b22ea2664b
fix: Add escapes to ML haplotype caller
2023-10-19 16:01:51 -05:00
3e411cc688
refactor: Switch to SRA direct download for samples
2023-10-19 11:39:20 -05:00
9f70b504e2
feat: Add fasterq-dump module
2023-10-19 11:39:19 -05:00
7e0f64f78b
feat: Add input schema to parameter schema
2023-10-19 11:39:18 -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
c55a854345
feat: Add input schema
2023-10-19 11:39:15 -05:00
93bd5cedec
chore: Replace results dir with parameterized outdir
2023-10-18 21:40:08 -05:00
b415c29ec0
feat: Add parameter schema
2023-10-18 21:33:58 -05:00
a5e2528781
chore: Add pre-commit config
...
In order to use nf-validation infrastructure, we have to have pre-commit
hooks installed, so add some basic hooks
2023-10-18 21:11:55 -05:00
41ac5852be
feat: Add parameters for input and output directories
2023-10-18 21:08:40 -05:00
21ef25be43
feat: Add nf-validation plugin
2023-10-18 21:06:48 -05:00
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
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
029f3a5126
feat: Add PREDICTHAPLO module
2023-09-26 08:49:23 -05:00
d8fee48c28
feat: Add CliqueSNV to pipeline
2023-09-26 08:49:22 -05:00
96471746b9
feat: Replace hard-coded singularity with profile-based containers
2023-09-26 08:49:20 -05:00
7f43f0282f
feat: Add nf-core resource allocation parameters
2023-09-26 08:49:17 -05:00
137804518f
feat: Add nf-core config parameters
2023-09-26 08:49:16 -05:00
3e6a0ca5df
feat: Add QuasiRecomb module
2023-09-26 08:49:14 -05:00
5ab64a8fea
feat: Add CliqueSNV haplotype calling to pipeline
2023-09-26 08:49:13 -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
52ca8f1528
refactor: Replace in-workflow HAPLINK processes with imported modules
2023-09-26 08:49:06 -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
