millironx/haplotyper-battle-royale
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Author SHA1 Message Date
Thomas A. Christensen II
b98a797701
feat: Add control flow for choosing haplotypers 2023-09-26 08:49:57 -05:00
Thomas A. Christensen II
9364225e74
fix: Change input cardinality on haplotyping modules 2023-09-26 08:49:56 -05:00
Thomas A. Christensen II
355ce9a00a
feat: Add SHORAH processes to pipeline 2023-09-26 08:49:55 -05:00
Thomas A. Christensen II
444001b499
feat: Add QUASIRECOMB to pipeline 2023-09-26 08:49:54 -05:00
Thomas A. Christensen II
5cc8867799
feat: Add PREDICTHAPLO to pipeline 2023-09-26 08:49:24 -05:00
Thomas A. Christensen II
029f3a5126
feat: Add PREDICTHAPLO module 2023-09-26 08:49:23 -05:00
Thomas A. Christensen II
d8fee48c28
feat: Add CliqueSNV to pipeline 2023-09-26 08:49:22 -05:00
Thomas A. Christensen II
96471746b9
feat: Replace hard-coded singularity with profile-based containers 2023-09-26 08:49:20 -05:00
Thomas A. Christensen II
7f43f0282f
feat: Add nf-core resource allocation parameters 2023-09-26 08:49:17 -05:00
Thomas A. Christensen II
137804518f
feat: Add nf-core config parameters 2023-09-26 08:49:16 -05:00
Thomas A. Christensen II
3e6a0ca5df
feat: Add QuasiRecomb module 2023-09-26 08:49:14 -05:00
Thomas A. Christensen II
5ab64a8fea
feat: Add CliqueSNV haplotype calling to pipeline 2023-09-26 08:49:13 -05:00
Thomas A. Christensen II
de853c2d22
feat: Add CliqueSNV module 2023-09-26 08:49:12 -05:00
Thomas A. Christensen II
5c4d02263b
refactor: Replace custom publish dirs with reference to task.process 2023-09-26 08:49:11 -05:00
Thomas A. Christensen II
002bd44975
refactor: Change output directory to match haplotypes 2023-09-26 08:49:10 -05:00
Thomas A. Christensen II
4751203579
feat: Add container directive to HAPLINK_SEQUENCES 2023-09-26 08:49:09 -05:00
Thomas A. Christensen II
095aff629d
refactor: Replace performance directives with process label 2023-09-26 08:49:09 -05:00
Thomas A. Christensen II
517b8eb66b
feat: Add method/prefix tag to HAPLINK_SEQUENCES 2023-09-26 08:49:08 -05:00
Thomas A. Christensen II
5162f649d8
refactor: Move HAPLINK_SEQUENCES module to its own file 2023-09-26 08:49:07 -05:00
Thomas A. Christensen II
52ca8f1528
refactor: Replace in-workflow HAPLINK processes with imported modules 2023-09-26 08:49:06 -05:00
Thomas A. Christensen II
47500bc986
feat: Add new HAPLINK_HAPLOTYPES module 2023-09-26 08:49:05 -05:00
Thomas A. Christensen II
abfed449f6
feat: Add prefix tag to SHORAH_SHOTGUN 2023-09-26 08:49:03 -05:00
Thomas A. Christensen II
db0255c54a
refactor: Move SHORAH_SHOTGUN to its own file 2023-09-26 08:49:02 -05:00
Thomas A. Christensen II
f6111f27c2
feat: Add prefix tag to SHORAH_AMPLICON 2023-09-23 16:09:47 -05:00
Thomas A. Christensen II
dbea6fb30a
refactor: Move SHORAH_AMPLICON to its own file 2023-09-23 16:09:21 -05:00
Thomas A. Christensen II
89323bf2c6
refactor: Replace MINIMAP2 performance directives with process label 2023-09-23 16:06:12 -05:00
Thomas A. Christensen II
b08d9df6a9
feat: Add prefix tag to MINIMAP2 2023-09-23 16:05:29 -05:00
Thomas A. Christensen II
a9aa590f00
refactor: Move MINIMAP2 module to separate file 2023-09-23 16:05:02 -05:00
Thomas A. Christensen II
d12a8b77d8
refactor: Replace NANOFILT performance directives with process label 2023-09-23 15:45:34 -05:00
Thomas A. Christensen II
461a4b64a3
feat: Add prefix tag to NANOFILT module 2023-09-23 15:44:40 -05:00
Thomas A. Christensen II
f157b0395e
refactor: Move NANOFILT module to its own file 2023-09-23 15:44:08 -05:00
Thomas A. Christensen II
0e822c2729
feat: Add genome tag to EFETCH 2023-09-23 15:43:10 -05:00
Thomas A. Christensen II
ec4414184b
refactor: Change output file name of EFETCH 2023-09-23 15:39:21 -05:00
Thomas A. Christensen II
b1ee784dac
refactor: Make reference genome an input for EFETCH 2023-09-23 15:38:55 -05:00
Thomas A. Christensen II
7a3744a3d3
refactor: Replace EFETCH performance directives with process label 2023-09-23 15:36:01 -05:00
Thomas A. Christensen II
18875ae1a6
refactor: Move EFETCH module to its own file 2023-09-23 15:34:27 -05:00
Thomas A. Christensen II
2c755dcd4f
refactor: Replace hard-coded performance directives with process label 2023-09-23 15:27:05 -05:00
Thomas A. Christensen II
cc433aaffe
feat: Add container directive to HAPLINK_VARIANTS 2023-09-23 15:23:45 -05:00
Thomas A. Christensen II
a223b87464
feat: Add tag directive to HAPLINK_VARIANTS module 2023-09-23 15:22:13 -05:00
Thomas A. Christensen II
2829d51533
refactor: Move HAPLINK_VARIANTS module to its own folder 2023-09-23 15:21:26 -05:00
Thomas A. Christensen II
a91632a883
feat: Force containerized R environments 2023-08-19 14:36:51 -05:00
Thomas A. Christensen II
1e741e1db1
fix: Copy over every directory in @INC 2023-08-10 23:17:21 -05:00
Thomas A. Christensen II
eb7cd4e382
fix: Remove undefined POSIX behavior 2023-08-09 23:39:02 -05:00
Thomas A. Christensen II
054c1853f5
fix: Change permissions on ViQuaS install 2023-08-09 23:36:24 -05:00
Thomas A. Christensen II
a4478cdf7f
fix: Add ps to final container 2023-08-09 23:25:43 -05:00
Thomas A. Christensen II
ebcbb53cb1
refactor: Switch to multi-stage build 2023-08-09 23:21:33 -05:00
Thomas A. Christensen II
58759e3314
fix: Add user permissions to ViQuas folder 2023-08-09 18:17:45 -05:00
Thomas A. Christensen II
0997616190
refactor: Add container declaration to ViQuas module 2023-08-09 18:09:31 -05:00
Thomas A. Christensen II
d0b25c41b9
fix: Add BAM index to ViQuas input 2023-08-09 17:53:07 -05:00
Thomas A. Christensen II
9198d1186c
feat: Add ViQuas to main pipeline 2023-08-09 16:09:55 -05:00