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246 commits

Author SHA1 Message Date
James A. Fellows Yates
d9003924be
Merge pull request #201 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
James Fellows Yates
c8f6d713a3 Add tool names to end of prefix files for easier distinguishing in general stats 2023-01-16 14:49:44 +01:00
James Fellows Yates
d6fa45b500 update MultiQC and include latest modules 2023-01-16 14:39:52 +01:00
James A. Fellows Yates
25bb4304e8
Merge pull request #187 from nf-core/revert-pep
Revert PEP validation back to python samplesheet check
2022-12-20 15:03:18 +01:00
Sofia Stamouli
c23eb968f9 Remove TODOs from test configs 2022-12-16 15:20:06 +01:00
James Fellows Yates
9e6a91aff9 Distinguish Kraken2 from Bracken 2022-12-15 13:25:01 +01:00
James Fellows Yates
3b86a22556 Fix falco publication names 2022-12-15 12:57:49 +01:00
James Fellows Yates
88589fbc53 Fix publishing of log files of rpreprocessing steps 2022-12-15 10:35:06 +01:00
James A. Fellows Yates
578081df2e
Merge pull request #189 from nf-core/database-check
Adds (native groovy!) database check
2022-12-13 08:43:00 +01:00
James Fellows Yates
3df0a383da Update combine bracken outputs to include meta for publishing purposes 2022-12-12 10:10:24 +01:00
James Fellows Yates
07bd989bc6 Start work on groovy native datbase checks 2022-12-12 10:02:22 +01:00
James Fellows Yates
4b68e95770 Revert PEP validation back to python samplesheet check 2022-12-12 08:49:13 +01:00
James Fellows Yates
8939ce3e20 Start adding bracken/combinebrackenreports (need smodule update) 2022-12-11 16:52:34 +01:00
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
Sofia Stamouli
7e7299203c
Set values to false 2022-12-02 08:55:23 +01:00
sofstam
6d140c683a Merge branch 'dev' into update_motus 2022-12-01 18:49:23 +01:00
James A. Fellows Yates
80c25008d0
Merge pull request #177 from nf-core/sep-krakenuniq-test
Separate KrakenUniq test run
2022-12-01 17:34:30 +01:00
James A. Fellows Yates
a34b240dfc
Merge pull request #174 from nf-core/malt-update
Update MALT
2022-12-01 13:58:30 +01:00
James Fellows Yates
f960c14caf Fix typos 2022-12-01 13:46:57 +01:00
sofstam
38a818fd17 Apply review suggestions 2022-12-01 13:42:21 +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
sofstam
e5bb627402 Apply review suggestions 2022-12-01 11:12:31 +01:00
James Fellows Yates
bc98f5b80f Separate KrakenUniq test run 2022-12-01 10:37:14 +01:00
James A. Fellows Yates
4f6eb6fd75
Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
2022-12-01 09:03:29 +01:00
sofstam
933b820c19 Apply review suggestions 2022-11-29 16:57:07 +01:00
James Fellows Yates
d7fbe55849 Add KU to the test profiles and add id to KU processes 2022-11-29 14:19:01 +01:00
Sofia Stamouli
7e3ece53bd
Update modules.config 2022-11-29 13:31:00 +01:00
Sofia Stamouli
0088b07220
Fix trailing whitespace 2022-11-29 13:28:04 +01:00
James A. Fellows Yates
770a35d7ac
Update conf/modules.config 2022-11-29 12:49:20 +01:00
Sofia Stamouli
ba727a81ae Fix left-padding spaces 2022-11-29 12:45:14 +01:00
Sofia Stamouli
71b52b9c94 Apply review suggestions 2022-11-29 11:58:23 +01:00
sofstam
49af33f68e Include NCBI_id, read counts and mgc arguments in motus 2022-11-29 11:07:29 +01:00
James A. Fellows Yates
f114cc4122
Apply suggestions from code review 2022-11-24 16:55:19 +01:00
James A. Fellows Yates
17b1e3df1c
Update test.config 2022-11-24 16:53:39 +01:00
James Fellows Yates
a20b3e3c58 Try to reduce MALT memory 2022-11-24 15:51:12 +01:00
James Fellows Yates
9feb6c2db6 Update MALT 2022-11-24 14:44:04 +01:00
Sofia Stamouli
d2195e9eda
Merge branch 'dev' into short_reads_samtools 2022-11-04 11:47:36 +01:00
Sofia Stamouli
b5e6639f9d
Apply review suggestions 2022-11-03 14:12:05 +01:00
James A. Fellows Yates
bc671c547d
Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict
Fix porechop conflict
2022-11-03 14:08:13 +01:00
James A. Fellows Yates
1f31f88635
Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
2022-11-03 11:36:14 +01:00
James Fellows Yates
d487a1ff2f Addd FASTP adadapter list 2022-11-02 12:39:34 +01:00
Sofia Stamouli
e4307ad8ab Change modules.config to include porechop_porechop 2022-11-01 20:50:42 +01:00
Mahwash Jamy
febcbfc057 add missing parameters to nextflow.config 2022-10-31 16:07:53 +00:00
Mahwash Jamy
3147a80a56 Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module 2022-10-31 15:36:57 +00:00
Sofia Stamouli
0e0c55d3b0
Update modules.config 2022-10-31 12:35:51 +01:00
Sofia Stamouli
a4b5fa9f57
Fix trailing space 2022-10-31 12:17:49 +01:00
Sofia Stamouli
1d1047374b
Fix EditorConfig format 2022-10-31 12:09:25 +01:00
Sofia Stamouli
c4a7d094c8 Fix EditorConfig check 2022-10-28 14:33:44 +02:00
Sofia Stamouli
5b99d9024a Add samtools stats for short-reads 2022-10-28 14:24:33 +02:00
Sofia Stamouli
f87131c7b1 Save samtools stats output 2022-10-28 14:10:24 +02:00
Moritz E. Beber
bf89525bc2
Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
2022-10-27 17:35:06 +02:00
James A. Fellows Yates
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Mahwash Jamy
f4717be9ab add krakenuniq to modules.config 2022-10-25 09:50:44 +00:00
Moritz E. Beber
60e369aa5c fix: set default run bracken to false 2022-10-21 10:47:51 +02:00
Moritz E. Beber
c7c7a7f678 refactor: change Bracken prefix to be more specific 2022-10-19 16:20:09 +02:00
Sofia Stamouli
7881ba9aef Fix the amount of left-padding spaces 2022-10-18 17:50:49 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
767663d975 chore: add Bracken to test configs 2022-10-14 12:18:55 +02:00
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +02:00
James A. Fellows Yates
3ca9058b9c
Merge pull request #133 from rafalstepien/add-pep-support
Add working version of PEP-nf-core integration
2022-09-30 10:21:15 +02:00
James Fellows Yates
43a8aa4405 Remove detect_reads.py and replace remaining checks with nextflow code instead 2022-09-27 15:32:51 +02:00
Rafal Stepien
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -04:00
James A. Fellows Yates
016efcb807
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-16 16:02:38 +02:00
James Fellows Yates
4e7857e2ed Standardise mOTUs table merge 2022-09-16 08:36:34 +02:00
James A. Fellows Yates
cdb21d17b3
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-15 13:08:57 +02:00
James Fellows Yates
19a195ed14 Append profiler to resulting file 2022-09-15 12:30:39 +02:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James Fellows Yates
05e9d92444 Add centrigue kreports 2022-09-13 16:47:19 +02:00
James Fellows Yates
c8dbf5be47 Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU 2022-09-13 15:47:28 +02:00
James Fellows Yates
a764bc4807 Start works - need updated module though t have meta 2022-09-09 13:57:06 +02:00
James A. Fellows Yates
cc5df924e4
Merge branch 'dev' into module-update 2022-09-08 13:36:21 +02:00
James Fellows Yates
fc26948950 Fix MultiQC 2022-09-08 12:49:38 +02:00
James Fellows Yates
832d981976 Don't have per sample directory as unnecessary if file names are unique with the db in them 2022-09-07 12:22:17 +02:00
James Fellows Yates
7c5f9d0c24 Start work on more merging tools 2022-09-06 17:34:45 +02:00
James A. Fellows Yates
dd194f3f47 Fix mOTUs CI and old param warn 2022-09-04 15:01:58 +00:00
James A. Fellows Yates
13e9957e14 Fixes process selector warning 2022-09-02 06:03:05 +00:00
James A. Fellows Yates
f7b7fd63a4
Merge pull request #114 from nf-core/nf-core-template-merge-2.5
Important! Template update for nf-core/tools v2.5
2022-08-31 10:28:14 +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
James Fellows Yates
afba604e8b Make everything within opt-out, once QC is opted-in 2022-08-30 14:04:34 +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
a3055bf6da
Update conf/test_nothing.config 2022-08-23 15:48:02 +02:00
James Fellows Yates
e6c7939305 Add test_nothing config profile for minimal testing 2022-08-23 14:37:01 +02:00
James Fellows Yates
a97bb69cd2 Prettier 2022-08-23 14:24:57 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc
Trying to get Centrifuge output into MQC
2022-07-29 13:36:25 +02:00
mjamy
5cdf5e958a Updated modules.config to add 'log' in diamond config 2022-07-28 16:08:15 +02:00
sofstam
71cf32cc6a Add error strategy for centrifuge/kreport 2022-07-28 08:54:32 +02:00
James A. Fellows Yates
65ae82efc4 Define separte krakena nd centrigfue modules 2022-07-26 18:37:33 +00:00
James A. Fellows Yates
e76b299705 Start working getting kraken and centrifuge working in MQC 2022-07-26 08:18:54 +00:00
James Fellows Yates
a0ee82bf43 Add motus/merge and biom support 2022-07-12 11:39:26 +02:00
James A. Fellows Yates
8082c7d108
Merge pull request #97 from nf-core/malt-to-krona
Add Krona support for MALT
2022-07-05 15:17:52 +02:00
James A. Fellows Yates
26e31c782d
Merge branch 'dev' into motus 2022-07-04 13:14:42 +02:00
James Fellows Yates
447b8f0905 Get fixed Krona module and add Krona taxonomy to test profile 2022-07-01 17:21:19 +02:00
James Fellows Yates
02c06b9f7b Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file 2022-06-30 18:33:11 +02:00
069370db86
Add unclassified and verbose flags to kaiju2krona 2022-06-28 09:00:42 -05:00
18284e6e32
Add run_krona option to allow skipping Krona chart creation 2022-06-27 08:45:08 -05:00
0e8edd5b2f
Add output configuration for Kraken Krona chart 2022-06-27 08:25:47 -05:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +02:00