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cutadapt #7

Merged
merged 41 commits into from
Jun 21, 2024
Merged

cutadapt #7

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954f8dc
First commit, clone of cutadapt in htrnaseq + help.txt
tverbeiren Jan 26, 2024
be3fb5a
Add config
tverbeiren Jan 30, 2024
ab57de3
Merge remote-tracking branch 'origin/main' into dev/cutadapt
rcannood Jan 30, 2024
0de2a36
Don't allow multiple: true when providing a FASTA file with adapters
tverbeiren Feb 6, 2024
e0685a5
First version of script
tverbeiren Feb 7, 2024
f67eeac
Merge remote-tracking branch 'origin/dev/cutadapt' into dev/cutadapt
tverbeiren Feb 7, 2024
b93f95c
Updates and fixes - se/pe
tverbeiren Feb 7, 2024
ac6e1c2
Add tests and fix --json argument
tverbeiren Feb 9, 2024
e68a038
Add software version
tverbeiren Feb 9, 2024
b2d3914
Better consistency in using snake_case
tverbeiren Feb 13, 2024
da46e66
Update src/cutadapt/config.vsh.yaml
tverbeiren Feb 13, 2024
e714e67
Update src/cutadapt/config.vsh.yaml
tverbeiren Feb 13, 2024
365215d
Update src/cutadapt/config.vsh.yaml
tverbeiren Feb 13, 2024
94ad54d
Specify --input and --input_r2 as separate arguments
tverbeiren Feb 13, 2024
d5af57e
Avoid specifying default arg values
tverbeiren Feb 13, 2024
8b6aa30
Add more information to `--minimum_length` and `maximum_length`
tverbeiren Feb 16, 2024
99b4f01
Add --cpus by means of $meta_cpus and set proper default
tverbeiren Feb 16, 2024
c864e5e
Allow multiple for adapters/fasta and add test
tverbeiren Feb 16, 2024
44d98ba
change multiple_sep to ';'
rcannood Feb 22, 2024
550d026
add example
rcannood Feb 22, 2024
65b47de
simplify code with a helper function
rcannood Feb 22, 2024
2f187ce
create directories in test
rcannood Feb 22, 2024
986a090
use a different output extension if --fasta is provided
rcannood Feb 22, 2024
6b76604
decrease code duplication by separating optional outputs from paired/…
rcannood Feb 22, 2024
4601f21
write custom tests for cutadapt
rcannood Feb 22, 2024
45d1989
fix _r2 arguments
rcannood Feb 22, 2024
22f99c6
add debug flag as not to always print the cli command
rcannood Feb 22, 2024
9f248c4
Merge remote-tracking branch 'origin/main' into dev/cutadapt
rcannood Feb 24, 2024
19da124
Merge branch 'dev/cutadapt' into dev/cutadapt_pr
rcannood Feb 24, 2024
8370251
remove comment
rcannood Feb 24, 2024
35e7f3c
Merge pull request #26 from viash-hub/dev/cutadapt_pr
rcannood Feb 27, 2024
d927b5e
Merge remote-tracking branch 'origin/main' into dev/cutadapt
tverbeiren Feb 28, 2024
e948215
Merge remote-tracking branch 'origin/main' into dev/cutadapt
tverbeiren Jun 5, 2024
e3204f9
Update to Viash 0.9.0-RC4
tverbeiren Jun 5, 2024
f399e38
Ability to specify output globbing patterns
tverbeiren Jun 5, 2024
58a9ec7
Avoid the need for both output_dir and output
tverbeiren Jun 6, 2024
d519a14
Move fields from `info` to `links`
tverbeiren Jun 7, 2024
200aa65
Move references back to the info field
tverbeiren Jun 7, 2024
9b89ace
Merge remote-tracking branch 'origin/main' into dev/cutadapt
rcannood Jun 21, 2024
417a559
apologies, I proposed a wrong syntax
rcannood Jun 21, 2024
00c97ae
Merge remote-tracking branch 'origin/main' into dev/cutadapt
rcannood Jun 21, 2024
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