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• b22ea2664b
  
  fix: Add escapes to ML haplotype caller master Thomas A. Christensen II 2023-10-19 16:01:51 -0500
• 3e411cc688
  
  refactor: Switch to SRA direct download for samples Thomas A. Christensen II 2023-10-19 11:38:43 -0500
• 9f70b504e2
  
  feat: Add fasterq-dump module Thomas A. Christensen II 2023-10-19 11:23:41 -0500
• 7e0f64f78b
  
  feat: Add input schema to parameter schema Thomas A. Christensen II 2023-10-18 22:11:47 -0500
• 77535ee726
  
  feat: Add parameter validation Thomas A. Christensen II 2023-10-18 22:08:27 -0500
• eddf9d21f6
  
  refactor: Change hard-coded reference into parameter Thomas A. Christensen II 2023-10-18 21:56:44 -0500
• c55a854345
  
  feat: Add input schema Thomas A. Christensen II 2023-10-18 21:45:52 -0500
• 93bd5cedec
  
  chore: Replace results dir with parameterized outdir Thomas A. Christensen II 2023-10-18 21:40:08 -0500
• b415c29ec0
  
  feat: Add parameter schema Thomas A. Christensen II 2023-10-18 21:33:58 -0500
• a5e2528781
  
  chore: Add pre-commit config Thomas A. Christensen II 2023-10-18 21:11:55 -0500
• 41ac5852be
  
  feat: Add parameters for input and output directories Thomas A. Christensen II 2023-10-18 21:08:40 -0500
• 21ef25be43
  
  feat: Add nf-validation plugin Thomas A. Christensen II 2023-10-18 21:06:48 -0500
• 38d779b1dc
  
  fix: Use GitHub containers registry for HapLink modules Thomas A. Christensen II 2023-09-30 16:01:09 -0500
• 2f96ba4e44
  
  feat!: Remove PREDICTHAPLO module Thomas A. Christensen II 2023-09-30 15:11:52 -0500
• 588d307ff6
  
  fix: Remove invalid shorah parameter Thomas A. Christensen II 2023-09-29 14:17:39 -0500
• b98a797701
  
  feat: Add control flow for choosing haplotypers Thomas A. Christensen II 2023-09-26 08:27:22 -0500
• 9364225e74
  
  fix: Change input cardinality on haplotyping modules Thomas A. Christensen II 2023-09-26 08:06:43 -0500
• 355ce9a00a
  
  feat: Add SHORAH processes to pipeline Thomas A. Christensen II 2023-09-25 18:51:58 -0500
• 444001b499
  
  feat: Add QUASIRECOMB to pipeline Thomas A. Christensen II 2023-09-25 18:50:37 -0500
• 5cc8867799
  
  feat: Add PREDICTHAPLO to pipeline Thomas A. Christensen II 2023-09-25 18:47:48 -0500
• 029f3a5126
  
  feat: Add PREDICTHAPLO module Thomas A. Christensen II 2023-09-25 18:46:38 -0500
• d8fee48c28
  
  feat: Add CliqueSNV to pipeline Thomas A. Christensen II 2023-09-25 18:44:50 -0500
• 96471746b9
  
  feat: Replace hard-coded singularity with profile-based containers Thomas A. Christensen II 2023-09-25 18:16:50 -0500
• 7f43f0282f
  
  feat: Add nf-core resource allocation parameters Thomas A. Christensen II 2023-09-25 18:05:10 -0500
• 137804518f
  
  feat: Add nf-core config parameters Thomas A. Christensen II 2023-09-25 17:59:14 -0500
• 3e6a0ca5df
  
  feat: Add QuasiRecomb module Thomas A. Christensen II 2023-09-23 16:54:49 -0500
• 5ab64a8fea
  
  feat: Add CliqueSNV haplotype calling to pipeline Thomas A. Christensen II 2023-09-23 16:43:02 -0500
• de853c2d22
  
  feat: Add CliqueSNV module Thomas A. Christensen II 2023-09-23 16:40:04 -0500
• 5c4d02263b
  
  refactor: Replace custom publish dirs with reference to task.process Thomas A. Christensen II 2023-09-23 16:32:29 -0500
• 002bd44975
  
  refactor: Change output directory to match haplotypes Thomas A. Christensen II 2023-09-23 16:30:24 -0500
• 4751203579
  
  feat: Add container directive to HAPLINK_SEQUENCES Thomas A. Christensen II 2023-09-23 16:28:57 -0500
• 095aff629d
  
  refactor: Replace performance directives with process label Thomas A. Christensen II 2023-09-23 16:28:12 -0500
• 517b8eb66b
  
  feat: Add method/prefix tag to HAPLINK_SEQUENCES Thomas A. Christensen II 2023-09-23 16:27:17 -0500
• 5162f649d8
  
  refactor: Move HAPLINK_SEQUENCES module to its own file Thomas A. Christensen II 2023-09-23 16:26:25 -0500
• 52ca8f1528
  
  refactor: Replace in-workflow HAPLINK processes with imported modules Thomas A. Christensen II 2023-09-23 16:24:57 -0500
• 47500bc986
  
  feat: Add new HAPLINK_HAPLOTYPES module Thomas A. Christensen II 2023-09-23 16:20:44 -0500
• abfed449f6
  
  feat: Add prefix tag to SHORAH_SHOTGUN Thomas A. Christensen II 2023-09-23 16:13:06 -0500
• db0255c54a
  
  refactor: Move SHORAH_SHOTGUN to its own file Thomas A. Christensen II 2023-09-23 16:12:40 -0500
• f6111f27c2
  
  feat: Add prefix tag to SHORAH_AMPLICON Thomas A. Christensen II 2023-09-23 16:09:47 -0500
• dbea6fb30a
  
  refactor: Move SHORAH_AMPLICON to its own file Thomas A. Christensen II 2023-09-23 16:09:21 -0500
• 89323bf2c6
  
  refactor: Replace MINIMAP2 performance directives with process label Thomas A. Christensen II 2023-09-23 16:06:12 -0500
• b08d9df6a9
  
  feat: Add prefix tag to MINIMAP2 Thomas A. Christensen II 2023-09-23 16:05:29 -0500
• a9aa590f00
  
  refactor: Move MINIMAP2 module to separate file Thomas A. Christensen II 2023-09-23 16:05:02 -0500
• d12a8b77d8
  
  refactor: Replace NANOFILT performance directives with process label Thomas A. Christensen II 2023-09-23 15:45:34 -0500
• 461a4b64a3
  
  feat: Add prefix tag to NANOFILT module Thomas A. Christensen II 2023-09-23 15:44:40 -0500
• f157b0395e
  
  refactor: Move NANOFILT module to its own file Thomas A. Christensen II 2023-09-23 15:44:08 -0500
• 0e822c2729
  
  feat: Add genome tag to EFETCH Thomas A. Christensen II 2023-09-23 15:43:10 -0500
• ec4414184b
  
  refactor: Change output file name of EFETCH Thomas A. Christensen II 2023-09-23 15:39:21 -0500
• b1ee784dac
  
  refactor: Make reference genome an input for EFETCH Thomas A. Christensen II 2023-09-23 15:38:55 -0500
• 7a3744a3d3
  
  refactor: Replace EFETCH performance directives with process label Thomas A. Christensen II 2023-09-23 15:36:01 -0500
• 18875ae1a6
  
  refactor: Move EFETCH module to its own file Thomas A. Christensen II 2023-09-23 15:34:27 -0500
• 2c755dcd4f
  
  refactor: Replace hard-coded performance directives with process label Thomas A. Christensen II 2023-09-23 15:27:05 -0500
• cc433aaffe
  
  feat: Add container directive to HAPLINK_VARIANTS Thomas A. Christensen II 2023-09-23 15:23:45 -0500
• a223b87464
  
  feat: Add tag directive to HAPLINK_VARIANTS module Thomas A. Christensen II 2023-09-23 15:22:13 -0500
• 2829d51533
  
  refactor: Move HAPLINK_VARIANTS module to its own folder Thomas A. Christensen II 2023-09-23 15:21:26 -0500
• a91632a883
  
  feat: Force containerized R environments Thomas A. Christensen II 2023-08-19 14:36:51 -0500
• 1e741e1db1
  
  fix: Copy over every directory in @INC Thomas A. Christensen II 2023-08-10 23:16:04 -0500
• eb7cd4e382
  
  fix: Remove undefined POSIX behavior Thomas A. Christensen II 2023-08-09 23:39:02 -0500
• 054c1853f5
  
  fix: Change permissions on ViQuaS install Thomas A. Christensen II 2023-08-09 23:36:24 -0500
• a4478cdf7f
  
  fix: Add ps to final container Thomas A. Christensen II 2023-08-09 23:25:43 -0500
• ebcbb53cb1
  
  refactor: Switch to multi-stage build Thomas A. Christensen II 2023-08-09 23:21:33 -0500
• 58759e3314
  
  fix: Add user permissions to ViQuas folder Thomas A. Christensen II 2023-08-09 18:17:45 -0500
• 0997616190
  
  refactor: Add container declaration to ViQuas module Thomas A. Christensen II 2023-08-09 18:05:22 -0500
• d0b25c41b9
  
  fix: Add BAM index to ViQuas input Thomas A. Christensen II 2023-08-09 17:53:07 -0500
• 9198d1186c
  
  feat: Add ViQuas to main pipeline Thomas A. Christensen II 2023-08-09 16:09:55 -0500
• 1e20488409
  
  feat: Add ViQuas module Thomas A. Christensen II 2023-08-09 16:07:54 -0500
• 108fb0dc5b
  
  refactor: Minimize Dockerfile layers Thomas A. Christensen II 2023-08-09 16:02:46 -0500
• a1d0348697
  
  feat: Create working Dockerfile for ViQuas Thomas A. Christensen II 2023-08-09 15:28:35 -0500
• ad10d46c87
  
  feat: Add SHORAH_SHOTGUN process Thomas A. Christensen II 2023-06-08 18:12:23 -0500
• feb051fc07
  
  feat: Add SHORAH_AMPLICON process Thomas A. Christensen II 2023-06-08 18:10:26 -0500
• 58b18cc2c9
  
  chore: Add gitignore Thomas A. Christensen II 2023-06-08 17:56:39 -0500
• 7743bf31c6
  
  feat: Import HapLink validation script Thomas A. Christensen II 2023-06-08 17:55:57 -0500