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857 commits 7 branches 0 tags 7.5 MiB
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51 commits

Author SHA1 Message Date
James Fellows Yates
2439aa69d0 Use specific samplesheet for MALT without LR reads due to GHA memory limits 2023-01-24 10:58:03 +01:00
Sofia Stamouli
d691b89727 Merge branch 'dev' into nf-core-template-merge-2.7.2 2022-12-20 15:14:41 +01:00
nf-core-bot
ab591e01ff Template update for nf-core/tools version 2.7.2 2022-12-19 12:10:58 +00:00
James Fellows Yates
dca0b86c78 Fix versions 2022-12-09 10:28:48 +01:00
James Fellows Yates
1ccd0a0767 Merge branch 'dev' into nf-core-template-merge-2.7.1 2022-12-09 10:16:17 +01:00
nf-core-bot
36f3b5723b Template update for nf-core/tools version 2.7.1 2022-12-08 13:18:23 +00:00
Moritz E. Beber
4529e7e545 refactor: change parameter exclude unmerged to include 2022-12-04 21:36:12 +01:00
James Fellows Yates
0a0dffa37c Try separating MALT 2022-12-04 12:06:33 +01:00
James A. Fellows Yates
ef1d2da179
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-12-01 12:53:34 +01:00
James Fellows Yates
bc98f5b80f Separate KrakenUniq test run 2022-12-01 10:37:14 +01:00
Moritz E. Beber
6b538d658a chore: let all tests run to completion 2022-11-22 10:13:10 +01:00
Sofia Stamouli
8c3e80b6ea Add helptest to nextflow_schema,add versions to longread_preprocessing 2022-10-25 11:13:26 +02:00
Sofia Stamouli
511cb16a61 Apply review suggestions 2022-10-20 16:55:57 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +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
James A. Fellows Yates
dd194f3f47 Fix mOTUs CI and old param warn 2022-09-04 15:01:58 +00:00
James A. Fellows Yates
331231ea28 Standardise CI execution 2022-09-04 14:02:54 +00:00
James Fellows Yates
c3427e44b3 Try with retries from sarek approach 2022-09-02 12:24:29 +02:00
James Fellows Yates
7917e1d656 Synronise mOTUs CI setup 2022-09-02 11:51:18 +02:00
James Fellows Yates
55d7919fa7 Revert "Update ci.yml" 
This reverts commit 176a0a6280.
 2022-09-02 11:48:57 +02:00
James Fellows Yates
c479714a5e Revert "Update ci.yml" 
This reverts commit 61560cf065.
 2022-09-02 11:48:49 +02:00
James A. Fellows Yates
61560cf065
Update ci.yml 2022-09-02 10:12:27 +02:00
James A. Fellows Yates
176a0a6280
Update ci.yml 2022-09-02 10:06:20 +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
JIANHONG OU
713a341e09 clean up ci.yml 2022-06-03 15:22:33 -04:00
JIANHONG OU
9fa6ecad56 debug for database csv file 2022-06-03 14:50:03 -04:00
JIANHONG OU
3cd3d2dad3 prettier write . 2022-06-03 14:38:59 -04:00
JIANHONG OU
22f65eedc7 fix the download address for downloadDB for mOTUs. 2022-06-03 14:16:25 -04:00
JIANHONG OU
c8a59adbce remove the database auto-download for mOTUs. 2022-06-03 14:13:58 -04:00
James A. Fellows Yates
53c4399052
Merge branch 'dev' into motus 2022-06-02 21:38:35 +02:00
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
Moritz E. Beber
a9fbe47992
Merge branch 'dev' into nf-core-template-merge-2.4 2022-05-19 08:42:28 +02:00
nf-core-bot
a560492353 Template update for nf-core/tools version 2.4 2022-05-16 10:22:38 +00:00
James Fellows Yates
3fa2181f49 Fix prinseq tool selection 2022-05-07 06:15:15 +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
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 Fellows Yates
29073e3c93 Update CI tests 2022-04-11 13:38:42 +02:00
James Fellows Yates
d130a72d74 Get this working 2022-04-08 13:09:23 +02:00
James Fellows Yates
7b08c49cd6 Re-add run merging and gonna let GHA see if it works >.> 2022-04-08 11:54:54 +02:00
James Fellows Yates
d46ddd972c Expand tests and fix schema after review 2022-04-05 11:04:30 +02:00
Moritz E. Beber
41526e8a64 try to fix locale 2022-04-02 15:44:39 +02:00
James Fellows Yates
0d0b377dfb Add additional test 2022-04-01 11:19:00 +02:00
nf-core-bot
feeb8ba8dd Template update for nf-core/tools version 2.3.2 2022-03-24 11:48:43 +00:00
nf-core-bot
6b939e6728 Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00
nf-core-bot
699d26b149 Template update for nf-core/tools version 2.3 2022-03-15 21:05:37 +00:00