James Fellows Yates
|
43a8aa4405
|
Remove detect_reads.py and replace remaining checks with nextflow code instead
|
2022-09-27 15:32:51 +02:00 |
|
Rafal Stepien
|
9349346864
|
Remove --pep parameter and leave just --input
|
2022-09-16 10:14:01 -04:00 |
|
James A. Fellows Yates
|
016efcb807
|
Merge branch 'dev' into metaphlan3/mergemetaphlantables
|
2022-09-16 16:02:38 +02:00 |
|
James Fellows Yates
|
4e7857e2ed
|
Standardise mOTUs table merge
|
2022-09-16 08:36:34 +02:00 |
|
James A. Fellows Yates
|
cdb21d17b3
|
Merge branch 'dev' into metaphlan3/mergemetaphlantables
|
2022-09-15 13:08:57 +02:00 |
|
James Fellows Yates
|
19a195ed14
|
Append profiler to resulting file
|
2022-09-15 12:30:39 +02:00 |
|
Rafal Stepien
|
5f3eee9a4a
|
Add working version of PEP-nf-core integration
|
2022-09-14 14:28:48 -04:00 |
|
James Fellows Yates
|
05e9d92444
|
Add centrigue kreports
|
2022-09-13 16:47:19 +02:00 |
|
James Fellows Yates
|
c8dbf5be47
|
Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
|
2022-09-13 15:47:28 +02:00 |
|
James Fellows Yates
|
a764bc4807
|
Start works - need updated module though t have meta
|
2022-09-09 13:57:06 +02:00 |
|
James A. Fellows Yates
|
cc5df924e4
|
Merge branch 'dev' into module-update
|
2022-09-08 13:36:21 +02:00 |
|
James Fellows Yates
|
fc26948950
|
Fix MultiQC
|
2022-09-08 12:49:38 +02:00 |
|
James Fellows Yates
|
832d981976
|
Don't have per sample directory as unnecessary if file names are unique with the db in them
|
2022-09-07 12:22:17 +02:00 |
|
James Fellows Yates
|
7c5f9d0c24
|
Start work on more merging tools
|
2022-09-06 17:34:45 +02:00 |
|
James A. Fellows Yates
|
dd194f3f47
|
Fix mOTUs CI and old param warn
|
2022-09-04 15:01:58 +00:00 |
|
James A. Fellows Yates
|
13e9957e14
|
Fixes process selector warning
|
2022-09-02 06:03:05 +00:00 |
|
James A. Fellows Yates
|
f7b7fd63a4
|
Merge pull request #114 from nf-core/nf-core-template-merge-2.5
Important! Template update for nf-core/tools v2.5
|
2022-08-31 10:28:14 +02:00 |
|
James A. Fellows Yates
|
28d8d3f8fb
|
Merge branch 'dev' into nf-core-template-merge-2.5
|
2022-08-31 09:16:34 +02:00 |
|
nf-core-bot
|
6dfca81761
|
Template update for nf-core/tools version 2.5
|
2022-08-30 13:43:03 +00:00 |
|
James Fellows Yates
|
afba604e8b
|
Make everything within opt-out, once QC is opted-in
|
2022-08-30 14:04:34 +02:00 |
|
James Fellows Yates
|
2cc07183a0
|
Standardise QC parameter system and turn on both porechop/filtlong in tests
|
2022-08-30 13:58:58 +02:00 |
|
James A. Fellows Yates
|
a3055bf6da
|
Update conf/test_nothing.config
|
2022-08-23 15:48:02 +02:00 |
|
James Fellows Yates
|
e6c7939305
|
Add test_nothing config profile for minimal testing
|
2022-08-23 14:37:01 +02:00 |
|
James Fellows Yates
|
a97bb69cd2
|
Prettier
|
2022-08-23 14:24:57 +02:00 |
|
James A. Fellows Yates
|
de70b0a01d
|
Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
|
2022-07-29 13:36:25 +02:00 |
|
mjamy
|
5cdf5e958a
|
Updated modules.config to add 'log' in diamond config
|
2022-07-28 16:08:15 +02:00 |
|
sofstam
|
71cf32cc6a
|
Add error strategy for centrifuge/kreport
|
2022-07-28 08:54:32 +02:00 |
|
James A. Fellows Yates
|
65ae82efc4
|
Define separte krakena nd centrigfue modules
|
2022-07-26 18:37:33 +00:00 |
|
James A. Fellows Yates
|
e76b299705
|
Start working getting kraken and centrifuge working in MQC
|
2022-07-26 08:18:54 +00:00 |
|
James Fellows Yates
|
a0ee82bf43
|
Add motus/merge and biom support
|
2022-07-12 11:39:26 +02:00 |
|
James A. Fellows Yates
|
8082c7d108
|
Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
|
2022-07-05 15:17:52 +02:00 |
|
James A. Fellows Yates
|
26e31c782d
|
Merge branch 'dev' into motus
|
2022-07-04 13:14:42 +02:00 |
|
James Fellows Yates
|
447b8f0905
|
Get fixed Krona module and add Krona taxonomy to test profile
|
2022-07-01 17:21:19 +02:00 |
|
James Fellows Yates
|
02c06b9f7b
|
Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
|
2022-06-30 18:33:11 +02:00 |
|
|
069370db86
|
Add unclassified and verbose flags to kaiju2krona
|
2022-06-28 09:00:42 -05:00 |
|
|
18284e6e32
|
Add run_krona option to allow skipping Krona chart creation
|
2022-06-27 08:45:08 -05:00 |
|
|
0e8edd5b2f
|
Add output configuration for Kraken Krona chart
|
2022-06-27 08:25:47 -05:00 |
|
James Fellows Yates
|
9462032d00
|
Fix MALT save_alignemnts reads and some clean up
|
2022-06-03 22:29:04 +02:00 |
|
JIANHONG OU
|
c8a59adbce
|
remove the database auto-download for mOTUs.
|
2022-06-03 14:13:58 -04:00 |
|
James A. Fellows Yates
|
96fecb2bfc
|
Merge branch 'dev' into support-aligned-reads
|
2022-06-03 13:48:54 +02:00 |
|
James A. Fellows Yates
|
53c4399052
|
Merge branch 'dev' into motus
|
2022-06-02 21:38:35 +02:00 |
|
James A. Fellows Yates
|
c9581b1796
|
Merge branch 'dev' into support-aligned-reads
|
2022-06-02 12:45:29 +02:00 |
|
James Fellows Yates
|
d3d28da1b1
|
Update after review
|
2022-06-02 11:53:53 +02:00 |
|
James Fellows Yates
|
16ec5bf74a
|
Update parameter names
|
2022-05-31 20:11:19 +02:00 |
|
JIANHONG OU
|
f0eb88cbe2
|
add mOTUs to modules.config
|
2022-05-31 08:57:00 -04:00 |
|
JIANHONG OU
|
4d77b47e8d
|
create a new test profile config for mOTUs.
|
2022-05-31 08:47:38 -04:00 |
|
James Fellows Yates
|
310ac6b450
|
Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
|
2022-05-31 13:05:52 +02:00 |
|
JIANHONG OU
|
68d0cc00fa
|
add motus profile.
|
2022-05-23 08:05:06 -04:00 |
|
James A. Fellows Yates
|
d67543503b
|
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
|
2022-05-07 13:15:21 +02:00 |
|
James Fellows Yates
|
0f651873dd
|
Linting
|
2022-05-07 06:12:24 +02:00 |
|
James Fellows Yates
|
47a5ae0cff
|
Add FASTP complexity option
|
2022-05-07 06:09:05 +02:00 |
|
James Fellows Yates
|
87a1d80519
|
Add working output for Kraken2/Centrifuge/DIAMOND
|
2022-05-07 05:22:35 +02:00 |
|
ljmesi
|
6618e8cac6
|
Change param to a more generic name
|
2022-05-05 13:20:34 +02:00 |
|
ljmesi
|
557d31dfd2
|
Add parameter for turning on longread host removal
|
2022-05-05 13:19:10 +02:00 |
|
ljmesi
|
d94534e8ac
|
Simplify params which control host removal publish
|
2022-05-05 09:07:33 +02:00 |
|
ljmesi
|
a821f748ee
|
Add modules
|
2022-05-03 09:28:46 +02:00 |
|
James Fellows Yates
|
031cb45934
|
Add initial longread QC filtering - requires filtlong module update
|
2022-05-01 07:18:14 +02:00 |
|
James Fellows Yates
|
0630fce3b5
|
Tweak based on official DIAMOND test-data
|
2022-04-30 08:11:40 +02:00 |
|
James Fellows Yates
|
a4a9b161d8
|
Lintin
|
2022-04-29 22:02:44 +02:00 |
|
James Fellows Yates
|
8126d16dee
|
Add draft version of DIAMOND
|
2022-04-29 21:59:42 +02:00 |
|
sofstam
|
d082d67bcb
|
Add kaiju2table to taxprofiler
|
2022-04-25 17:36:29 +02:00 |
|
Sofia Stamouli
|
e7e24c2d95
|
Prettier and suggestions from review
|
2022-04-25 09:21:29 +02:00 |
|
sofstam
|
c00ca1c2b8
|
Add centrifuge kreport in taxprofiler
|
2022-04-22 15:24:10 +02:00 |
|
James A. Fellows Yates
|
63230c3254
|
Merge pull request #63 from nf-core/maxforks
Update test.config to only allow maxFork to 1 for MALT_RUN
|
2022-04-21 12:57:37 +02:00 |
|
James A. Fellows Yates
|
cd3c8f6a89
|
Merge branch 'dev' into hostremoval-publish-fix
|
2022-04-21 11:43:06 +02:00 |
|
James A. Fellows Yates
|
d850333e11
|
Linting
|
2022-04-20 13:42:26 +02:00 |
|
James A. Fellows Yates
|
d031322c16
|
Update test.config
|
2022-04-20 13:41:01 +02:00 |
|
Sofia Stamouli
|
236141f065
|
Resolve conflicts with dev
|
2022-04-20 10:17:10 +02:00 |
|
James A. Fellows Yates
|
d16cd75652
|
Merge branch 'dev' into hostremoval-publish-fix
|
2022-04-20 09:53:51 +02:00 |
|
sofstam
|
1b7ff2265d
|
Update usage.md, reformat test.config and modules.config
|
2022-04-19 13:04:58 +02:00 |
|
James Fellows Yates
|
9880baa0b8
|
Get build directory working
|
2022-04-18 06:37:23 +02:00 |
|
James Fellows Yates
|
2cfcdf2dd2
|
Add finer controler over for hostremoval saving
|
2022-04-17 22:27:04 +02:00 |
|
James Fellows Yates
|
cc73cdd51d
|
Add generation of taxon-table like output for MALT
|
2022-04-16 07:42:30 +02:00 |
|
sofstam
|
68ce5843a4
|
Add kaiju in taxprofiler
|
2022-04-13 18:51:56 +02:00 |
|
James A. Fellows Yates
|
5e80df0f94
|
Apply suggestions from code review
|
2022-04-13 15:27:53 +02:00 |
|
James Fellows Yates
|
aa2d07c42a
|
Fix merge cockup
|
2022-04-13 14:19:19 +02:00 |
|
James A. Fellows Yates
|
70f94603b0
|
Merge branch 'dev' into hostremoval
|
2022-04-13 13:59:51 +02:00 |
|
James Fellows Yates
|
dfeaa0d1fe
|
Rename subworkflow parameters for consistency
|
2022-04-13 12:00:28 +02:00 |
|
James A. Fellows Yates
|
967b1f7d6e
|
Merge branch 'dev' into run-merging
|
2022-04-12 09:28:10 +02:00 |
|
James Fellows Yates
|
a5f4fc42d5
|
Fix run merging for unmerged PE data
|
2022-04-12 09:25:27 +02:00 |
|
James A. Fellows Yates
|
025083061e
|
Merge branch 'dev' into hostremoval
|
2022-04-11 13:36:03 +02:00 |
|
James Fellows Yates
|
082093f3de
|
Prettier
|
2022-04-10 06:44:10 +02:00 |
|
James Fellows Yates
|
ecf0eea4f9
|
Move profiling to subworkflow and standardise outputs
|
2022-04-10 06:43:30 +02:00 |
|
James Fellows Yates
|
ca011ccc5b
|
Fix cat_fastq naming logic?
|
2022-04-08 13:28:37 +02:00 |
|
James Fellows Yates
|
d130a72d74
|
Get this working
|
2022-04-08 13:09:23 +02:00 |
|
Sofia Stamouli
|
48d28cf8d4
|
Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-04-08 10:00:10 +02:00 |
|
Sofia Stamouli
|
2dfe3b3cc1
|
Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-04-08 10:00:04 +02:00 |
|
sofstam
|
26779a4420
|
Remove db_name from nextflow.config
|
2022-04-07 16:27:19 +02:00 |
|
sofstam
|
606e5da7d5
|
Check if PR works with centrifuge/centrifuge module
|
2022-04-07 16:13:17 +02:00 |
|
James A. Fellows Yates
|
b554aa3e4d
|
Merge branch 'dev' into hostremoval
|
2022-04-07 14:00:10 +02:00 |
|
Moritz E. Beber
|
7ab3aa546b
|
refactor: use flags to publish reads
|
2022-04-06 10:27:11 +02:00 |
|
Moritz E. Beber
|
018b9a8ea6
|
refactor: do not generally publish output
|
2022-04-06 10:21:43 +02:00 |
|
Moritz E. Beber
|
8827b143a2
|
fix: disable publishing correctly
|
2022-04-05 20:56:19 +02:00 |
|
Moritz E. Beber
|
af12435fa5
|
fix: use parameter for publish mode everywhere
|
2022-04-05 20:56:19 +02:00 |
|
Moritz E. Beber
|
c40a9a0011
|
refactor: avoid publishing unpacked databases
|
2022-04-05 20:54:32 +02:00 |
|
James Fellows Yates
|
d46ddd972c
|
Expand tests and fix schema after review
|
2022-04-05 11:04:30 +02:00 |
|
James A. Fellows Yates
|
3d662d2e06
|
Merge branch 'dev' into complexity-filter-bbduk
|
2022-04-04 21:19:36 +02:00 |
|
James Fellows Yates
|
a384162810
|
Add prinseq as alternative complexity filtering
|
2022-04-04 21:16:51 +02:00 |
|
sofstam
|
d897c922b2
|
Add centrifuge classificatioN
|
2022-04-04 13:51:51 +02:00 |
|
James A. Fellows Yates
|
b2e29ea23a
|
Merge branch 'dev' into hostremoval
|
2022-04-03 17:24:07 +02:00 |
|
James Fellows Yates
|
066ceb2bca
|
Remove flagstat as bowtie2 reports this itself
|
2022-04-03 17:23:14 +02:00 |
|
James Fellows Yates
|
02d950c58c
|
Fix test so complexity filter actually executes
|
2022-04-02 17:18:20 +02:00 |
|
James Fellows Yates
|
7f1a7fb4e7
|
Add complexity filtering to test profile
|
2022-04-02 17:05:54 +02:00 |
|
James Fellows Yates
|
b055df5ea0
|
Add bbduk complexity (entropy-based) filtering
|
2022-04-02 17:02:05 +02:00 |
|
Moritz E. Beber
|
70862570e0
|
fix: use same naming scheme
|
2022-04-02 15:00:26 +02:00 |
|
Moritz E. Beber
|
817678d870
|
chore: add metaphlan3 run to test profile
|
2022-04-02 15:00:26 +02:00 |
|
Moritz E. Beber
|
b0b5936fe8
|
chore: configure output for metaphlan3
|
2022-04-02 15:00:26 +02:00 |
|
James Fellows Yates
|
dcda815bfb
|
Add final adapterremoval options to match fastp functionality
|
2022-04-01 09:50:08 +02:00 |
|
James Fellows Yates
|
76e9624e3f
|
NOW commit the adapte rtrim flag
|
2022-03-30 11:31:37 +02:00 |
|
James Fellows Yates
|
98a9688329
|
Change CPUs back to template, update skiptrim fiag
|
2022-03-29 15:18:06 +02:00 |
|
James Fellows Yates
|
04fb6f4127
|
Use new resources for test data
|
2022-03-28 20:38:16 +02:00 |
|
James Fellows Yates
|
94e5cfef4a
|
Filter long reads for MALT, bump cpus for FastQC for minigut to pass
|
2022-03-28 18:20:10 +02:00 |
|
James Fellows Yates
|
231253227c
|
Remove run merging for now due to complexity
|
2022-03-28 16:38:10 +02:00 |
|
James Fellows Yates
|
8dc9e583ad
|
Debugging run merging
|
2022-03-27 09:30:23 +02:00 |
|
James A. Fellows Yates
|
e6e8ed7cc9
|
Add some debugging notes
|
2022-03-26 20:54:50 +00:00 |
|
sofstam
|
37a70dc3e3
|
Merge branch 'dev' into classification_centrifuge
|
2022-03-25 16:18:35 +01:00 |
|
James Fellows Yates
|
ede362dbf9
|
Remove duplicate config and sync longread fastqc
|
2022-03-25 15:28:30 +01:00 |
|
James Fellows Yates
|
dfcf8f7b1a
|
Prettier
|
2022-03-25 15:10:52 +01:00 |
|
James Fellows Yates
|
ff1f28f4f0
|
Update schema
|
2022-03-25 15:01:25 +01:00 |
|
James Fellows Yates
|
4e93abc7c0
|
Add read improved read preprocessing
|
2022-03-25 14:58:06 +01:00 |
|
sofstam
|
3ff54e620e
|
Add centrifuge classification
|
2022-03-24 13:02:25 +01:00 |
|
James A. Fellows Yates
|
038a8d106a
|
Fix test with correct URL
|
2022-03-23 11:25:47 +01:00 |
|
James Fellows Yates
|
48b6ef508d
|
Update path to samplesheet
|
2022-03-23 10:06:01 +01:00 |
|
James Fellows Yates
|
358b89a4c6
|
Linting
|
2022-03-21 20:30:29 +01:00 |
|
James Fellows Yates
|
81bfb629ca
|
Add working basic test to begin
|
2022-03-21 20:28:09 +01:00 |
|
James A. Fellows Yates
|
3079f16861
|
Merge branch 'dev' into database-untar
|
2022-03-21 19:55:36 +01:00 |
|
James Fellows Yates
|
8012998542
|
Make parameter naming more consistent for clipmerge
|
2022-03-21 19:52:50 +01:00 |
|
James A. Fellows Yates
|
631c115e10
|
Adds PoC of untarring system
|
2022-03-21 14:58:19 +00:00 |
|
ljmesi
|
16be676d72
|
Add Porechop module
|
2022-03-18 14:34:10 +01:00 |
|
James A. Fellows Yates
|
ac77676d2b
|
Merge branch 'dev' into nf-core-template-merge-2.3
|
2022-03-17 13:11:34 +01:00 |
|
nf-core-bot
|
699d26b149
|
Template update for nf-core/tools version 2.3
|
2022-03-15 21:05:37 +00:00 |
|
James Fellows Yates
|
2c183ed2ed
|
Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue)
|
2022-03-03 17:42:02 +01:00 |
|
James Fellows Yates
|
cf55cc592c
|
Get skeleton read processing to input for profiling
|
2022-02-18 16:51:01 +01:00 |
|
James Fellows Yates
|
12e7b428f2
|
initial template build from nf-core/tools, version 2.2
|
2022-02-18 07:55:14 +01:00 |
|