Nfcore and structuring modules for collaboration #157

chasemc · 2021-04-28T20:28:48Z

Execution Details

task_id	hash	native_id	name	status	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
1	4c/06205c	2237350	AUTOMETA:LENGTH_FILTER (filtering metagenome metagenome)	COMPLETED	2021-04-28 14:39:08.950	3.6s	3s	153.8%	218.6 MB	3.3 GB	184.4 MB	76.1 MB
2	0d/5d13c8	2237734	AUTOMETA:KMER_COVERAGE (Calculating k-mer coverage for metagenome)	COMPLETED	2021-04-28 14:39:12.594	1.2s	625ms	305.4%	11.3 MB	15.9 MB	85.4 MB	281.7 KB
8	b8/4fa560	2238087	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.843	5.1s	3.5s	97.7%	57.3 MB	113.8 MB	1.3 MB	2.3 MB
10	e0/c30153	2238159	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.856	6.8s	5.2s	96.2%	57.9 MB	114.1 MB	1.1 MB	1.8 MB
5	77/b83513	2238019	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.831	7.7s	6.7s	97.8%	66.5 MB	120 MB	1.1 MB	1.7 MB
9	2c/62c9bc	2238120	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.849	8.1s	6.4s	97.5%	60.6 MB	114.1 MB	1.2 MB	1.9 MB
3	af/66baae	2237997	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.822	9.3s	8.5s	97.3%	70.8 MB	127.2 MB	1.4 MB	2.3 MB
14	18/cadcec	2238260	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.869	9.8s	7.8s	97.6%	58.1 MB	113.9 MB	1.2 MB	1.9 MB
20	44/abd8ae	2238508	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.921	11s	7.9s	96.2%	55.7 MB	113.7 MB	1.1 MB	1.8 MB
18	49/089aac	2238449	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.911	11.1s	7.8s	95.6%	56.6 MB	113.9 MB	1.1 MB	1.7 MB
25	35/618b16	2238627	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.941	12s	10.2s	97.7%	55.1 MB	113.6 MB	1.2 MB	1.9 MB
24	dd/194b84	2238590	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.936	12.6s	10.6s	96.0%	55.1 MB	113.7 MB	1.1 MB	1.8 MB
7	0c/930231	2238059	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.838	12.9s	11.3s	96.4%	63.1 MB	114.3 MB	1.5 MB	2.5 MB
26	e6/131a95	2238640	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.945	13s	9.3s	94.5%	54.9 MB	113.6 MB	1.1 MB	1.8 MB
19	94/adb728	2238477	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.915	13.2s	10.6s	96.6%	56.4 MB	113.7 MB	1.2 MB	2 MB
6	62/29d31c	2238040	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.835	13.9s	12.3s	96.7%	66.1 MB	119.4 MB	2 MB	3.2 MB
23	74/de3f57	2238572	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.932	14s	10.4s	96.5%	55.6 MB	113.6 MB	1.1 MB	1.8 MB
17	82/0c5366	2238345	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.883	14.5s	12.2s	97.3%	57.3 MB	113.8 MB	1.2 MB	1.9 MB
22	bb/b00cae	2238552	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.928	15.7s	12s	96.6%	55.7 MB	113.6 MB	1.2 MB	1.9 MB
28	68/656ba9	2247386	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:20.639	9.1s	7.8s	94.7%	54.5 MB	113.6 MB	1.1 MB	1.8 MB
16	0e/77bad2	2238388	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.889	15.9s	12.9s	96.8%	57 MB	113.8 MB	1.3 MB	2.1 MB
11	68/bcd2bb	2238185	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.859	16.5s	13.9s	96.1%	59.6 MB	114.3 MB	1.4 MB	2.3 MB
30	08/941745	2248986	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:21.943	8.5s	7.5s	93.4%	54.4 MB	113.6 MB	1.1 MB	1.8 MB
34	90/610e41	2252749	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:24.966	6.4s	5.5s	96.6%	53.8 MB	113.6 MB	1.1 MB	1.8 MB
27	af/3f1e8d	2245277	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:18.931	13.3s	11.8s	96.6%	54.7 MB	113.6 MB	1.1 MB	1.7 MB
21	d4/473943	2238529	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.925	18.4s	15.2s	96.0%	55.9 MB	113.7 MB	1.2 MB	2 MB
32	c1/4c0b26	2251057	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:23.698	9.6s	8s	97.0%	54.1 MB	113.6 MB	1.1 MB	1.8 MB
33	35/45607f	2252682	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:24.928	8.5s	6.8s	97.3%	54.2 MB	113.6 MB	1.1 MB	1.7 MB
31	44/4ed54b	2250515	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:23.138	10.6s	8.7s	96.5%	54.3 MB	113.6 MB	1.2 MB	1.8 MB
36	fb/b1d701	2255064	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:26.564	7.3s	5.6s	96.4%	53 MB	113.4 MB	1.1 MB	1.7 MB
13	4b/dc5bd4	2238242	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.866	20.1s	16.8s	97.3%	58.9 MB	113.9 MB	1.3 MB	2.1 MB
15	d2/68e084	2238326	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.874	20.3s	17.3s	98.0%	57.9 MB	113.8 MB	1.4 MB	2.2 MB
4	4b/fdbf01	2238004	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.826	20.5s	19.4s	97.7%	71.6 MB	122.7 MB	1.2 MB	1.9 MB
29	b2/b2f6f3	2248518	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:21.539	12.9s	11.6s	97.3%	54.8 MB	113.6 MB	1.1 MB	1.8 MB
38	9d/0ee178	2255454	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:26.947	8.2s	6.9s	96.9%	53.7 MB	113.4 MB	1.1 MB	1.8 MB
40	ac/7f21e3	2256649	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:27.767	8.1s	6.3s	98.7%	53.4 MB	113.4 MB	1.1 MB	1.8 MB
39	88/22f7ad	2255609	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:27.100	9.1s	7s	97.7%	53.5 MB	113.4 MB	1.1 MB	1.8 MB
12	eb/196c48	2238206	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:13.863	22.7s	20s	97.7%	60.1 MB	114 MB	1.4 MB	2.2 MB
41	d8/86f4d7	2256916	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:27.947	8.7s	7s	98.1%	53.5 MB	113.4 MB	1.1 MB	1.8 MB
35	ed/0eb013	2254166	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:25.972	10.9s	8.8s	98.3%	53.6 MB	113.4 MB	1.1 MB	1.9 MB
37	be/e827d3	2255264	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:26.717	10.3s	8.1s	98.9%	53.3 MB	113.4 MB	1.1 MB	1.8 MB
47	43/a0aa5e	2259898	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:30.475	6.6s	5.1s	98.7%	52.7 MB	113.4 MB	1.1 MB	1.7 MB
43	79/2835ca	2258890	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:29.633	7.7s	6s	97.9%	53.1 MB	113.4 MB	1.1 MB	1.7 MB
46	7b/fa805d	2259612	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:30.317	7.2s	5.9s	99.3%	53.2 MB	113.4 MB	1.1 MB	1.7 MB
42	a3/277152	2257645	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:28.414	9.6s	8.5s	98.7%	53.4 MB	113.4 MB	1.1 MB	1.7 MB
48	b6/9f5857	2261138	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:31.400	7.1s	5.2s	99.5%	52.8 MB	113.4 MB	1.1 MB	1.7 MB
45	6b/9a61f3	2259064	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:29.781	8.9s	7.1s	99.8%	52.7 MB	113.4 MB	1.1 MB	1.8 MB
44	2c/09d655	2258967	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:29.699	9.3s	7.4s	99.9%	53.4 MB	113.4 MB	1.1 MB	1.8 MB
50	57/4b41cd	2262101	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:32.328	7.1s	5.6s	100.6%	52.5 MB	113.4 MB	1.1 MB	1.8 MB
49	b1/9f4290	2261914	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:32.188	7.3s	5.4s	100.0%	52.5 MB	113.4 MB	1.1 MB	1.7 MB
53	43/5a4ed6	2263892	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:33.748	6.9s	4.6s	100.0%	52.8 MB	113.4 MB	1.1 MB	1.7 MB
51	f4/076c1a	2263259	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:33.269	8.1s	6.5s	99.9%	52.9 MB	113.4 MB	1.1 MB	1.8 MB
62	72/36cc8f	2267547	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:36.596	5.6s	3.6s	100.3%	52.8 MB	113.4 MB	1.1 MB	1.7 MB
56	49/b59d3a	2264404	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:34.175	8.2s	6.1s	99.9%	52.3 MB	113.4 MB	1.1 MB	1.7 MB
54	90/f44b80	2263974	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:33.858	8.7s	6.2s	100.6%	52.9 MB	113.4 MB	1.1 MB	1.7 MB
52	c9/54ddc0	2263408	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:33.445	9.5s	6.7s	100.6%	52.9 MB	113.4 MB	1.1 MB	1.7 MB
71	7a/cebb94	2270206	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:38.678	4.3s	1.9s	99.6%	52 MB	113.4 MB	735.9 KB	1.2 MB
57	97/b28bce	2264569	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:34.344	8.8s	6.1s	100.0%	52.3 MB	113.4 MB	1.1 MB	1.7 MB
55	eb/313464	2264150	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:33.960	9.4s	6.4s	100.2%	52.3 MB	113.4 MB	1.1 MB	1.7 MB
59	d7/d02065	2265770	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:35.149	8.5s	4.5s	100.4%	52.3 MB	113.4 MB	1.1 MB	1.7 MB
60	d4/d5af07	2266728	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:35.827	8.2s	3.9s	99.7%	52.5 MB	113.4 MB	1.1 MB	1.7 MB
63	a5/03380c	2267700	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:36.693	7.4s	4s	99.7%	52.6 MB	113.4 MB	1.1 MB	1.7 MB
58	aa/0f0e00	2264669	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:34.446	9.7s	5.6s	100.2%	52.3 MB	113.4 MB	1.1 MB	1.7 MB
66	e2/cd8c58	2268159	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:37.082	7.1s	3.6s	100.1%	51.8 MB	113.4 MB	1.1 MB	1.7 MB
68	c1/3159a8	`2268723`	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:37.542	6.7s	3s	99.1%	52.1 MB	113.4 MB	1.1 MB	1.7 MB
67	1d/9b4439	2268375	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:37.293	7s	3.2s	99.6%	52 MB	113.4 MB	1.1 MB	1.7 MB
69	fd/8a0127	2269335	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:38.032	6.4s	3.1s	99.6%	52 MB	113.4 MB	1.1 MB	1.8 MB
70	1c/19bd66	2269817	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:38.455	6s	2.8s	100.0%	52 MB	113.4 MB	1.1 MB	1.8 MB
65	c6/5e3849	2268036	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:36.982	7.5s	3.9s	99.1%	52 MB	113.4 MB	1.1 MB	1.7 MB
61	4f/9a736c	2267091	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:36.174	8.4s	4.7s	100.1%	52.7 MB	113.4 MB	1.1 MB	1.7 MB
64	50/94b2fd	2267989	AUTOMETA:ORFS (Calling orfs for metagenome)	COMPLETED	2021-04-28 14:39:36.890	7.8s	4.1s	99.4%	52 MB	113.4 MB	1.1 MB	1.7 MB
72	00/2bf5aa	2275661	AUTOMETA:TAXON_ASSIGNMENT:DIAMOND (diamond blastp on metagenome)	COMPLETED	2021-04-28 14:39:44.737	5s	4.4s	1982.4%	726.3 MB	3.1 GB	115.6 MB	82 MB
73	a8/d34ed8	2277515	AUTOMETA:MARKERS (Finding markers for metagenome)	COMPLETED	2021-04-28 14:39:49.743	4m 6s	4m 5s	239.1%	93 MB	3.5 GB	159.6 GB	105.2 MB
74	c0/8e1fb1	4038042	AUTOMETA:TAXON_ASSIGNMENT:LCA (Assigning LCA to metagenome)	COMPLETED	2021-04-28 14:43:55.264	7m 37s	7m 37s	100.4%	3.8 GB	7 GB	34.2 GB	5.1 MB
75	a7/86babd	4043735	AUTOMETA:TAXON_ASSIGNMENT:MAJORITY_VOTE (Performing taxon majority vote on metagenome)	COMPLETED	2021-04-28 14:51:32.394	7.5s	7s	123.3%	1.3 GB	4.5 GB	369.6 MB	80.8 KB
76	23/10de17	4044339	AUTOMETA:TAXON_ASSIGNMENT:SPLIT_KINGDOMS (Splitting votes into kingdoms for metagenome)	COMPLETED	2021-04-28 14:51:39.935	7.5s	7s	123.1%	1.3 GB	4.5 GB	435.5 MB	76 MB
77	0c/7d0367	4044951	AUTOMETA:KMERS (counting kmers for metagenome)	COMPLETED	2021-04-28 14:51:47.505	1m 1s	1m 1s	704.0%	4.1 GB	81.1 GB	180.8 MB	99.7 MB
78	9f/86e4f8	4051768	AUTOMETA:BINNING (Performing Autometa binning)	COMPLETED	2021-04-28 14:52:48.842	17m 17s	17m 16s	108.6%	357.7 MB	5.1 GB	29.5 MB	452.4 KB
79	e4/3aa9de	4136136	AUTOMETA:UNCLUSTERED_RECRUITMENT (Performing Autometa unclustered recruitment)	COMPLETED	2021-04-28 15:10:05.602	2.3s	1.7s	345.0%	144.1 MB	3.4 GB	38 MB	987.6 KB
80	5b/002dd2	4136121	AUTOMETA:BINNING_SUMMARY (Binning summary for metagenome)	COMPLETED	2021-04-28 15:10:05.592	8.3s	7.7s	118.5%	1.3 GB	4.5 GB	435.9 MB	75.8 MB

Will come back around to this right before PR in case things change

This still needs work. Plan: - true = default to "${params.outdir}/interim_outputs" - false = switch off publishDir for intermediates - path = store intermediates at specified path

Move main.nf to nextflow/autometa.nf Change config so that main script is found and the different config files are included

A decent amount of text in here can be removed/is specific to nf-core.

…-like-nfcore

Originally was main.nf and may revert to autometa.nf later. Bringing stuff from another repo where I tested the layout first

nf-core requires having an `params.input` so may as well change the input argument to that

Lots of changes here. Still a work in progress (WIP)

Leftover from testing output/publish directories

Co-authored-by: Evan Rees <25933122+WiscEvan@users.noreply.github.com>

subworkflows/local/prepare_ncbi_taxinfo.nf

https://github.com/KwanLab/Autometa/pull/157/files#r696981913

evanroyrees

Will be merging by EOTD

modules/local/diamond_blastp.nf

nextflow.config

nextflow_schema.json

conf/base.config

chasemc · 2021-09-28T19:11:11Z

Will be merging by EOTD

Add other kmer embedding options in embedding method description

Fix typo

🐛 Fix typo/bug

chasemc added 30 commits April 19, 2021 15:52

🎨 Add informational Autometa header to main nextflow script

5800488

🎨 Move and add comment about include statement

c7ffaef

🎨 change params.interim to params.interim_dir

f076907

🎨 change params.processed to params.outdir

1d41cd6

🎨 change params.metagenome to params.input_fna

b1d9625

🎨 Add help function. WIP, will need to be updated.

82a295d

Will come back around to this right before PR in case things change

🎨 Update documentation and function names in validation

6907bfb

🎨 Modify interim directory value meaning

602e49d

This still needs work. Plan: - true = default to "${params.outdir}/interim_outputs" - false = switch off publishDir for intermediates - path = store intermediates at specified path

🎨 WIP: organizing configs and help

b7e3da6

🎨 Minimize Nextflow file presence in top git directory

968f76b

Move main.nf to nextflow/autometa.nf Change config so that main script is found and the different config files are included

Add nf-core boilerplate files and functions

3cad58b

Add nf-core boilerplate files and functions

0137389

A decent amount of text in here can be removed/is specific to nf-core.

Merge remote-tracking branch 'KwanLab/format-like-nfcore' into format…

a94ebe5

…-like-nfcore

🍏 Create ignore file for nf-core linter

da781b6

🍏 replaced autometa.nf with main.nf

6e24b8d

Originally was main.nf and may revert to autometa.nf later. Bringing stuff from another repo where I tested the layout first

🍏 🎨 Change input_fna to input

819fae5

nf-core requires having an `params.input` so may as well change the input argument to that

🍏 Add schema validation back to linting

810554e

🍏 Add nf-core schema.json

4053b85

WIP- nextflow configuration

17d059e

🍏 move def check_max() from base to hardware config

ec4c675

🍏 Add config profile options

249ac60

🍏 remove nf-core generated autometa logo

1e34af6

🍏 Update docker repo path

e517607

🍏 🐛 Fix version check

39aa764

🍏 Update nextflow schema

7b34a10

🍏 create nf-core output docuementation process

04bfd57

🍏 🎨 Format comment block

27a5e60

🍏 Add nf-core parameter validator to main.nf

85e0070

🍏 nf-core templating

83a83b3

Lots of changes here. Still a work in progress (WIP)

🍏 🎨 Streamline required config

dbb594e

chasemc and others added 8 commits September 1, 2021 19:10

🍏 remove mkdir

2a815b6

Leftover from testing output/publish directories

🍏 comment WIP files

284ca19

🍏 Remove unnecessary intermediate fasta

7d014f4

🍏 bump 2.0.0-alpha.0 to 2.0.0 in nf-manifest

455e38e

Update subworkflows/local/align_reads.nf

e1d31b9

Co-authored-by: Evan Rees <25933122+WiscEvan@users.noreply.github.com>

🍏 🎨 Update line continuation within nf script

9b62d3e

Update subworkflows/local/prepare_ncbi_taxinfo.nf

0e8f4fc

Co-authored-by: Evan Rees <25933122+WiscEvan@users.noreply.github.com>

🍏 remove redundant collect

3e72080

chasemc commented Sep 2, 2021

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subworkflows/local/prepare_ncbi_taxinfo.nf Show resolved Hide resolved

chasemc added 2 commits September 2, 2021 11:36

🍏 fix lint

59b7308

🍏 Split Binning/UR subworkflow

d547946

https://github.com/KwanLab/Autometa/pull/157/files#r696981913

chasemc mentioned this pull request Sep 2, 2021

Decide on how output directories should be created/handled #188

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evanroyrees approved these changes Sep 28, 2021

View reviewed changes

evanroyrees and others added 8 commits September 28, 2021 15:19

Update nextflow_schema.json

7de0dbe

Update nextflow_schema.json

e86a096

Update nextflow_schema.json

2dfbbb3

Add other kmer embedding options in embedding method description

Update nextflow.config

5f0b12d

Fix typo

Update modules/local/diamond_blastp.nf

a9bbebe

🐛 Fix typo/bug

🎨 Restrict diamond blastp process to run only one task at a time

4044a1f

🎨🍎⬆️ resolve merge conflicts with dev

97cd1cd

🔥🍏 Fix linting by removing invalid benchmarking tasks nf script

f50b573

evanroyrees merged commit 92179f5 into dev Sep 28, 2021

evanroyrees deleted the nfcore branch December 2, 2021 20:07

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Nfcore and structuring modules for collaboration #157

Nfcore and structuring modules for collaboration #157

chasemc commented Apr 28, 2021 •

edited by evanroyrees

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chasemc commented Sep 28, 2021

Nfcore and structuring modules for collaboration #157

Nfcore and structuring modules for collaboration #157

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chasemc commented Sep 28, 2021

chasemc commented Apr 28, 2021 •

edited by evanroyrees

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