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Klinische Genetica
capture-lumc
hutspot
Commits
7fd2ca3d
Commit
7fd2ca3d
authored
Feb 19, 2019
by
Sander Bollen
Browse files
use tags
parent
d3be2d28
Pipeline
#2383
failed with stage
in 1 minute and 3 seconds
Changes
3
Pipelines
1
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Inline
Side-by-side
.gitlab-ci.yml
View file @
7fd2ca3d
...
...
@@ -6,4 +6,8 @@ before_script:
test_sanities
:
script
:
-
py.test
-
py.test --tag sanity
test_dry_run
:
script
:
-
py.test --tag dry-run
tests/test_dry_run.yml
View file @
7fd2ca3d
...
...
@@ -15,3 +15,5 @@
stderr
:
must_not_contain
:
-
"
rror"
tags
:
-
dry-run
tests/test_sanity_checks.yml
View file @
7fd2ca3d
...
...
@@ -4,12 +4,16 @@
stdout
:
contains
:
-
"
You
must
set
--config
OUT_DIR=<path>"
tags
:
-
sanity
-
name
:
test-no-reference
command
:
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/teststtest/
exit_code
:
1
stdout
:
contains
:
-
"
You
must
set
--config
REFERENCE=<path>"
tags
:
-
sanity
-
name
:
test-reference-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/teststtest/
...
...
@@ -18,6 +22,8 @@
stdout
:
contains
:
-
"
Reference
file
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
-
name
:
test-no-java
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -26,6 +32,8 @@
stdout
:
contains
:
-
"
You
must
set
--config
JAVA=<path>"
tags
:
-
sanity
-
name
:
test-java-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -34,6 +42,8 @@
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
-
name
:
test-no-gatk
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -42,6 +52,8 @@
stdout
:
contains
:
-
"
You
must
set
--config
GATK=<path>"
tags
:
-
sanity
-
name
:
test-gatk-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -50,6 +62,8 @@
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
-
name
:
test-no-dbsnp
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -58,6 +72,8 @@
stdout
:
contains
:
-
"
You
must
set
--config
DBSNP=<path>"
tags
:
-
sanity
-
name
:
test-dbsnp-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -67,6 +83,8 @@
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
-
name
:
test-no-onethousand
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -75,6 +93,8 @@
stdout
:
contains
:
-
"
You
must
set
--config
ONETHOUSAND=<path>"
tags
:
-
sanity
-
name
:
test-onethousand-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -84,6 +104,8 @@
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
-
name
:
test-no-hapmap
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -93,6 +115,8 @@
stdout
:
contains
:
-
"
You
must
set
--config
HAPMAP=<path>"
tags
:
-
sanity
-
name
:
test-hapmap-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -102,6 +126,8 @@
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
-
name
:
test-no-sample-config
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -111,6 +137,8 @@
stdout
:
contains
:
-
"
You
must
set
--config
SAMPLE_CONFIG=<path>"
tags
:
-
sanity
-
name
:
test-sample-config-does-not-exist
command
:
>
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
...
...
@@ -121,3 +149,5 @@
stdout
:
contains
:
-
"
/very/unlikely/to/exist
does
not
exist"
tags
:
-
sanity
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