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

Closed

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

chase's nextflow project tracking automation moved this from To do to Done 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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