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Commit bad01b38 authored by van den Berg's avatar van den Berg
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Run sanity and dry-run test for each module

parent 539d2452
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.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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