millironx/taxprofiler
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533 commits 7 branches 0 tags 7.5 MiB
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22 commits

Author SHA1 Message Date
Moritz E. Beber
f5af9fd939 fix: adjust import paths to re-organization 2022-10-05 13:40:43 +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 A. Fellows Yates
f48b22d615
Apply suggestions from code review 2022-07-29 09:52:49 +02:00
James A. Fellows Yates
64f01fcfe0
Merge branch 'dev' into porechop-log 2022-07-20 14:05:23 +02:00
James Fellows Yates
255afee4c7 Re-add the collects 2022-07-19 17:10:10 +02:00
Sofia Stamouli
237e9aa623
Update longread_preprocessing.nf 2022-07-19 16:44:08 +02:00
James A. Fellows Yates
8d7ddb5847
Apply suggestions from code review 2022-07-19 16:30:13 +02:00
sofstam
171258d545 Fix typos 2022-07-19 14:07:13 +02:00
sofstam
25bc01f9c4 Fix typos 2022-07-19 14:04:49 +02:00
sofstam
8147dba0b4 Fix typos 2022-07-19 14:03:10 +02:00
sofstam
526ed79763 Fix filtlong logs 2022-07-19 14:01:11 +02:00
sofstam
1ba6a08135 Seperate multiqc for filtlong 2022-07-19 13:53:29 +02:00
James Fellows Yates
33a5402b25 Add emitting porechop logs to multiqc and fix collection of others 2022-07-19 13:50:39 +02:00
sofstam
5a2fd260fd Log file into multiqc channel 2022-07-15 12:50:50 +02:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +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
b055df5ea0 Add bbduk complexity (entropy-based) filtering 2022-04-02 17:02:05 +02:00
James Fellows Yates
93aaa9eeac Clean up AdapterRemoval and remove all debugging dumps 2022-04-01 21:36:22 +02:00
James Fellows Yates
ede362dbf9 Remove duplicate config and sync longread fastqc 2022-03-25 15:28:30 +01:00
James Fellows Yates
b5f5c75504 Fix file header descriptions 2022-03-25 15:21:52 +01:00
ljmesi
1e42f1d9f2 Add long read preprocessing subworkflow 2022-03-18 15:10:44 +01:00