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244 commits

Author SHA1 Message Date
James A. Fellows Yates
ee76a5f38b
Update conf/modules.config
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-04-21 13:44:03 +02:00
James Fellows Yates
31e3c21dcb Make all saveAs conditions consistent 2023-04-20 15:10:39 +02:00
James Fellows Yates
5d90c775e9 Logic safety! 2023-04-20 14:59:07 +02:00
James A. Fellows Yates
0245c4880b
Merge branch 'dev' into final-reads-saving 2023-04-20 14:18:10 +02:00
James Fellows Yates
94e88d788d Everywhere account when no-runmerging for single libs 2023-04-04 18:36:37 +02:00
James Fellows Yates
e5e0aab59d More tweaks 2023-04-04 16:29:37 +02:00
James Fellows Yates
ca9c0cf8fd Further fixes 2023-04-04 15:52:23 +02:00
sofstam
e274823f73 Add conf for samtools/fastq 2023-03-27 12:42:28 +02:00
James Fellows Yates
6895e45768 Fix a few conditional bugs and related 2023-03-23 15:46:02 +01:00
James Fellows Yates
3b90064ba4 Start adding conditions in modules.conf - non-cat not working 2023-03-22 15:39:45 +01:00
James A. Fellows Yates
142ff2f099
Apply suggestions from code review 2023-03-17 10:26:38 +01:00
James Fellows Yates
577d270423 Deactivate saving of reads and other large files for full tests 2023-03-17 10:14:40 +01:00
James Fellows Yates
8ca9fad3b1 move errorStrategy to config 2023-03-07 11:09:25 +01:00
James Fellows Yates
b5a2983c5f Make modules entries consistent 2023-03-07 11:06:35 +01:00
James Fellows Yates
a5138ed6e0 Fix ugly warn when KAIJU2TABLE not run 2023-03-06 08:17:50 +01:00
James A. Fellows Yates
6c2ce4a1c9
Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-03-03 08:37:31 +01:00
James Fellows Yates
5c549e5ce3 Remove TODOs and references to under development 2023-03-02 13:49:03 +01:00
Sofia Stamouli
d96e0a17a5
Update conf/modules.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-02-27 10:39:10 +01:00
sofstam
2f0c68a833 Last review suggestions 2023-02-27 10:15:42 +01:00
sofstam
a7ae57c94e Fix linting 2023-02-24 15:53:54 +01:00
sofstam
e18e68faa5 Apply review suggestion 2023-02-24 15:50:24 +01:00
sofstam
5dc3cbc278 Rename taxonomy argument 2023-02-24 13:04:38 +01:00
sofstam
5a6fcf1f42 Update taxpasta/merge to version 0.2.0 and add taxonomy argument 2023-02-24 11:44:07 +01:00
James A. Fellows Yates
9847b8d9a7
Fix label base.config for MEGAN_RMA2INFO 2023-02-20 20:35:22 +01:00
sofstam
04bc978ef6 Remove taxonomy parameter from taxpasta 2023-02-20 11:56:06 +01:00
sofstam
90a5668007 run_malt false in test and add text in output.md 2023-02-17 15:38:36 +01:00
sofstam
f0aa89cb87 Rename taxpasta parameters and remove samplesheet parameter 2023-02-17 14:47:29 +01:00
sofstam
27b7171b96 Apply review suggestions 2023-02-17 09:16:58 +01:00
sofstam
2456038567 Merge branch 'dev' into add_taxpasta_merge 2023-02-16 15:07:51 +01:00
sofstam
de6a4214ef Add taxpasta_merge to taxprofiler 2023-02-16 14:29:52 +01:00
James Fellows Yates
7dfcdd015b Re-add the 'native' combined kaiju output 2023-02-16 14:02:13 +01:00
James Fellows Yates
79b4db9a34 Move kaiju2table to profiling 2023-02-16 13:39:05 +01:00
James Fellows Yates
ce1118930d Resource optimisation 2023-02-09 13:33:39 +01:00
James Fellows Yates
cc7d219267 Revert "optimisation for single-cpu processes"
This reverts commit a731669b8e.
2023-02-09 13:32:29 +01:00
James Fellows Yates
a731669b8e optimisation for single-cpu processes 2023-02-09 13:31:57 +01:00
James A. Fellows Yates
45ac6fedc2
Merge pull request from nf-core/bracken-params
Support Kraken and Bracken db_params in database sheet
2023-02-09 10:59:27 +01:00
James A. Fellows Yates
70eb84b8d5
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2023-02-09 08:01:52 +01:00
James Fellows Yates
18886c0cbc Start trying a different method with maps in profiling 2023-02-07 15:51:25 +01:00
James Fellows Yates
059cd17114 Fix exporting of mapped/unmapped reads for consistency across both short and long reads 2023-02-07 11:43:40 +01:00
sofstam
5363274867 Add some last documentation 2023-02-02 13:58:48 +01:00
James Fellows Yates
7ce55a99e8 Fix linting 2023-02-02 13:08:16 +01:00
James A. Fellows Yates
c4e366d47d
Add full test data and documentation of the test data 2023-02-02 11:59:26 +01:00
James A. Fellows Yates
1d7da61801
Merge pull request from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
2023-01-30 11:25:28 +01:00
James A. Fellows Yates
098ec087c9
Merge pull request from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
2023-01-25 13:48:06 +01:00
James Fellows Yates
a993300099 Tweaks to MultiQC based on full test experiments 2023-01-24 15:06:42 +01:00
James Fellows Yates
e7d7affcd0 Pick up Kraken2 files correctly 2023-01-24 14:44:14 +01:00
Moritz E. Beber
40f1e7b27a fix: correct pattern to publish minimap2 index 2023-01-24 14:15:51 +01:00
James Fellows Yates
1c820f21b3 Dont fail on divide by 0 errors on centrifuge 2023-01-20 17:53:55 +01:00
James A. Fellows Yates
d9003924be
Merge pull request from genomic-medicine-sweden/removo_todo
Remove TODOs from test configs
2023-01-19 13:15:14 +01:00
James Fellows Yates
92dff9b453 Standardise file names using only underscore 2023-01-17 10:58:30 +01:00