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1037 commits 7 branches 0 tags 7.5 MiB
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Author SHA1 Message Date
James Fellows Yates
df4f13319f More linting 2022-04-01 11:13:57 +02:00
James Fellows Yates
b04cfec2c2 Prettier linting 2022-04-01 11:13:36 +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 A. Fellows Yates
323883bd3e
Merge pull request #33 from nf-core/improve-shortread-input 
Improve shortread input preprocessing
 2022-03-30 11:48:32 +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
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
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
eada201eb2 Prettier 2022-03-28 16:47:37 +02:00
James Fellows Yates
98dc8014a5 Fix kraken2 module 2022-03-28 16:46:45 +02:00
James Fellows Yates
231253227c Remove run merging for now due to complexity 2022-03-28 16:38:10 +02:00
sofstam
0e0e8128e8 Prettier format 2022-03-28 13:53:16 +02:00
James Fellows Yates
ee53283696 Debugging comment 2022-03-28 09:13:05 +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
James A. Fellows Yates
622fafedc8 Prempt centrifuge database untar crash 2022-03-26 20:22:35 +00:00
James Fellows Yates
120382f51d Fix input channels to kraken2 2022-03-26 06:45:16 +01:00
sofstam
59d3f18a75 Update nextflow_schema.json 2022-03-25 17:18:04 +01:00
sofstam
16bdc79cc0 Apply prettier 2022-03-25 16:30:26 +01:00
sofstam
37a70dc3e3 Merge branch 'dev' into classification_centrifuge 2022-03-25 16:18:35 +01:00
James A. Fellows Yates
000f129dab
Apply suggestions from code review 2022-03-25 15:32:56 +01:00
James Fellows Yates
ede362dbf9 Remove duplicate config and sync longread fastqc 2022-03-25 15:28:30 +01:00
James Fellows Yates
b763bfa2c0 More cleanup 2022-03-25 15:26:57 +01:00
James Fellows Yates
0e6f7e2ca1 Revert "Some more cleanup" 
This reverts commit 7ddcb09a85.
 2022-03-25 15:24:10 +01:00
James Fellows Yates
7ddcb09a85 Some more cleanup 2022-03-25 15:22:41 +01:00
James Fellows Yates
b5f5c75504 Fix file header descriptions 2022-03-25 15:21:52 +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 A. Fellows Yates
fafb7e0f6f
Update README.md 2022-03-24 16:59:12 +01:00
James A. Fellows Yates
f3c21203c8
Merge pull request #32 from nf-core/nf-core-template-merge-2.3.2 
Important! Template update for nf-core/tools v2.3.2
 2022-03-24 15:50:38 +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 Fellows Yates
203cd2e7d3 Prettier 2022-03-24 14:31:53 +01:00
James Fellows Yates
e3be393f16 Fix broken json 2022-03-24 14:18:15 +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
sofstam
3ff54e620e Add centrifuge classification 2022-03-24 13:02:25 +01:00
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
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
cd9e3c604c
Merge pull request #30 from nf-core/database-untar 
Adds ability to conditionally untar databases TAR files that contain DB directories
 2022-03-21 19:56:22 +01:00
James A. Fellows Yates
3079f16861
Merge branch 'dev' into database-untar 2022-03-21 19:55:36 +01:00
James Fellows Yates
07eed435c6 Replace set with explicity assignment 2022-03-21 19:54:51 +01:00