	2023-10-06T07:28:09	COMPLETED	0:0
5257970	sv_annotate_justhusky	developme+	core	3	29:43.765	00:18:53	2023-10-06T07:30:17	2023-10-06T07:49:10	COMPLETED	0:0
5257971	sv_varianteffectpredictor_justhusky	developme+	core	25	10:30.095	00:01:13	2023-10-06T12:01:35	2023-10-06T12:02:48	COMPLETED	0:0
5257972	sv_vcfparser_justhusky	developme+	core	13	03:00.955	00:00:38	2023-10-06T12:03:06	2023-10-06T12:03:44	COMPLETED	0:0
5257973	sv_rankvariant_justhusky	developme+	core	16	00:51.290	00:00:18	2023-10-06T12:32:49	2023-10-06T12:33:07	COMPLETED	0:0
5257974	sv_reformat_justhusky	developme+	core	5	00:17.123	00:00:15	2023-10-06T12:40:27	2023-10-06T12:40:42	COMPLETED	0:0
5257975	vcf2cytosure_ar_justhusky	developme+	core	4	54:43.261	00:18:25	2023-10-06T16:09:13	2023-10-06T16:27:38	COMPLETED	0:0
5257976	me_merge_bam_earlycasualcaiman	developme+	core	5	04:13.999	00:09:46	2023-10-06T02:34:29	2023-10-06T02:44:15	COMPLETED	0:0
5257977	me_merge_bam_hugelymodelbat	developme+	core	5	04:15.149	00:09:54	2023-10-06T02:34:29	2023-10-06T02:44:23	COMPLETED	0:0
5257978	me_merge_bam_slowlycivilbuck	developme+	core	5	04:58.957	00:10:27	2023-10-06T02:40:56	2023-10-06T02:51:23	COMPLETED	0:0
5257979	retroseq_earlycasualcaiman	developme+	core	2	03:49:41	03:40:55	2023-10-06T05:16:58	2023-10-06T08:57:53	COMPLETED	0:0
5257980	retroseq_hugelymodelbat	developme+	core	2	04:02:54	03:48:51	2023-10-06T05:16:58	2023-10-06T09:05:49	COMPLETED	0:0
5257981	retroseq_slowlycivilbuck	developme+	core	2	03:50:29	03:35:04	2023-10-06T05:16:58	2023-10-06T08:52:02	COMPLETED	0:0
5257982	me_merge_vcfs_justhusky	developme+	core	2	00:17.737	00:00:21	2023-10-06T09:06:10	2023-10-06T09:06:31	COMPLETED	0:0
5257983	me_annotate_justhusky	developme+	core	2	00:42.933	00:00:47	2023-10-06T09:08:14	2023-10-06T09:09:01	COMPLETED	0:0
5257984	me_varianteffectpredictor_justhusky	developme+	core	4	10:19.742	00:03:57	2023-10-06T09:09:44	2023-10-06T09:13:41	COMPLETED	0:0
5257985	me_filter_justhusky	developme+	core	2	00:41.889	00:00:44	2023-10-06T09:14:00	2023-10-06T09:14:44	COMPLETED	0:0
5257986	deepvariant_earlycasualcaiman	developme+	core	36	4-17:39:44	04:47:34	2023-10-06T05:05:55	2023-10-06T09:53:29	COMPLETED	0:0
5257987	deepvariant_hugelymodelbat	developme+	core	36	4-17:53:37	04:54:34	2023-10-06T05:05:59	2023-10-06T10:00:33	COMPLETED	0:0
5257988	deepvariant_slowlycivilbuck	developme+	core	36	4-17:35:19	04:51:44	2023-10-06T05:06:46	2023-10-06T09:58:30	COMPLETED	0:0
5257989	glnexus_merge_justhusky	developme+	core	32	55:38.601	00:21:19	2023-10-06T12:03:05	2023-10-06T12:24:24	COMPLETED	0:0
5257990	gatk_combinevariantcallsets_justhusky	developme+	core	5	01:23.476	00:01:08	2023-10-06T12:24:59	2023-10-06T12:26:07	COMPLETED	0:0
5257991	peddy_ar_justhusky	developme+	core	4	00:25.282	00:00:18	2023-10-06T12:26:22	2023-10-06T12:26:40	COMPLETED	0:0
5257992	plink_justhusky	developme+	core	2	01:08.209	00:01:21	2023-10-06T12:26:22	2023-10-06T12:27:43	COMPLETED	0:0
5257993	gatk_variantevalall_earlycasualcaiman	developme+	core	1	03:09.590	00:03:16	2023-10-06T12:26:22	2023-10-06T12:29:38	COMPLETED	0:0
5257994	gatk_variantevalall_hugelymodelbat	developme+	core	1	03:46.100	00:04:08	2023-10-06T12:26:22	2023-10-06T12:30:30	COMPLETED	0:0
5257995	gatk_variantevalall_slowlycivilbuck	developme+	core	1	03:44.940	00:04:10	2023-10-06T12:26:22	2023-10-06T12:30:32	COMPLETED	0:0
5257996	gatk_collectreadcounts_earlycasualcaiman	developme+	core	3	27:03.351	00:22:30	2023-10-06T12:26:22	2023-10-06T12:48:52	COMPLETED	0:0
5257997	gatk_collectreadcounts_hugelymodelbat	developme+	core	3	28:01.821	00:22:39	2023-10-06T12:26:22	2023-10-06T12:49:01	COMPLETED	0:0
5257998	gatk_collectreadcounts_slowlycivilbuck	developme+	core	3	26:26.621	00:21:33	2023-10-06T12:26:22	2023-10-06T12:47:55	COMPLETED	0:0
5257999	gatk_denoisereadcounts_earlycasualcaiman	developme+	core	9	05:58.091	00:03:26	2023-10-06T12:51:36	2023-10-06T12:55:02	COMPLETED	0:0
5258000	gatk_denoisereadcounts_hugelymodelbat	developme+	core	9	05:17.821	00:03:14	2023-10-06T12:51:36	2023-10-06T12:54:50	COMPLETED	0:0
5258001	gatk_denoisereadcounts_slowlycivilbuck	developme+	core	9	05:27.549	00:02:44	2023-10-06T12:48:19	2023-10-06T12:51:03	COMPLETED	0:0
5258002	gens_generatedata_earlycasualcaiman	developme+	core	2	15:24.554	00:15:48	2023-10-06T12:59:44	2023-10-06T13:15:32	COMPLETED	0:0
5258003	gens_generatedata_hugelymodelbat	developme+	core	2	15:21.827	00:15:49	2023-10-06T12:59:44	2023-10-06T13:15:33	COMPLETED	0:0
5258004	gens_generatedata_slowlycivilbuck	developme+	core	2	16:11.852	00:16:23	2023-10-06T12:51:36	2023-10-06T13:07:59	COMPLETED	0:0
5258005	prepareforvariantannotationblock_justhusky	developme+	core	25	01:11.421	00:00:08	2023-10-06T12:40:26	2023-10-06T12:40:34	COMPLETED	0:0
5258006	rhocall_ar_justhusky	developme+	core	13	03:52.656	00:00:22	2023-10-06T12:41:52	2023-10-06T12:42:14	COMPLETED	0:0
5258007	bcftools_norm_justhusky	developme+	core	13	01:06.522	00:00:07	2023-10-06T12:48:19	2023-10-06T12:48:26	COMPLETED	0:0
5258008	variant_annotation_justhusky	developme+	core	13	04:28:49	00:22:33	2023-10-06T12:52:24	2023-10-06T13:14:57	COMPLETED	0:0
5258009	rhocall_viz_earlycasualcaiman	developme+	core	1	02:54.646	00:03:10	2023-10-06T13:17:24	2023-10-06T13:20:34	COMPLETED	0:0
5258010	rhocall_viz_hugelymodelbat	developme+	core	1	03:15.914	00:03:30	2023-10-06T13:17:24	2023-10-06T13:20:54	COMPLETED	0:0
5258011	rhocall_viz_slowlycivilbuck	developme+	core	1	02:34.932	00:02:53	2023-10-06T13:17:24	2023-10-06T13:20:17	COMPLETED	0:0
5258012	chromograph_rhoviz_earlycasualcaiman	developme+	core	1	00:12.104	00:00:19	2023-10-06T13:21:39	2023-10-06T13:21:58	COMPLETED	0:0
5258013	chromograph_rhoviz_hugelymodelbat	developme+	core	1	00:10.824	00:00:18	2023-10-06T13:21:39	2023-10-06T13:21:57	COMPLETED	0:0
5258014	chromograph_rhoviz_slowlycivilbuck	developme+	core	1	00:10.783	00:00:18	2023-10-06T13:21:39	2023-10-06T13:21:57	COMPLETED	0:0
5258015	upd_ar_hugelymodelbat	developme+	core	1	07:12.696	00:07:23	2023-10-06T13:17:24	2023-10-06T13:24:47	COMPLETED	0:0
5258016	chromograph_upd_hugelymodelbat	developme+	core	1	01:52.276	00:01:56	2023-10-06T13:25:07	2023-10-06T13:27:03	COMPLETED	0:0
5258017	mt_annotation_justhusky	developme+	core	1	00:06.361	00:00:12	2023-10-06T13:17:24	2023-10-06T13:17:36	COMPLETED	0:0
5258018	frequency_filter_justhusky	developme+	core	13	01:33.469	00:00:12	2023-10-06T13:21:39	2023-10-06T13:21:51	COMPLETED	0:0
5258019	cadd_ar_justhusky	developme+	core	16	1-00:34:23	02:40:17	2023-10-06T13:23:11	2023-10-06T16:03:28	COMPLETED	0:0
5258020	varianteffectpredictor_justhusky	developme+	core	25	1-15:10:26	01:47:54	2023-10-06T16:09:13	2023-10-06T17:57:07	COMPLETED	0:0
5258021	vcfparser_ar_justhusky	developme+	core	25	03:43:49	00:17:25	2023-10-06T18:11:01	2023-10-06T18:28:26	COMPLETED	0:0
5258022	rankvariant_justhusky	developme+	core	36	03:37:05	00:24:21	2023-10-06T20:56:17	2023-10-06T21:20:38	COMPLETED	0:0
5258023	endvariantannotationblock_justhusky	developme+	core	2	04:27.828	00:07:09	2023-10-06T21:21:11	2023-10-06T21:28:20	COMPLETED	0:0
5258024	gatk_variantevalexome_earlycasualcaiman	developme+	core	1	02:10.559	00:02:29	2023-10-06T21:28:32	2023-10-06T21:31:01	COMPLETED	0:0
5258025	gatk_variantevalexome_hugelymodelbat	developme+	core	1	03:00.759	00:04:14	2023-10-06T21:28:32	2023-10-06T21:32:46	COMPLETED	0:0
5258026	gatk_variantevalexome_slowlycivilbuck	developme+	core	1	03:04.131	00:04:15	2023-10-06T21:28:32	2023-10-06T21:32:47	COMPLETED	0:0
5258027	qccollect_ar_justhusky	developme+	core	1	00:27.217	00:00:39	2023-10-06T21:33:18	2023-10-06T21:33:57	COMPLETED	0:0
5258028	version_collect_ar_justhusky	developme+	core	2	01:17.068	00:01:37	2023-10-06T21:34:28	2023-10-06T21:36:05	COMPLETED	0:0
5258029	multiqc_ar_justhusky	developme+	core	1	02:01.630	00:03:11	2023-10-06T21:36:35	2023-10-06T21:39:46	COMPLETED	0:0
5258030	analysisrunstatus_justhusky	developme+	core	1	00:32.390	00:00:45	2023-10-06T21:40:18	2023-10-06T21:41:03	COMPLETED	0:0

QC deliverables file contains value

...
  - header: first_of_pair
    id: earlycasualcaiman
    input: earlycasualcaiman_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.023422'
  - header: second_of_pair
    id: earlycasualcaiman
    input: earlycasualcaiman_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.020379'
  - header: pair
    id: earlycasualcaiman
    input: earlycasualcaiman_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.021903'
  - header: first_of_pair
    id: slowlycivilbuck
    input: slowlycivilbuck_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.02499'
  - header: second_of_pair
    id: slowlycivilbuck
    input: slowlycivilbuck_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.021568'
  - header: pair
    id: slowlycivilbuck
    input: slowlycivilbuck_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.023282'
  - header: first_of_pair
    id: hugelymodelbat
    input: hugelymodelbat_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.023798'
  - header: second_of_pair
    id: hugelymodelbat
    input: hugelymodelbat_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.020421'
  - header: pair
    id: hugelymodelbat
    input: hugelymodelbat_lanes_1_sorted_md_collectmultiplemetrics
    name: PCT_PF_READS_IMPROPER_PAIRS
    step: collectmultiplemetrics
    value: '0.022112'
...
```

@jemten jemten marked this pull request as ready for review October 9, 2023 08:29
@jemten jemten requested a review from ramprasadn as a code owner October 9, 2023 08:29
@jemten jemten merged commit ef074ab into master Oct 9, 2023
@jemten jemten deleted the release/12.0.1 branch October 9, 2023 08:30
@jemten jemten restored the release/12.0.1 branch October 9, 2023 08:30
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3 participants