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hem
hamlet
Commits
1d3e9215
Unverified
Commit
1d3e9215
authored
May 11, 2021
by
van den Berg
Committed by
GitHub
May 11, 2021
Browse files
Merge pull request
#13
from LUMC/github-workflow
Enable testing via github workflows
parents
f5e6b40a
7bd0af2e
Changes
10
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Inline
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.github/PULL_REQUEST_TEMPLATE.md
0 → 100644
View file @
1d3e9215
### Checklist
-
[ ] Pull request details were added to CHANGELOG.md.
-
[ ] Documentation was updated (if required).
-
[ ] New test have been properly tagged with the test (
`sanity`
,
`dry-run`
or
`intergration`
)
**and**
the apropriate module (
`qc`
,
`itd`
,
`fusion`
,
`expression`
,
`snv-indels`
or
`hamlet`
).
.github/workflows/ci.yml
0 → 100644
View file @
1d3e9215
name
:
Continuous Integration
on
:
[
push
,
pull_request
]
defaults
:
run
:
# This is needed for miniconda, see:
# https://github.com/marketplace/actions/setup-miniconda#important.
shell
:
bash -l {0}
jobs
:
test
:
runs-on
:
ubuntu-latest
strategy
:
matrix
:
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
:
submodules
:
recursive
-
name
:
Set up Conda environment
uses
:
conda-incubator/setup-miniconda@v2.0.1
# https://github.com/conda-incubator/setup-miniconda.
with
:
activate-environment
:
HAMLET
environment-file
:
environment.yml
auto-activate-base
:
false
-
name
:
Install singularity
uses
:
eWaterCycle/setup-singularity@v6
with
:
singularity-version
:
3.6.4
-
name
:
Run test in conda environment
# Use --symlink to limit disk usage.
run
:
>-
pytest --keep-workflow-wd-on-fail
--tag ${{ matrix.test }}
--tag ${{ matrix.module }}
--symlink test/
-
name
:
Check cromwell log in case of failure.
if
:
${{ failure() }}
# Get the last 1000 lines of the cromwell log to catch the error.
run
:
bash -c 'tail -n 1000 /tmp/pytest_workflow_*/*/log.out'
-
name
:
Check pytest stdout messages in case of failure
if
:
${{ failure() }}
run
:
>-
bash -c '
for file in $(find /tmp -name log.out);
do echo $file; cat $file; done'
-
name
:
Check pytest stderr messages in case of failure
if
:
${{ failure() }}
run
:
>-
bash -c '
for file in $(find /tmp -name log.err);
do echo $file; cat $file; done'
README.md
View file @
1d3e9215
[

](https://github.com/HAMLET/actions/workflows/ci.yml)
# Hamlet
Hamlet is a pipeline for analysis of human acute myeloid leukemia RNA-seq samples. Please use the
...
...
environment.yml
View file @
1d3e9215
# This file may be used to create an environment using:
# $ conda create -
-name <env> --file <this file>
# $ conda
env
create -
f environment.yml
# platform: linux-64
name
:
HAMLET
channels
:
-
bioconda
-
conda-forge
-
defaults
dependencies
:
-
pytest-workflow>=1.4.0
-
python>3.6
-
snakemake=5.9
-
snakemake
-minimal
=5.9
test/test_expression.yml
View file @
1d3e9215
-
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 @
1d3e9215
-
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 @
1d3e9215
-
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 @
1d3e9215
-
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 @
1d3e9215
-
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 @
1d3e9215
-
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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