Warning: with resume, the figure 38 is not the good one taken -> problem with...

Warning: with resume, the figure 38 is not the good one taken -> problem with the cache. Otherwise, goalign added. Remains to create empty png from gogalign and to insert into the markdown

bin/motif.R

@@ -416,7 +416,7 @@ b$orient[b$orient == 0] <- "Forward"
 b$orient[b$orient == 16] <- "Reverse"
 
 # verifications right of Ori
-fun_report(data = "\n\nOn the right of the Ori and the left of the ter:\n<br />Forward insertion = Leading (aka 0)\n<br />Reverse insertion = Lagging (aka 16)", output = report.rmd, path = "./", overwrite = FALSE)
+fun_report(data = "\n\nOn the right of the Ori and the left of the ter:\n<br />Forward insertion = Leading (i.e., reads with FLAG=0 are leading strand)\n<br />Reverse insertion = Lagging (i.e., reads with FLAG=16 are lagging strand)", output = report.rmd, path = "./", overwrite = FALSE)
 d <- b[b$Position > ori.center & b$Position < ter.center,]
 options(scipen = 1000) # to avoid writing of scientific numbers in tables, see https://stackoverflow.com/questions/3978266/number-format-writing-1e-5-instead-of-0-00001
 write.table(as.data.frame.matrix(addmargins(table(d[, c("fork", "orient")]))), file = paste0("./table1.txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t")
@@ -443,7 +443,7 @@ fun_report(data = tempo.cat, output = report.rmd, path = "./", overwrite = FALSE
 
 
 # verifications left of Ori
-fun_report(data = "\n\nOn the left of the Ori and the right of the ter:\n<br />Forward insertion = Lagging (aka 16)\n<br />Reverse insertion = Leading (aka 0)", output = report.rmd, path = "./", overwrite = FALSE)
+fun_report(data = "\n\nOn the left of the Ori and the right of the ter:\n<br />Forward insertion = Lagging (i.e., reads with FLAG=0 are lagging strand)\n<br />Reverse insertion = Leading (i.e., reads with FLAG=16 are lagging strand)", output = report.rmd, path = "./", overwrite = FALSE)
 e<- b[b$Position < ori.center | b$Position > ter.center,]
 options(scipen = 1000) # to avoid writing of scientific numbers in tables, see https://stackoverflow.com/questions/3978266/number-format-writing-1e-5-instead-of-0-00001
 write.table(as.data.frame.matrix(addmargins(table(e[, c("fork", "orient")]))), file = paste0("./table3.txt"), row.names = TRUE, col.names = NA, append = FALSE, quote = FALSE, sep = "\t")

example_of_result/20220120_test_1648711903/reports/nf_trace.txt

-task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
-3	c6/b5a87f	233	report1	COMPLETED	0	2022-03-31 09:31:45.419	1.6s	18ms	5.2%	0	0	104.6 KB	694 B
-1	b0/6d17f5	202	init	COMPLETED	0	2022-03-31 09:31:45.385	1.7s	11ms	6.0%	0	0	104.2 KB	676 B
-5	6a/41b53f	357	backup	COMPLETED	0	2022-03-31 09:31:45.602	1.6s	14ms	5.6%	0	0	104.4 KB	511 B
-2	60/ec2927	181	Nremove (1)	COMPLETED	0	2022-03-31 09:31:45.348	1.9s	438ms	47.9%	11.8 MB	70.6 MB	16.8 MB	14.5 MB
-6	21/fc97ed	394	workflowVersion	COMPLETED	0	2022-03-31 09:31:45.630	2.4s	962ms	12.1%	4.8 MB	38.4 MB	133.5 KB	2.1 KB
-7	f6/1888ae	1135	trim (1)	COMPLETED	0	2022-03-31 09:31:47.349	3.3s	2.2s	42.6%	38.8 MB	5.6 GB	16.4 MB	12 MB
-10	90/fb9dd7	1715	kraken (1)	COMPLETED	0	2022-03-31 09:31:50.658	167ms	8ms	64.0%	0	0	151 KB	231 B
-8	21/3c2e17	1739	fivep_filtering (1)	COMPLETED	0	2022-03-31 09:31:50.692	2.9s	1.9s	26.7%	9.6 MB	61.4 MB	28 MB	15.3 MB
-12	fc/7433af	2536	cutoff (1)	COMPLETED	0	2022-03-31 09:31:53.762	2s	712ms	18.6%	9.6 MB	61.3 MB	7 MB	3.9 MB
-9	97/f9aa8f	1807	fastqc1 (1)	COMPLETED	0	2022-03-31 09:31:50.716	7.6s	6.6s	65.4%	189.7 MB	3.1 GB	13.9 MB	1.2 MB
-11	59/c4b7ed	2509	fastqc2 (1)	COMPLETED	0	2022-03-31 09:31:53.700	6.2s	5.1s	62.5%	143.5 MB	3.1 GB	12.2 MB	1.2 MB
-4	12/9d071e	335	motif	COMPLETED	0	2022-03-31 09:31:45.576	18.4s	17s	47.3%	209.1 MB	407.3 MB	48.8 MB	39.7 MB
-13	45/ae26f7	3940	plot_fivep_filtering_stat (1)	COMPLETED	0	2022-03-31 09:32:03.942	13.8s	12.9s	52.6%	181.7 MB	427 MB	19.5 MB	812.8 KB
-15	a6/6f3471	4649	bowtie2 (1)	COMPLETED	0	2022-03-31 09:32:17.704	4.3s	3.4s	57.9%	112.8 MB	239.5 MB	35 MB	16.2 MB
-16	a5/b0a651	5106	Q20 (1)	COMPLETED	0	2022-03-31 09:32:22.078	1.5s	363ms	18.7%	5.8 MB	42.8 MB	3.2 MB	2.2 MB
-19	8b/ffe2b3	5641	no_soft_clipping (1)	COMPLETED	0	2022-03-31 09:32:24.630	1.5s	270ms	13.4%	3.4 MB	38.4 MB	2.1 MB	1.5 MB
-20	c7/508005	5663	duplicate_removal (1)	COMPLETED	0	2022-03-31 09:32:24.650	2.9s	1.8s	26.6%	6.4 MB	38.4 MB	12.9 MB	6.6 MB
-22	f0/f80457	6730	insertion (1)	COMPLETED	0	2022-03-31 09:32:28.515	1.6s	521ms	19.1%	9.2 MB	65.6 MB	2.5 MB	1.7 MB
-24	91/41d9a8	6736	insertion (2)	COMPLETED	0	2022-03-31 09:32:28.533	1.7s	574ms	20.4%	7.8 MB	65.6 MB	3 MB	2.2 MB
-18	bc/6f4ebe	5139	multiQC	COMPLETED	0	2022-03-31 09:32:22.098	8.4s	8s	40.8%	71.9 MB	82.3 MB	28.3 MB	2.3 MB
-14	be/6a3fa2	5068	plot_read_length (1)	COMPLETED	0	2022-03-31 09:32:22.034	14.8s	13.9s	58.0%	181.9 MB	417.7 MB	20 MB	712.6 KB
-17	db/29996f	7537	coverage (1)	COMPLETED	0	2022-03-31 09:32:36.842	1.6s	629ms	17.9%	5.1 MB	44.6 MB	479.8 KB	91 KB
-21	ce/89bb59	7693	coverage (2)	COMPLETED	0	2022-03-31 09:32:38.401	1.3s	542ms	20.8%	5.1 MB	44.6 MB	335.2 KB	82.4 KB
-23	c7/7907eb	7847	coverage (3)	COMPLETED	0	2022-03-31 09:32:39.731	1.4s	545ms	19.1%	5.1 MB	44.6 MB	310.4 KB	82.1 KB
-25	44/a1b906	7998	final_insertion_files (1)	COMPLETED	0	2022-03-31 09:32:41.142	6.4s	5.7s	41.2%	134.1 MB	332.2 MB	18.4 MB	318.2 KB
-31	6a/9443e7	8456	report3 (1)	COMPLETED	0	2022-03-31 09:32:47.564	971ms	29ms	13.3%	0	0	176.9 KB	535 B
-26	44/c4b2cf	8432	final_insertion_files (2)	COMPLETED	0	2022-03-31 09:32:47.541	6.5s	5.7s	41.5%	135.1 MB	333.3 MB	18.4 MB	318.2 KB
-27	cf/b9fba8	8998	plot_coverage (1)	COMPLETED	0	2022-03-31 09:32:54.043	16s	15.3s	47.0%	146 MB	391.7 MB	19.5 MB	460.6 KB
-28	e8/72aa08	9711	plot_coverage (2)	COMPLETED	0	2022-03-31 09:33:10.063	12.5s	11.8s	58.6%	224.6 MB	436.6 MB	19.5 MB	454.7 KB
-29	a1/4547ae	10417	plot_coverage (3)	COMPLETED	0	2022-03-31 09:33:22.594	12.8s	12s	58.3%	220.4 MB	431.4 MB	19.5 MB	455.3 KB
-30	95/3650da	11124	seq_around_insertion (1)	COMPLETED	0	2022-03-31 09:33:35.366	6.6s	5.9s	42.7%	133.8 MB	331.7 MB	18.4 MB	229.5 KB
-32	6b/1a0ec6	11558	random_insertion (1)	COMPLETED	0	2022-03-31 09:33:42.025	10.7s	9.9s	53.8%	367.8 MB	577.1 MB	31.2 MB	1.2 MB
-33	30/f186d8	12208	seq_around_insertion (2)	COMPLETED	0	2022-03-31 09:33:52.713	6.7s	6s	42.0%	133.5 MB	331.6 MB	18.4 MB	163.4 KB
-34	d5/add756	12654	dup_insertion_and_logo (1)	COMPLETED	0	2022-03-31 09:33:59.434	13.1s	12.4s	60.0%	176.3 MB	387.8 MB	17.8 MB	526.6 KB
-35	0f/010866	13383	extract_seq (1)	COMPLETED	0	2022-03-31 09:34:12.542	1.7s	815ms	20.1%	5.9 MB	50.4 MB	9.1 MB	4.5 MB
-38	ea/138194	13651	base_freq (1)	COMPLETED	0	2022-03-31 09:34:14.293	1.4s	96ms	9.9%	0	0	279.8 KB	16.8 KB
-41	5d/a11b6c	13590	base_freq (4)	COMPLETED	0	2022-03-31 09:34:14.250	1.6s	99ms	12.0%	0	0	282.1 KB	19 KB
-40	32/dba095	13693	base_freq (3)	COMPLETED	0	2022-03-31 09:34:14.315	1.6s	99ms	11.0%	0	0	282.7 KB	19.7 KB
-39	04/a23943	13742	base_freq (2)	COMPLETED	0	2022-03-31 09:34:14.337	1.6s	101ms	11.1%	0	0	281.9 KB	18.9 KB
-36	07/07d7b0	13577	plot_insertion (1)	COMPLETED	0	2022-03-31 09:34:14.226	3m 38s	3m 37s	32.7%	1.1 GB	1.3 GB	59.1 MB	17.7 MB
-37	18/3237c2	18231	extract_seq (2)	COMPLETED	0	2022-03-31 09:37:52.165	1.4s	468ms	19.7%	5.9 MB	50.4 MB	9 MB	4.5 MB
-49	0d/8a0c99	18454	base_freq (8)	COMPLETED	0	2022-03-31 09:37:53.563	1.5s	41ms	11.3%	0	0	180.5 KB	7 KB
-47	0c/b8dd30	18514	base_freq (6)	COMPLETED	0	2022-03-31 09:37:53.610	1.5s	38ms	11.0%	0	0	178.7 KB	5.1 KB
-48	e6/ef7c36	18567	base_freq (7)	COMPLETED	0	2022-03-31 09:37:53.629	1.7s	41ms	10.9%	0	0	176.4 KB	2.8 KB
-46	44/4501dd	18603	base_freq (5)	COMPLETED	0	2022-03-31 09:37:53.648	1.7s	50ms	8.0%	0	0	182.5 KB	8.9 KB
-50	d6/eb7d31	19171	report2	COMPLETED	0	2022-03-31 09:37:56.354	960ms	22ms	9.3%	0	0	131.9 KB	2 KB
-42	49/87dc82	18440	logo (1)	COMPLETED	0	2022-03-31 09:37:53.542	12.2s	11.2s	27.4%	184.9 MB	395.7 MB	15.1 MB	1023.2 KB
-43	85/acf092	19803	logo (2)	COMPLETED	0	2022-03-31 09:38:05.751	7.3s	6.6s	45.7%	183.1 MB	394 MB	15.1 MB	904.1 KB
-44	6a/37a6b6	20291	logo (3)	COMPLETED	0	2022-03-31 09:38:13.101	7.3s	6.6s	45.0%	182.6 MB	393.6 MB	15.1 MB	894.6 KB
-45	3e/6f606f	20781	logo (4)	COMPLETED	0	2022-03-31 09:38:20.371	7.2s	6.5s	46.0%	184.4 MB	393.4 MB	15.1 MB	874 KB
-51	47/e9041b	21265	global_logo (1)	COMPLETED	0	2022-03-31 09:38:27.562	7.5s	6.8s	47.9%	179.6 MB	390.3 MB	15.1 MB	867.7 KB
-52	7c/d7021a	21760	global_logo (2)	COMPLETED	0	2022-03-31 09:38:35.091	7.5s	6.9s	48.6%	181.3 MB	392.6 MB	15.1 MB	988 KB
-53	0b/7d3032	22259	print_report (1)	COMPLETED	0	2022-03-31 09:38:42.977	11s	10.3s	39.8%	222.7 MB	1 TB	44.2 MB	19.9 MB