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172 commits

Author SHA1 Message Date
James Fellows Yates
c5e5696f84 Fix parameter name 2022-11-03 14:58:03 +01:00
James Fellows Yates
21a76c2449 Fix cardinality issue 2022-11-03 14:56:26 +01:00
James Fellows Yates
6459d8920f Linting! 2022-11-03 14:05:43 +01:00
James A. Fellows Yates
1f31f88635
Merge pull request #158 from nf-core/adapterremoval-fix 
Fix adapterremoval adapter conflict and add optional adapter list file
 2022-11-03 11:36:14 +01:00
James A. Fellows Yates
24dc2a2cec
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-11-03 10:03:07 +01:00
James Fellows Yates
d487a1ff2f Addd FASTP adadapter list 2022-11-02 12:39:34 +01:00
Mahwash Jamy
851016e497 Update nextflow_scheme.json 2022-10-31 16:17:40 +00:00
Moritz E. Beber
bf89525bc2
Merge pull request #146 from nf-core/feat-bracken 
add Bracken to the profiling workflow
 2022-10-27 17:35:06 +02:00
nf-core-bot
a402ee3be2 [automated] Fix linting with Prettier 2022-10-27 12:20:08 +00:00
James A. Fellows Yates
733d3dc8c5
Apply suggestions from code review 2022-10-27 14:19:28 +02:00
James A. Fellows Yates
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Sofia Stamouli
de6816ec49
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-25 11:19:16 +02:00
Sofia Stamouli
7b1a53b062
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-25 11:19:08 +02:00
Sofia Stamouli
8c3e80b6ea Add helptest to nextflow_schema,add versions to longread_preprocessing 2022-10-25 11:13:26 +02:00
Sofia Stamouli
19231538da Prettier 2022-10-20 16:59:32 +02:00
Sofia Stamouli
511cb16a61 Apply review suggestions 2022-10-20 16:55:57 +02:00
Sofia Stamouli
0481bb9449 Prettier 2022-10-18 17:48:40 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
9dc819ceff style: reformat schema 2022-10-14 13:16:54 +02:00
Moritz E. Beber
c4f6468275 chore: update parameters schema 2022-10-14 12:55:26 +02:00
Moritz E. Beber
fdb8a7f740 Merge branch 'devel' into nf-core-template-merge-2.6 2022-10-05 12:21:54 +02:00
nf-core-bot
51bacb00e6 Template update for nf-core/tools version 2.6 2022-10-05 03:30:53 +00:00
Rafal Stepien
bfd260e9c8 Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-28 12:40:43 -04:00
Rafal Stepien
0ccbf50938
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 09:49:37 -04:00
Rafal Stepien
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -04:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James Fellows Yates
806208c4b1 Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected 2022-08-31 08:30:26 +02:00
James Fellows Yates
acd0570b4a Finalise first pass of nextflow json documentation 2022-08-31 07:56:39 +02:00
James Fellows Yates
bdcae4f934 More docs and tweat to usage.md 2022-08-30 16:04:05 +02:00
James Fellows Yates
c2eaa3f6b0 Prettier 2022-08-30 14:33:40 +02:00
James Fellows Yates
d19a473c59 Merge branch 'filtlong-in-tests' into json-schema 2022-08-30 14:33:19 +02:00
James Fellows Yates
8917e29e35 Fix accidental overly zelous search-and-replace 2022-08-30 14:11:48 +02:00
James Fellows Yates
3f8f32cba8 Make longread quality ftilering opt out 2022-08-30 14:08:05 +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 Fellows Yates
d4af88e3ff Make kaiju parameter clearer for documentation purpses and update documentation 2022-08-25 15:50:28 +02:00
James Fellows Yates
d6d51e0e43 Start work on reordering json schema parameters 2022-08-24 15:23:51 +02:00
James Fellows Yates
d8c0e9e7fe Prettier 2022-07-12 11:41:07 +02:00
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
97e6cdf4b4 Add Krona taxonomy DB to schema build 2022-06-30 18:36:13 +02:00
James Fellows Yates
af854f5f34 Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files 2022-06-28 12:42:41 +02:00
Thomas A. Christensen II
18284e6e32
Add run_krona option to allow skipping Krona chart creation 2022-06-27 08:45:08 -05:00
JIANHONG OU
c8a59adbce remove the database auto-download for mOTUs. 2022-06-03 14:13:58 -04:00
James Fellows Yates
3313b90453 Fix JSOn schema 2022-06-03 13:50:48 +02:00
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 Fellows Yates
2838c136bd Prettier 2022-06-02 12:51:39 +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
792e2d019b Fix merge error in schema 2022-05-31 13:06:48 +02:00
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 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
c833d4fd9a Fix issues found with prettier 2022-05-03 11:42:05 +02:00
ljmesi
17039ebc6b Fix type to boolean for flags 2022-05-03 11:07:23 +02:00
ljmesi
fa1c132635 Update nextflow_schema 2022-05-03 11:03:25 +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
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
Sofia Stamouli
194b89e66a Prettier 2022-04-26 12:53:39 +02:00
Sofia Stamouli
7afda265c5 Enumerating taxon 2022-04-26 11:27:18 +02:00
Sofia Stamouli
f4480feb9b Prettier 2022-04-25 17:45:26 +02:00
sofstam
d082d67bcb Add kaiju2table to taxprofiler 2022-04-25 17:36:29 +02:00
James A. Fellows Yates
cd3c8f6a89
Merge branch 'dev' into hostremoval-publish-fix 2022-04-21 11:43:06 +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
Sofia Stamouli
4e1b1269be Apply prettier 2022-04-19 13:11:43 +02:00
James Fellows Yates
b036ed5b73 Prettier 2022-04-17 22:28:18 +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
0e5c9e7bdd Type:boolean for kaiju in nextflow_schema.json 2022-04-14 09:14:05 +02:00
sofstam
6736a2a980 Update README.md, nextflow_schema.json 2022-04-13 19:00:52 +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 A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval 2022-04-11 13:36:03 +02:00
James Fellows Yates
a634814d84 Formatting and fix fastp output 2022-04-08 13:34:00 +02:00
James Fellows Yates
ca011ccc5b Fix cat_fastq naming logic? 2022-04-08 13:28:37 +02:00
Sofia Stamouli
3d45ac57ae Prettier 2022-04-07 16:42:22 +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
James Fellows Yates
d46ddd972c Expand tests and fix schema after review 2022-04-05 11:04:30 +02:00
James Fellows Yates
bb6dd738bd Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk 2022-04-04 21:21:34 +02:00
James Fellows Yates
613f6a5565 Prettier 2022-04-04 21:21:29 +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
3a56206513 Centrifuge classification 2022-04-04 16:55:48 +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
b055df5ea0 Add bbduk complexity (entropy-based) filtering 2022-04-02 17:02:05 +02:00