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176 commits 7 branches 0 tags 7.5 MiB
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53 commits

Author SHA1 Message Date
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 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
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 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