feat: add maftools output #297

dlaehnemann · 2024-04-18T13:08:32Z

No description provided.

keep it set to false, so users have to actively turn it on

…vate in config-simple

config/config.yaml

johanneskoester

Just one thing

.test/config-giab/config.yaml

workflow/rules/maftools.smk

…ance improvement

…d INFO (and ANN) field names for vcf2maf conversion

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

…config

…nt users to see and fix this

…ig/config.yaml

…ing lookup functions with defaults for all the fields

…f2maf

…in `config.yaml`

…it is `activate: false`, except for one case (to test that syntax, as well)

.test/config-chm-eval/config.yaml

.test/config-giab/config.yaml

.test/config-sra/config.yaml

.test/config-target-regions/config_multiple_beds.yaml

.test/config_primers/config.yaml

…tion

…the default expected `--vcf-normal-id` that is checked for, even if the optional `--normal-id` is not specified

workflow/rules/common.smk

config/config.yaml

workflow/rules/common.smk

… we need this Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

…al_alias to control_alias, to make it clear that maf format and plotting can be used more generally

dlaehnemann added 11 commits April 18, 2024 14:49

feat: add rules to generate maftools input files

c17b9a3

request maftools input files in common.smk

7de7dac

include maftools activate option in default config.yaml

d9d6335

keep it set to false, so users have to actively turn it on

add maftools activation option to all testing config.yaml files, acti…

ab969a4

…vate in config-simple

add wildcard into maftools input file generation rules

95dcd7f

fix missing quote and snakefmt

9145b3c

rename results folder for maftools to maftools

f627a82

actually include maftools.smk in Snakefile

822beb8

fix: remove module reference not needed after integration into workflow

24c594b

fix: add forgotten conda environment def for vcf2maf

de248aa

fix: path to newly included env

bb1b918

johanneskoester reviewed May 4, 2024

View reviewed changes

config/config.yaml Outdated Show resolved Hide resolved

dlaehnemann marked this pull request as draft May 7, 2024 07:03

dlaehnemann added 3 commits May 28, 2024 12:40

feat: make freebayes configurable via config.params.freebayes.extra

7364276

fix typo: extra " in config.yaml

0791fb8

Merge branch 'master' into feat/add-maftools-output

3b14b11

dlaehnemann marked this pull request as ready for review June 13, 2024 11:32

johanneskoester requested changes Jun 13, 2024

View reviewed changes

dlaehnemann and others added 12 commits June 17, 2024 11:20

perf: switch to latest datavzrd wrapper to profit from recent perform…

5830147

…ance improvement

feat: refactor get_vembrane_config to allow re-use of plain FORMAT an…

c75f8fa

…d INFO (and ANN) field names for vcf2maf conversion

fix: levels if f and format in append_items() calls

e77caaf

chore: snakefmt workflow/rules/common.smk

5522d02

fix: remove superfluous params: section

080a9fc

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

fix: address requeste refactoring from amftools to maf

d38cced

fix: address update on main branch

4165a0c

Merge branch 'master' into feat/add-maftools-output

5020b5b

chore: manually follow snakefmt, as versions seem to diverge

9c1daee

fix: pass along the input

c6bdadf

fix: search and replace didn't go into .test/ folder...

3a8914b

fix: properly pass on wildcards variable to get fusion info fields

8a97d60

dlaehnemann added 11 commits August 22, 2024 16:17

fix: make alias selection tumor and alias selection for maf work via …

b3d4ff2

…config

fix: catch vcf2maf warnings, if tumor or normal alias is wrong; we wa…

96fed24

…nt users to see and fix this

chore: also mention maf: tumor_alias and normal_alias in default conf…

ce20880

…ig/config.yaml

chore: address review comment

cce39c9

chore: snakefmt

b2914a7

perf: update datavzrd version

d82c479

fix: make maf: introduction in config.yaml backwards compatible by us…

eec9ed6

…ing lookup functions with defaults for all the fields

fix: try providing False as default for vcf_normal_alias lookup in vc…

8e0a325

…f2maf

fix: also test case where only a tumor_alias is specified for maf: …

f977602

…in `config.yaml`

chore: remove maf: entry from all .test/ config.yaml files where …

c599f92

…it is `activate: false`, except for one case (to test that syntax, as well)

docs: indicate that maf output and plots are optional

91c9456