James Fellows Yates
a634814d84
Formatting and fix fastp output
2022-04-08 13:34:00 +02:00
James Fellows Yates
d130a72d74
Get this working
2022-04-08 13:09:23 +02:00
James Fellows Yates
82aa89ad63
re add missing switch meta of merged reads to true
2022-04-05 13:55:11 +02:00
James Fellows Yates
98f082d7b6
Fix mistake in previous upstream merge with AR2 output channel for settings file
2022-04-05 13:17:54 +02:00
James A. Fellows Yates
23fb319779
Merge branch 'dev' into complexity-filter-bbduk
2022-04-05 13:11:15 +02:00
James Fellows Yates
245a4d1f5d
Fix MQC staging and remove debugging dump
2022-04-05 13:08:44 +02:00
Moritz E. Beber
39e5e802c7
refactor: make code more explicit, add comment
2022-04-05 11:29:39 +02:00
Moritz E. Beber
0e9b2989e3
refactor: remove superfluous ENSURE_FASTQ_EXTENSION
2022-04-05 10:53:04 +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
James Fellows Yates
d3572e1878
Final MQC fix for AR2 (remove too-early collect)
2022-04-03 07:28:01 +02:00
Moritz E. Beber
f5baf910be
Apply suggestions from code review
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-03 00:21:09 +02:00
Moritz E. Beber
be93eae640
fix: insert .fastq
file extension
...
The MetaPhlAn3 module computes the input type from the file extension
without the possibility to configure an override. Since AdapterRemoval2
creates files without `.fastq` extensions, MetaPhlAn3 input was determined
to be SAM.
2022-04-02 21:50:13 +02:00
Moritz E. Beber
4eab257d68
style: prettify comment
2022-04-02 17:05:46 +02:00
James Fellows Yates
b055df5ea0
Add bbduk complexity (entropy-based) filtering
2022-04-02 17:02:05 +02:00
Moritz E. Beber
a425a322f2
refactor: make metaphlan3 run in workflow
2022-04-02 14:59:44 +02:00
James Fellows Yates
93aaa9eeac
Clean up AdapterRemoval and remove all debugging dumps
2022-04-01 21:36:22 +02:00
James A. Fellows Yates
03e832954f
Update subworkflows/local/shortread_adapterremoval.nf
...
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-04-01 20:55:33 +02:00
James A. Fellows Yates
14f2b7bd84
Apply suggestions from code review
...
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-04-01 15:34:05 +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 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
622fafedc8
Prempt centrifuge database untar crash
2022-03-26 20:22:35 +00:00
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
4e93abc7c0
Add read improved read preprocessing
2022-03-25 14:58:06 +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
07eed435c6
Replace set with explicity assignment
2022-03-21 19:54:51 +01:00
James Fellows Yates
8012998542
Make parameter naming more consistent for clipmerge
2022-03-21 19:52:50 +01:00
ljmesi
5b1b48e59e
Update subworkflow name to be more consistent
2022-03-21 18:29:47 +01:00
ljmesi
f6fe26de46
Rename shortread subworkflow to be more consistent
2022-03-21 18:25:56 +01:00
James A. Fellows Yates
631c115e10
Adds PoC of untarring system
2022-03-21 14:58:19 +00:00
James Fellows Yates
c7f022008c
Start getting database prep ready
2022-03-21 15:07:59 +01:00
ljmesi
1e42f1d9f2
Add long read preprocessing subworkflow
2022-03-18 15:10:44 +01:00
ljmesi
41b3d8db82
Add nanopore channel
2022-03-18 10:47:41 +01:00
ljmesi
0f0ed6cd46
Fix function name
2022-03-18 10:45:06 +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
James Fellows Yates
278f5605ca
Added database preparation and final channel for profiling
2022-02-19 12:36:08 +01:00
James Fellows Yates
cf55cc592c
Get skeleton read processing to input for profiling
2022-02-18 16:51:01 +01:00
James Fellows Yates
12e7b428f2
initial template build from nf-core/tools, version 2.2
2022-02-18 07:55:14 +01:00