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hem
hamlet
Commits
bad01b38
Commit
bad01b38
authored
May 11, 2021
by
van den Berg
Browse files
Run sanity and dry-run test for each module
parent
539d2452
Changes
7
Hide whitespace changes
Inline
Side-by-side
.github/workflows/ci.yml
View file @
bad01b38
...
...
@@ -16,6 +16,13 @@ jobs:
test
:
-
sanity
-
dry-run
module
:
-
qc
-
itd
-
fusion
-
expression
-
snv-indels
-
hamlet
steps
:
-
uses
:
actions/checkout@v2.3.4
# https://github.com/actions/checkout.
with
:
...
...
@@ -36,7 +43,9 @@ jobs:
-
name
:
Run test in conda environment
# Use --symlink to limit disk usage.
run
:
>-
pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }}
pytest --keep-workflow-wd-on-fail
--tag ${{ matrix.test }}
--tag ${{ matrix.module }}
--symlink test/
-
name
:
Check cromwell log in case of failure.
...
...
test/test_expression.yml
View file @
bad01b38
-
name
:
test-expression-dry-run-single
tags
:
-
dry-run
-
expression
command
:
>
snakemake -n
--snakefile includes/expression/Snakefile
...
...
@@ -17,6 +18,7 @@
-
name
:
test-expression-dry-run-trio
tags
:
-
dry-run
-
expression
command
:
>
snakemake -n
--snakefile includes/expression/Snakefile
...
...
@@ -43,6 +45,7 @@
-
name
:
test-expression-sanity-snakemake
tags
:
-
sanity
-
expression
command
:
>
snakemake --version
stdout
:
...
...
@@ -52,6 +55,7 @@
-
name
:
test-expression-sanity-singularity
tags
:
-
sanity
-
expression
command
:
>
singularity --version
stdout
:
...
...
@@ -61,6 +65,7 @@
-
name
:
test-expression-integration-HEL
tags
:
-
integration
-
expression
command
:
>
snakemake -rp
--snakefile includes/expression/Snakefile
...
...
@@ -101,6 +106,7 @@
-
name
:
test-expression-MECOM-vs-MECOM
tags
:
-
integration
-
expression
command
:
>
snakemake -rp
--snakefile includes/expression/Snakefile
...
...
test/test_fusion.yml
View file @
bad01b38
-
name
:
test-fusion-dry-run-single
tags
:
-
dry-run
-
fusion
command
:
>
snakemake -n
--snakefile includes/fusion/Snakefile
...
...
@@ -23,6 +24,7 @@
-
name
:
test-fusion-dry-run-trio
tags
:
-
dry-run
-
fusion
command
:
>
snakemake -n
--snakefile includes/fusion/Snakefile
...
...
@@ -69,6 +71,7 @@
-
name
:
test-fusion-sanity-snakemake
tags
:
-
sanity
-
fusion
command
:
>
snakemake --version
stdout
:
...
...
@@ -78,6 +81,7 @@
-
name
:
test-fusion-sanity-singularity
tags
:
-
sanity
-
fusion
command
:
>
singularity --version
stdout
:
...
...
@@ -87,6 +91,7 @@
-
name
:
test-fusion-integration-NB-4-dry-run
tags
:
-
dry-run
-
fusion
command
:
>
snakemake -rpn
--snakefile includes/fusion/Snakefile
...
...
@@ -97,6 +102,7 @@
-
name
:
test-fusion-integration-NB-4
tags
:
-
integration
-
fusion
command
:
>
snakemake -rp
--snakefile includes/fusion/Snakefile
...
...
test/test_hamlet.yml
View file @
bad01b38
-
name
:
test-hamlet-dry-run-single
tags
:
-
dry-run
-
hamlet
command
:
>
snakemake -n
--snakefile Snakefile
...
...
@@ -16,6 +17,7 @@
-
name
:
test-hamlet-dry-run-trio
tags
:
-
dry-run
-
hamlet
command
:
>
snakemake -n
--snakefile Snakefile
...
...
@@ -41,6 +43,7 @@
-
name
:
test-hamlet-sanity-snakemake
tags
:
-
sanity
-
hamlet
command
:
>
snakemake --version
stdout
:
...
...
@@ -50,6 +53,7 @@
-
name
:
test-hamlet-sanity-singularity
tags
:
-
sanity
-
hamlet
command
:
>
singularity --version
stdout
:
...
...
@@ -59,6 +63,7 @@
-
name
:
test-hamlet-frankenstein-integration
tags
:
-
integration
-
hamlet
command
:
>
snakemake -rp
--snakefile Snakefile
...
...
test/test_itd.yml
View file @
bad01b38
-
name
:
test-itd-dry-run-single
tags
:
-
dry-run
-
itd
command
:
>
snakemake -n
--snakefile includes/itd/Snakefile
...
...
@@ -18,6 +19,7 @@
-
name
:
test-itd-dry-run-trio
tags
:
-
dry-run
-
itd
command
:
>
snakemake -n
--snakefile includes/itd/Snakefile
...
...
@@ -47,6 +49,7 @@
-
name
:
test-itd-sanity-snakemake
tags
:
-
sanity
-
itd
command
:
>
snakemake --version
stdout
:
...
...
@@ -56,6 +59,7 @@
-
name
:
test-itd-sanity-singularity
tags
:
-
sanity
-
itd
command
:
>
singularity --version
stdout
:
...
...
@@ -65,6 +69,7 @@
-
name
:
test-itd-MV4-11-flt3
tags
:
-
integration
-
itd
-
flt3
command
:
>
snakemake -rp
...
...
@@ -92,6 +97,7 @@
-
name
:
test-ptd-EoL-1-KMT2A
tags
:
-
integration
-
itd
-
kmt2a
command
:
>
snakemake -rp
...
...
@@ -117,6 +123,7 @@
-
name
:
test-flt3-kmt2a-no-reads
tags
:
-
integration
-
itd
command
:
>
snakemake -rp
--snakefile includes/itd/Snakefile
...
...
test/test_qc_seq.yml
View file @
bad01b38
-
name
:
test-qc-dry-run-single
tags
:
-
dry-run
-
qc
command
:
>
snakemake -n
--snakefile includes/qc-seq/Snakefile
...
...
@@ -12,6 +13,7 @@
-
name
:
test-qc-dry-run-trio
tags
:
-
dry-run
-
qc
command
:
>
snakemake -n
--snakefile includes/qc-seq/Snakefile
...
...
@@ -23,6 +25,7 @@
-
name
:
test-qc-sanity-snakemake
tags
:
-
sanity
-
qc
command
:
>
snakemake --version
stdout
:
...
...
@@ -32,6 +35,7 @@
-
name
:
test-qc-sanity-singularity
tags
:
-
sanity
-
qc
command
:
>
singularity --version
stdout
:
...
...
@@ -41,6 +45,7 @@
-
name
:
test-qc-single
tags
:
-
integration
-
qc
command
:
>
snakemake -rp
--snakefile includes/qc-seq/Snakefile
...
...
@@ -60,6 +65,7 @@
-
name
:
test-qc-duo
tags
:
-
functional
-
qc
command
:
>
snakemake -rp
--snakefile includes/qc-seq/Snakefile
...
...
@@ -79,6 +85,7 @@
-
name
:
test-qc-trio
tags
:
-
functional
-
qc
command
:
>
snakemake -rp
--snakefile includes/qc-seq/Snakefile
...
...
@@ -93,6 +100,7 @@
-
name
:
test-qc-single-low-qual-adapters
tags
:
-
functional
-
qc
command
:
>
snakemake -rp
--snakefile includes/qc-seq/Snakefile
...
...
test/test_snv_indels.yml
View file @
bad01b38
-
name
:
test-snv-indels-dry-run-single
tags
:
-
dry-run
-
snv-indels
command
:
>
snakemake -n
--snakefile includes/snv-indels/Snakefile
...
...
@@ -15,6 +16,7 @@
-
name
:
test-snv-indels-dry-run-trio
tags
:
-
dry-run
-
snv-indels
command
:
>
snakemake -n
--snakefile includes/snv-indels/Snakefile
...
...
@@ -37,6 +39,7 @@
-
name
:
test-snv-indels-sanity-snakemake
tags
:
-
sanity
-
snv-indels
command
:
>
snakemake --version
stdout
:
...
...
@@ -46,6 +49,7 @@
-
name
:
test-snv-indels-sanity-singularity
tags
:
-
sanity
-
snv-indels
command
:
>
singularity --version
stdout
:
...
...
@@ -56,6 +60,7 @@
tags
:
-
integration
-
p53
-
snv-indels
command
:
>
snakemake -rp
--snakefile includes/snv-indels/Snakefile
...
...
@@ -108,8 +113,9 @@
-
name
:
test-flt3-integration-MV4-11
tags
:
-
flt3
-
integration
-
flt3
-
snv-indels
command
:
>
snakemake -rp
--snakefile includes/snv-indels/Snakefile
...
...
@@ -128,6 +134,7 @@
-
name
:
test-TET2-insertion-config
tags
:
-
integration
-
snv-indels
command
:
>
snakemake -rp
--snakefile includes/snv-indels/Snakefile
...
...
@@ -150,6 +157,7 @@
-
name
:
test-RUNX1-insertion
tags
:
-
integration
-
snv-indels
command
:
>
snakemake -rp
--snakefile includes/snv-indels/Snakefile
...
...
@@ -165,6 +173,7 @@
-
name
:
test-TET2-false-positive-mutation
tags
:
-
integration
-
snv-indels
command
:
>
snakemake -rp
--snakefile includes/snv-indels/Snakefile
...
...
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