3e411cc688
refactor: Switch to SRA direct download for samples
2023-10-19 11:39:20 -05:00
77535ee726
feat: Add parameter validation
2023-10-19 11:39:17 -05:00
eddf9d21f6
refactor: Change hard-coded reference into parameter
2023-10-19 11:39:16 -05:00
2f96ba4e44
feat!: Remove PREDICTHAPLO module
...
The developers no longer publish a single-end version of predicthaplo (see
https://github.com/cbg-ethz/PredictHaplo/issues/1 ). Since this pipeline is
targeting single-end read technologies, drop predicthaplo from the list.
2023-09-30 15:11:52 -05:00
355ce9a00a
feat: Add SHORAH processes to pipeline
2023-09-26 08:49:55 -05:00
444001b499
feat: Add QUASIRECOMB to pipeline
2023-09-26 08:49:54 -05:00
5cc8867799
feat: Add PREDICTHAPLO to pipeline
2023-09-26 08:49:24 -05:00
d8fee48c28
feat: Add CliqueSNV to pipeline
2023-09-26 08:49:22 -05:00
5ab64a8fea
feat: Add CliqueSNV haplotype calling to pipeline
2023-09-26 08:49:13 -05:00
002bd44975
refactor: Change output directory to match haplotypes
2023-09-26 08:49:10 -05:00
5162f649d8
refactor: Move HAPLINK_SEQUENCES module to its own file
2023-09-26 08:49:07 -05:00
52ca8f1528
refactor: Replace in-workflow HAPLINK processes with imported modules
2023-09-26 08:49:06 -05:00
db0255c54a
refactor: Move SHORAH_SHOTGUN to its own file
2023-09-26 08:49:02 -05:00
dbea6fb30a
refactor: Move SHORAH_AMPLICON to its own file
2023-09-23 16:09:21 -05:00
a9aa590f00
refactor: Move MINIMAP2 module to separate file
2023-09-23 16:05:02 -05:00
f157b0395e
refactor: Move NANOFILT module to its own file
2023-09-23 15:44:08 -05:00
b1ee784dac
refactor: Make reference genome an input for EFETCH
2023-09-23 15:38:55 -05:00
18875ae1a6
refactor: Move EFETCH module to its own file
2023-09-23 15:34:27 -05:00
2829d51533
refactor: Move HAPLINK_VARIANTS module to its own folder
2023-09-23 15:21:26 -05:00
9198d1186c
feat: Add ViQuas to main pipeline
2023-08-09 16:09:55 -05:00
ad10d46c87
feat: Add SHORAH_SHOTGUN process
2023-06-08 18:12:23 -05:00
feb051fc07
feat: Add SHORAH_AMPLICON process
2023-06-08 18:11:33 -05:00
7743bf31c6
feat: Import HapLink validation script
2023-06-08 17:55:57 -05:00
