v7.7.0 release: Kraken added and multiQC fixed

README.md

@@ -146,7 +146,7 @@ Then run:
 
 ```bash
 # distant main.nf file
-HOME="$ZEUSHOME/14985_loot/" ; nextflow run --modules ${MODULES} -hub pasteur gmillot/14985_loot -r v7.0.0 ; HOME="/pasteur/appa/homes/gmillot/"
+HOME="$ZEUSHOME/14985_loot/" ; nextflow run --modules ${MODULES} -hub pasteur gmillot/14985_loot -r v7.6.0 ; HOME="/pasteur/appa/homes/gmillot/"
 
 # local main.nf file ($HOME changed to allow the creation of .nextflow into /$ZEUSHOME/14985_loot/. See NFX_HOME in the nextflow soft script)
 HOME="$ZEUSHOME/14985_loot/" ; nextflow run --modules ${MODULES} main.nf ; HOME="/pasteur/appa/homes/gmillot/"
@@ -198,6 +198,11 @@ Gitlab developers
 
 ## WHAT'S NEW IN
 
+### v7.7.0
+
+1) Kraken added and multiQC fixed
+
+
 ### v7.6.0
 
 1) Everything's fine, except the multiQC

example_of_result/20220120_res_CL14985_B4985_4_1645109072/reports/nf_trace.txt

-task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
-2	d9/630746	7684	Nremove (1)	CACHED	0	2022-02-16 20:35:30.818	1.8s	424ms	52.5%	12.2 MB	70.6 MB	16.8 MB	14.5 MB
-4	b3/1c2ef7	8608	trim (1)	CACHED	0	2022-02-16 20:35:32.710	2.8s	1.9s	48.3%	42.6 MB	5.6 GB	16.4 MB	12 MB
-6	18/0f169c	13823	fivep_filtering (1)	CACHED	0	2022-02-17 14:36:41.956	3.4s	1.9s	22.7%	9.5 MB	61.4 MB	26 MB	14.3 MB
-5	96/df49e5	9178	fastqc1 (1)	CACHED	0	2022-02-16 20:35:35.529	5.7s	4.8s	85.2%	183.9 MB	3.1 GB	13.7 MB	1.2 MB
-9	2b/ed3a2a	14926	cutoff (1)	CACHED	0	2022-02-17 14:36:46.438	1.6s	607ms	19.8%	9.6 MB	61.3 MB	7 MB	3.9 MB
-8	b0/42cb74	17030	plot_read_length_fivep_filtering (1)	CACHED	0	2022-02-17 14:37:13.806	12.5s	11.4s	69.6%	233.2 MB	2.4 GB	19.1 MB	384.1 KB
-11	15/e3b952	12600	plot_fivep_filtering_stat (1)	CACHED	0	2022-02-16 20:36:10.915	12.2s	11.5s	75.1%	243.3 MB	2.4 GB	19.1 MB	816.6 KB
-10	d5/2de795	18246	plot_read_length_ini (1)	CACHED	0	2022-02-17 14:37:26.306	11.8s	11.1s	72.2%	233.4 MB	2.4 GB	19.1 MB	387.9 KB
-12	33/aa8574	24116	plot_read_length_cutoff (1)	CACHED	0	2022-02-17 14:40:57.228	12.1s	11.3s	70.1%	231.4 MB	2.4 GB	19.1 MB	376.7 KB
-13	69/7168f4	24843	bowtie2 (1)	CACHED	0	2022-02-17 14:41:09.287	4s	3.2s	60.9%	111.8 MB	239.5 MB	35 MB	16.2 MB
-7	0f/b81485	14947	fastqc2 (1)	CACHED	0	2022-02-17 14:36:46.456	5.6s	4.8s	76.4%	178 MB	3.1 GB	12 MB	1.2 MB
-18	68/f70403	25264	Q20 (1)	CACHED	0	2022-02-17 14:41:13.366	1.4s	327ms	21.7%	5.8 MB	42.8 MB	3.2 MB	2.2 MB
-17	c1/24d1cb	25236	coverage (1)	CACHED	0	2022-02-17 14:41:13.342	1.9s	728ms	18.8%	5 MB	44.6 MB	479.7 KB	91 KB
-20	a1/ab5068	25680	no_soft_clipping (1)	CACHED	0	2022-02-17 14:41:14.827	1.5s	274ms	14.5%	3.5 MB	38.4 MB	2.1 MB	1.5 MB
-22	8e/8c39fc	25863	coverage (2)	CACHED	0	2022-02-17 14:41:15.208	1.7s	686ms	16.8%	5.1 MB	44.6 MB	335.1 KB	82.4 KB
-23	ad/de823c	26426	plot_coverage (1)	CACHED	0	2022-02-17 14:41:16.956	12.6s	11.8s	70.7%	241.8 MB	2.4 GB	19.1 MB	464.3 KB
-21	3a/566af1	25706	duplicate_removal (1)	CACHED	0	2022-02-17 14:41:14.851	2.9s	1.7s	26.1%	10.4 MB	68.1 MB	12.9 MB	6.6 MB
-24	e0/5349ee	27505	plot_coverage (2)	CACHED	0	2022-02-17 14:41:29.547	12.2s	11.5s	72.0%	248.7 MB	2.4 GB	19.1 MB	455.9 KB
-26	aa/521edd	26735	insertion (1)	CACHED	0	2022-02-17 14:41:18.765	1.3s	437ms	22.2%	9.1 MB	65.7 MB	2.5 MB	1.7 MB
-25	44/f43ca7	28226	coverage (3)	CACHED	0	2022-02-17 14:41:41.776	1.4s	556ms	19.0%	5.1 MB	44.6 MB	310.3 KB	82.1 KB
-28	2d/74a6a2	28379	seq_around_insertion (1)	CACHED	0	2022-02-17 14:41:43.165	6.2s	5.5s	72.8%	156.3 MB	2.3 GB	17.9 MB	229.4 KB
-27	bd/2be631	28830	final_insertion_files (1)	CACHED	0	2022-02-17 14:41:49.355	6.3s	5.6s	72.2%	159.7 MB	2.3 GB	18 MB	266 KB
-29	fe/2ad1c2	29282	plot_coverage (3)	CACHED	0	2022-02-17 14:41:55.645	12.5s	11.7s	71.6%	263.5 MB	2.4 GB	19.1 MB	459.1 KB
-30	95/5c3641	30005	extract_seq (1)	CACHED	0	2022-02-17 14:42:08.124	1.7s	805ms	20.3%	5.8 MB	50.2 MB	9.1 MB	4.5 MB
-31	15/73b0fa	30224	base_freq (2)	CACHED	0	2022-02-17 14:42:09.881	1.4s	98ms	12.3%	0	0	281.7 KB	18.9 KB
-33	25/ce933f	30254	base_freq (4)	CACHED	0	2022-02-17 14:42:09.897	1.7s	89ms	9.4%	0	0	281.9 KB	19 KB
-32	da/9b485c	30341	base_freq (3)	CACHED	0	2022-02-17 14:42:09.935	1.7s	92ms	11.3%	0	0	282.5 KB	19.7 KB
-34	d8/137e70	30301	base_freq (1)	CACHED	0	2022-02-17 14:42:09.915	1.5s	87ms	14.9%	0	0	279.6 KB	16.8 KB
-39	b3/389d31	1073	global_logo	CACHED	0	2022-02-17 14:42:49.105	7.5s	6.8s	74.2%	202.8 MB	2.4 GB	14.6 MB	850.3 KB
-36	a3/f197a4	32028	logo (2)	CACHED	0	2022-02-17 14:42:27.726	7.2s	6.5s	73.5%	206.4 MB	2.4 GB	14.6 MB	1002.2 KB
-38	61/960392	32534	logo (3)	CACHED	0	2022-02-17 14:42:34.924	7.1s	6.4s	72.7%	203.6 MB	2.4 GB	14.6 MB	882.6 KB
-37	ab/988fed	569	logo (4)	CACHED	0	2022-02-17 14:42:42.065	7s	6.3s	73.6%	202.2 MB	2.4 GB	14.6 MB	873.7 KB
-35	81/d19fa7	31517	logo (1)	CACHED	0	2022-02-17 14:42:20.555	7.2s	6.5s	72.8%	203.5 MB	2.4 GB	14.6 MB	852.9 KB
-1	94/1749aa	18166	init	COMPLETED	0	2022-02-17 15:44:34.526	1.7s	14ms	8.1%	0	0	104.2 KB	673 B
-3	92/6c8320	18185	report1	COMPLETED	0	2022-02-17 15:44:34.568	1.7s	22ms	5.3%	0	0	104.5 KB	687 B
-15	68/5cb5a7	18300	backup	COMPLETED	0	2022-02-17 15:44:34.739	1.8s	14ms	5.1%	0	0	104.4 KB	522 B
-40	2d/c6de43	18543	report2	COMPLETED	0	2022-02-17 15:44:35.058	1.6s	34ms	7.7%	0	0	130.9 KB	1.3 KB
-16	13/0f76a4	18334	workflowVersion	COMPLETED	0	2022-02-17 15:44:34.780	2.4s	690ms	12.2%	3.2 MB	19.2 MB	135.3 KB	1.7 KB
-19	eb/621cc4	18381	multiQC	FAILED	1	2022-02-17 15:44:34.837	3.2s	3.1s	-	-	-	-	-
-14	58/5a238e	18288	motif	COMPLETED	0	2022-02-17 15:44:34.698	15.9s	14.7s	63.1%	217.9 MB	2.4 GB	48.3 MB	39.7 MB
-41	51/d8ad3f	19903	random_insertion (1)	COMPLETED	0	2022-02-17 15:44:50.654	10.4s	9.7s	70.7%	387.2 MB	2.7 GB	30.7 MB	1.2 MB
-42	fe/4bc2ef	20574	plot_insertion (1)	COMPLETED	0	2022-02-17 15:45:01.154	34.2s	33.5s	77.2%	999.3 MB	3.2 GB	40.3 MB	9.7 MB
-43	2b/e700a5	21541	print_report (1)	COMPLETED	0	2022-02-17 15:45:35.629	10.1s	9.4s	56.7%	286.9 MB	1 TB	29.8 MB	10.3 MB