millironx/taxprofiler
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553 commits 7 branches 0 tags 7.5 MiB
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112 commits

Author SHA1 Message Date
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
Moritz E. Beber
e579f9f5f3 style: apply prettier 2022-04-02 14:59:44 +02:00
Moritz E. Beber
fb9afa013a fix: add metaphlan parameter to schema 2022-04-02 14:59:44 +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
c4c93bd59d Start working on adding adapterremoval 2022-03-31 15:31:45 +02:00
James Fellows Yates
76e9624e3f NOW commit the adapte rtrim flag 2022-03-30 11:31:37 +02:00
Sofia Stamouli
c552819c72 Apply prettier again 2022-03-28 22:15:31 +02:00
sofstam
d25f97c506 Prettier format 2022-03-28 22:08:05 +02:00
sofstam
0e0e8128e8 Prettier format 2022-03-28 13:53:16 +02:00
sofstam
59d3f18a75 Update nextflow_schema.json 2022-03-25 17:18:04 +01:00
sofstam
37a70dc3e3 Merge branch 'dev' into classification_centrifuge 2022-03-25 16:18:35 +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
James Fellows Yates
92a3c8ec8d Prettier 2022-03-24 15:40:14 +01:00
James Fellows Yates
494c641fb8 Prettier 2022-03-24 15:37:42 +01:00
James Fellows Yates
cc9368ee52 Prettier linting and update schema 2022-03-24 15:35:09 +01:00
James A. Fellows Yates
edce6603ef
Merge branch 'dev' into nf-core-template-merge-2.3.2 2022-03-24 14:10:58 +01:00
nf-core-bot
6b939e6728 Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00
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
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