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fix: update parameters and callsets #34

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fix: update parameters and callsets #34

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34a54e1
fix: increase max read depth
FelixMoelder Aug 4, 2023
8ec4865
update release
FelixMoelder Aug 7, 2023
dbece4e
update github action
FelixMoelder Aug 7, 2023
1a0a08e
Update Snakefile
FelixMoelder Aug 28, 2023
c447e75
minor changes
FelixMoelder Sep 21, 2023
6c48ff1
Merge branch 'fix/update_config' of github.com:snakemake-workflows/dn…
FelixMoelder Sep 21, 2023
2266cc0
update varlociraptor params
FelixMoelder Sep 21, 2023
1a4d9c8
clean
FelixMoelder Sep 21, 2023
64d771f
Fix scenario
FelixMoelder Sep 21, 2023
6830c58
update pathogenic callset
FelixMoelder Nov 13, 2023
69d1374
update callset
FelixMoelder Nov 14, 2023
2e84e7d
Merge branch 'main' into fix/update_config
FelixMoelder Feb 9, 2024
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18 changes: 11 additions & 7 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
steps:
- uses: actions/checkout@v2
- name: Lint workflow
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.0
with:
directory: .
snakefile: workflow/Snakefile
Expand All @@ -40,42 +40,46 @@ jobs:
- uses: actions/checkout@v2

- name: Test workflow (tumor/normal)
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-tumor_normal/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true

- name: Test report
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-tumor_normal/config.yaml --report report.zip"

- name: Test workflow (tumor/normal, ffpe)
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-tumor_normal_ffpe/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
stagein: |
rm -rf .test/results
show-disk-usage-on-error: true

- name: Test workflow (tumor only)
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-tumor_only/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
stagein: |
rm -rf .test/results
show-disk-usage-on-error: true

- name: Test workflow (tumor only, ffpe)
uses: snakemake/snakemake-github-action@v1.24.0
uses: snakemake/snakemake-github-action@v1.25.0
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-tumor_only_ffpe/config.yaml --use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
stagein: |
rm -rf .test/results
rm -rf .test/results
show-disk-usage-on-error: true
4 changes: 2 additions & 2 deletions config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -48,9 +48,9 @@ params:
# which might be misleading because all reads of an amplicon have the same start
# position, strand etc. (--omit-strand-bias, --omit-read-position-bias,
# --omit-softclip-bias, --omit-read-orientation-bias).
call: ""
call: "--omit-read-position-bias"
# Add extra arguments for varlociraptor preprocess. By default, we limit the depth to 200.
# Increase this value for panel sequencing!
preprocess: "--max-depth 200"
preprocess: "--max-depth 30000"
freebayes:
min_alternate_fraction: 0.01 # Reduce for calling variants with lower VAFs
1 change: 1 addition & 0 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ module dna_seq_varlociraptor:
github(
"snakemake-workflows/dna-seq-varlociraptor",
path="workflow/Snakefile",

tag="v5.2.0",
)
config:
Expand Down
4 changes: 2 additions & 2 deletions workflow/resources/config/default.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -411,9 +411,9 @@ params:
# which might be misleading because all reads of an amplicon have the sample start
# position, strand etc. (--omit-strand-bias, --omit-read-position-bias,
# --omit-softclip-bias, --omit-read-orientation-bias).
call: ""
call: "--omit-read-position-bias"
# Add extra arguments for varlociraptor preprocess. By default, we limit the depth to 200.
# Increase this value for panel sequencing!
preprocess: "--max-depth 200"
preprocess: "--max-depth 30000"
freebayes:
min_alternate_fraction: 0.05 # Reduce for calling variants with lower VAFs
28 changes: 17 additions & 11 deletions workflow/resources/config/scenario.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,20 @@ __definitions__:
samples = params.samples.set_index("alias")
if "ffpe" not in samples.columns:
samples["ffpe"] = pd.NA
- sex = samples.loc["tumor", "sex"]
- sex = samples.loc[["tumor"], "sex"]
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Why the brackets?

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@FelixMoelder FelixMoelder Nov 13, 2023 •
edited
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In case of groups with just one entry sample.loc["tumor", "sex"] will just return sex as a string.
But if there are multiple entries for a group sex will become a series.
In the previous implementation rendering the scenario only worked for groups with a single entry.
Changing sex to sample.loc[["tumor"], "sex"] will always return a series allowing to render single and multiple entries correctly.

Edit: In your other comment you mentioned that each alias should only occur once. So if we handle multiple panels by prefix this change probably also becomes unnecessary.

- |
if pd.isna(sex) or sex not in ["male", "female"]:
raise ValueError(f"Unsupported sex in sample sheet (also ensure that sample sheet is entirely tab separated): {sex}")
- is_ffpe = samples.loc["tumor", "ffpe"]
if pd.isna(sex).any() or len(sex.unique()) != 1 or sex.iloc[0] not in ["male", "female"]:
raise ValueError(f"Unsupported sex in sample sheet (also ensure that sample sheet is entirely tab separated): {sex}")
- is_ffpe = samples.loc[["tumor"], "ffpe"].all()
- |
if len(samples.loc[["tumor"], "ffpe"].unique()) != 1:
raise ValueError(f"All samples within a group must to be either ffpe or not.")
- |
if len(samples.loc[["tumor"], "purity"].unique()) != 1:
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Each alias should occur only once in a group. We should also check for that when validating the sample sheet. If there are two panels for a patient we could name the two tumors tumor_panelname1 and 2. the scenario could support that by looking for the prefix tumor.

raise ValueError(f"All samples within a group need to have the same purity.")
- |
def contamination():
return 1.0 - float(samples.loc["tumor", "purity"])
return 1.0 - float(samples.loc[["tumor"], "purity"].iloc[0])

species:
heterozygosity: 0.001
Expand All @@ -41,7 +47,7 @@ species:
?if "normal" in samples.index:
samples:
tumor:
sex: ?sex
sex: ?sex.iloc[0]
somatic-effective-mutation-rate: 1e-6
inheritance:
clonal:
Expand All @@ -51,7 +57,7 @@ species:
by: normal
fraction: ?contamination()
normal:
sex: ?sex
sex: ?sex.iloc[0]
somatic-effective-mutation-rate: 1e-6

events:
Expand All @@ -61,7 +67,7 @@ species:
loh_or_amplification: "normal:0.5 & tumor:[0.9,1.0["
germline: "(normal:0.5 & tumor:[0.0,0.9[) | (normal:1.0 & tumor:[0.0,1.0])"
?if is_ffpe:
ffpe_artifact: "($ffpe_subst) & tumor:]0.0,0.05["
ffpe_artifact: "normal:0.0 & (($ffpe_subst) & tumor:]0.0,0.05[)"
somatic_tumor_low: "normal:0.0 & ((($ffpe_subst) & tumor:]0.05,0.1[) | (!($ffpe_subst) & tumor:]0.0,0.1[))"
?else:
somatic_tumor_low: "normal:0.0 & tumor:]0.0,0.1["
Expand All @@ -71,19 +77,19 @@ species:
tumor:
resolution: 0.01
universe: "[0.0,1.0]"
sex: ?sex
sex: ?sex.iloc[0]
contamination:
by: normal
fraction: ?contamination()
normal:
universe: "0.0 | 0.5 | 1.0"
sex: ?sex
sex: ?sex.iloc[0]

events:
somatic_tumor_high: "normal:0.0 & tumor:[0.1,1.0]"
germline: "(normal:0.5 & tumor:0.5) | (normal:1.0 & tumor:1.0)"
?if is_ffpe:
ffpe_artifact: "($ffpe_subst) & tumor:]0.0,0.05["
ffpe_artifact: "normal:0.0 & (($ffpe_subst) & tumor:]0.0,0.05[)"
somatic_tumor_low: "normal:0.0 & ((($ffpe_subst) & tumor:]0.05,0.1[) | (!($ffpe_subst) & tumor:]0.0,0.1[))"
?else:
somatic_tumor_low: "normal:0.0 & tumor:]0.0,0.1["
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