38d779b1dc
fix: Use GitHub containers registry for HapLink modules
...
There are still issues with using the Biocontainers build of HapLink within
certain container platforms (cough, Singularity). Use the more exotic, but
more stable, one directly from the lab.
2023-09-30 16:19:28 -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
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
