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
588d307ff6
fix: Remove invalid shorah parameter
...
It turns out that -t threads only works for shorah shotgun, not shorah
amplicon. Remove the invalid parameter.
2023-09-29 14:17:39 -05:00
b98a797701
feat: Add control flow for choosing haplotypers
2023-09-26 08:49:57 -05:00
9364225e74
fix: Change input cardinality on haplotyping modules
2023-09-26 08:49:56 -05:00
029f3a5126
feat: Add PREDICTHAPLO module
2023-09-26 08:49:23 -05:00
3e6a0ca5df
feat: Add QuasiRecomb module
2023-09-26 08:49:14 -05:00
de853c2d22
feat: Add CliqueSNV module
2023-09-26 08:49:12 -05:00
5c4d02263b
refactor: Replace custom publish dirs with reference to task.process
2023-09-26 08:49:11 -05:00
002bd44975
refactor: Change output directory to match haplotypes
2023-09-26 08:49:10 -05:00
4751203579
feat: Add container directive to HAPLINK_SEQUENCES
2023-09-26 08:49:09 -05:00
095aff629d
refactor: Replace performance directives with process label
2023-09-26 08:49:09 -05:00
517b8eb66b
feat: Add method/prefix tag to HAPLINK_SEQUENCES
2023-09-26 08:49:08 -05:00
5162f649d8
refactor: Move HAPLINK_SEQUENCES module to its own file
2023-09-26 08:49:07 -05:00
47500bc986
feat: Add new HAPLINK_HAPLOTYPES module
2023-09-26 08:49:05 -05:00
abfed449f6
feat: Add prefix tag to SHORAH_SHOTGUN
2023-09-26 08:49:03 -05:00
db0255c54a
refactor: Move SHORAH_SHOTGUN to its own file
2023-09-26 08:49:02 -05:00
f6111f27c2
feat: Add prefix tag to SHORAH_AMPLICON
2023-09-23 16:09:47 -05:00
dbea6fb30a
refactor: Move SHORAH_AMPLICON to its own file
2023-09-23 16:09:21 -05:00
89323bf2c6
refactor: Replace MINIMAP2 performance directives with process label
2023-09-23 16:06:12 -05:00
b08d9df6a9
feat: Add prefix tag to MINIMAP2
2023-09-23 16:05:29 -05:00
a9aa590f00
refactor: Move MINIMAP2 module to separate file
2023-09-23 16:05:02 -05:00
d12a8b77d8
refactor: Replace NANOFILT performance directives with process label
2023-09-23 15:45:34 -05:00
461a4b64a3
feat: Add prefix tag to NANOFILT module
2023-09-23 15:44:40 -05:00
f157b0395e
refactor: Move NANOFILT module to its own file
2023-09-23 15:44:08 -05:00
0e822c2729
feat: Add genome tag to EFETCH
2023-09-23 15:43:10 -05:00
ec4414184b
refactor: Change output file name of EFETCH
2023-09-23 15:39:21 -05:00
b1ee784dac
refactor: Make reference genome an input for EFETCH
2023-09-23 15:38:55 -05:00
7a3744a3d3
refactor: Replace EFETCH performance directives with process label
2023-09-23 15:36:01 -05:00
18875ae1a6
refactor: Move EFETCH module to its own file
2023-09-23 15:34:27 -05:00
2c755dcd4f
refactor: Replace hard-coded performance directives with process label
2023-09-23 15:27:05 -05:00
cc433aaffe
feat: Add container directive to HAPLINK_VARIANTS
2023-09-23 15:23:45 -05:00
a223b87464
feat: Add tag directive to HAPLINK_VARIANTS module
2023-09-23 15:22:13 -05:00
2829d51533
refactor: Move HAPLINK_VARIANTS module to its own folder
2023-09-23 15:21:26 -05:00
1e741e1db1
fix: Copy over every directory in @INC
2023-08-10 23:17:21 -05:00
eb7cd4e382
fix: Remove undefined POSIX behavior
2023-08-09 23:39:02 -05:00
054c1853f5
fix: Change permissions on ViQuaS install
2023-08-09 23:36:24 -05:00
a4478cdf7f
fix: Add ps to final container
2023-08-09 23:25:43 -05:00
ebcbb53cb1
refactor: Switch to multi-stage build
2023-08-09 23:21:33 -05:00
58759e3314
fix: Add user permissions to ViQuas folder
2023-08-09 18:17:45 -05:00
0997616190
refactor: Add container declaration to ViQuas module
2023-08-09 18:09:31 -05:00
d0b25c41b9
fix: Add BAM index to ViQuas input
2023-08-09 17:53:07 -05:00
1e20488409
feat: Add ViQuas module
2023-08-09 16:07:54 -05:00
108fb0dc5b
refactor: Minimize Dockerfile layers
2023-08-09 16:02:46 -05:00
a1d0348697
feat: Create working Dockerfile for ViQuas
2023-08-09 15:28:35 -05:00
