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adding viloca to the workflow #150

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merged 89 commits into from
Jun 7, 2024
Merged

adding viloca to the workflow #150

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41e0b53
Version bump COJAC 0.9.2
DrYak Jun 4, 2024
34a3e36
[method] cliquesnv with output snvs -- create empyt file if cliquesnv…
LaraFuhrmann Oct 17, 2023
c6e555d
exclude shorah_amplicon since it fails on the illumina populations du…
LaraFuhrmann Oct 17, 2023
66a0d0a
vary population parameters and coverage
LaraFuhrmann Oct 17, 2023
ee6ddf8
subsample hiv mix
LaraFuhrmann Oct 17, 2023
d5733fc
exlcude viloca_multi since the cluster allocation of multiple threads…
LaraFuhrmann Oct 17, 2023
671d37e
add rerun-triggers mtime snakemake command
LaraFuhrmann Oct 17, 2023
de4354e
[viloca] set higher win_min_ext threshold for 10-IAV-mix
LaraFuhrmann Oct 17, 2023
960fa5b
updates
LaraFuhrmann Oct 17, 2023
5a87288
conda enviroment
LaraFuhrmann Oct 17, 2023
a322f7b
viloca with older configuration
LaraFuhrmann Oct 19, 2023
193b691
exclude indels configuration for now
LaraFuhrmann Oct 27, 2023
8ae9839
PVY mix with uniform tiling
LaraFuhrmann Oct 27, 2023
c6f221f
add another sars-mix
LaraFuhrmann Oct 27, 2023
ef801f4
update resources
LaraFuhrmann Oct 27, 2023
92e34db
add older viloca configuration
LaraFuhrmann Oct 27, 2023
24432ad
more methods + updated populations
LaraFuhrmann Oct 30, 2023
0d57c99
run indel also
LaraFuhrmann Nov 7, 2023
bbd0355
rename methods, since bash takes files names of length max 255
LaraFuhrmann Nov 7, 2023
709bcf7
method names updated
LaraFuhrmann Nov 7, 2023
035b154
method names updated
LaraFuhrmann Nov 7, 2023
e33697b
b2w multi
LaraFuhrmann Nov 8, 2023
3ec6395
fix: in case no mutations are in vcf
LaraFuhrmann Nov 10, 2023
a27917d
[update] distance populations for conference figures
LaraFuhrmann Nov 13, 2023
d92d46b
[viloca method] also report posterior of haplotypes
LaraFuhrmann Nov 17, 2023
9410d2b
[varyvilocaparams] update config and params
LaraFuhrmann Nov 17, 2023
4f6d22d
[realdata] don't use SARS-CoV-2-Two-Strain-Mix -- since we don't have…
LaraFuhrmann Nov 17, 2023
532ebd9
[HIV-5-mix] update ground truth - exclude deletions since they are no…
LaraFuhrmann Nov 17, 2023
6885afd
[single_bed_file] fix
LaraFuhrmann Nov 17, 2023
119c821
[single_bed_file] fix int
LaraFuhrmann Nov 17, 2023
b95c288
[performance_global] save posterior of predictions
LaraFuhrmann Nov 17, 2023
df54361
[method_def] viloca with posterior threshold
LaraFuhrmann Nov 17, 2023
726635b
[method_def] viloca with posterior threshold
LaraFuhrmann Nov 17, 2023
5eeb1c4
[experimental data] 5-virus-mix correct ground truth
LaraFuhrmann Nov 20, 2023
cd19f16
[local_haplo] add predicthaplo
LaraFuhrmann Jan 3, 2024
2330800
add method: strainline
LaraFuhrmann Jan 9, 2024
5d9420e
update method strainline
LaraFuhrmann Jan 9, 2024
40a2c7d
update method strainline
LaraFuhrmann Jan 9, 2024
6d78436
remove rules for 2 strain sars-cov2 mix
LaraFuhrmann Jan 19, 2024
c7216ca
add predicthaplo
LaraFuhrmann Feb 9, 2024
955001d
remove old methods that are not used anywhere
LaraFuhrmann Apr 16, 2024
434c82c
correct output name for different applications and improved comments
LaraFuhrmann Apr 16, 2024
3f3a144
[shorah] reduce window size for illumina samples
LaraFuhrmann Apr 16, 2024
ca27a1a
[fix] simulation of deletions and insertions into the haplotypes
LaraFuhrmann Apr 17, 2024
04beff2
[add] extra performance measures for local_haplo_setup
LaraFuhrmann Apr 18, 2024
5bd565d
fix illumina simulation with indels in haplotypes, bwa is not alignin…
LaraFuhrmann Apr 18, 2024
2168ebb
fix indel simulation, ground truth table, simulate missing codon or i…
LaraFuhrmann Apr 18, 2024
b86677c
[remove] rule to provide curlcakes ont data
LaraFuhrmann Apr 18, 2024
71f57bf
[remove] rule to provide wastewater sars-cov2 data
LaraFuhrmann Apr 18, 2024
b3123ac
[remove] rule to provide wastewater sars-cov2 data
LaraFuhrmann Apr 18, 2024
4bfc2d6
[remove] rule to provide wastewater sars-cov2 data
LaraFuhrmann Apr 18, 2024
3eade89
[remove] rule to provide wastewater sars-cov2 data
LaraFuhrmann Apr 18, 2024
7223f86
[fix groud truth list for distance haplo generation]
LaraFuhrmann Apr 18, 2024
26ddd53
[clean-up] ground_truth_corrected.csv not neeeded anymore, since grou…
LaraFuhrmann Apr 18, 2024
5fba0ba
config_distance: final version as in manuscript
LaraFuhrmann Apr 18, 2024
b29db53
remove cliquesnv version that returns snvs wrt consensus seq
LaraFuhrmann Apr 18, 2024
2c5f604
distance config: final methods
LaraFuhrmann Apr 18, 2024
fb55348
remove corrected groundtruth file
LaraFuhrmann Apr 18, 2024
32265a2
final methods list and simulated dataset for varyvilocaparams
LaraFuhrmann Apr 18, 2024
f595971
realdata update to final method versions
LaraFuhrmann Apr 18, 2024
fb54a42
call indels
LaraFuhrmann Apr 18, 2024
2804035
remove outdated methods
LaraFuhrmann Apr 18, 2024
40bea26
method_definitions: cliquesnv
LaraFuhrmann Apr 18, 2024
d76f40d
update method defintions as run on cluster
LaraFuhrmann Apr 18, 2024
d7cc318
generate haplotypes: correct deletion position in ground truth
LaraFuhrmann Apr 19, 2024
7814934
[local_haplo_setup] add readme
LaraFuhrmann Apr 19, 2024
c5fbce1
fix indel ground truth and performance evaluationa
LaraFuhrmann Apr 23, 2024
a388f4e
fix indel ground truth and performance evaluationa
LaraFuhrmann Apr 23, 2024
c533f17
indel config
LaraFuhrmann Apr 23, 2024
ebe53e5
remove isfile() tst
LaraFuhrmann Apr 23, 2024
00ed959
update viloca ewm for amplicon
LaraFuhrmann Apr 25, 2024
1b257c0
add indel settings and performance eval
LaraFuhrmann May 2, 2024
56ff76d
typo
LaraFuhrmann May 2, 2024
21977cd
[real data] complete insert file
LaraFuhrmann May 2, 2024
04ca094
[add] notebooks for figures in manuscript
LaraFuhrmann May 2, 2024
9ab7264
Keep the linter happy
DrYak Jun 7, 2024
416efeb
adding viloca to the workflow
LaraFuhrmann Feb 5, 2024
13aee8e
fix file paths
LaraFuhrmann Feb 6, 2024
7ddb320
update conig_schema
LaraFuhrmann Mar 5, 2024
17f779c
adding paired_end_read_merger
LaraFuhrmann Jun 4, 2024
15d75b3
update rule for paired_en_read_merger + add conda env definition
LaraFuhrmann Jun 5, 2024
c2c2ae7
update rule for paired_en_read_merger + add conda env definition
LaraFuhrmann Jun 5, 2024
5174e9a
update enviroment
LaraFuhrmann Jun 5, 2024
3e79e5e
add paired_end_read_merger
LaraFuhrmann Jun 5, 2024
206e056
update paired_end_read_merger rule
LaraFuhrmann Jun 6, 2024
4ccd9d8
add conda package to env
LaraFuhrmann Jun 6, 2024
2af73f9
Viloca touch ups
DrYak Jun 7, 2024
59386c7
Linting
DrYak Jun 7, 2024
c948d2e
Generate copnfig manual
DrYak Jun 7, 2024
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230 changes: 116 additions & 114 deletions config/config.html
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8 changes: 0 additions & 8 deletions resources/auxiliary_workflows/benchmark/config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,6 @@ method_list: [haploclique,
cliquesnv,
lofreq_local_haplo,
shorah_default,
qualhap_use_quality_scores_unique_tiling,
qualhap_learn_error_params_unique_tiling,
qualhap_learn_error_params_tiling,
qualhap_use_quality_scores_tiling,
qualhap_use_quality_scores_unique,
qualhap_learn_error_params_unique,
qualhap_learn_error_params,
qualhap_use_quality_scores,
viloca,
]

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