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Commit 2fa4b6d6 authored by van den Berg's avatar van den Berg
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Update test cases so all tests pass

Remove deprecated sanity checks for the GAKT jar file and the different
VCF files that are used for BQSR.
Remove the 'functional' tag since it was identical to integration.
Remove the conda specific test cases, since conda has been deprecated.
parent b4c11f69
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1 merge request!13Deprecate conda, make pipeline more general
- name: test-integration-run
command: >-
snakemake
--use-singularity
--singularity-prefix /tmp/singularity
--jobs 10 -w 120
-r -p -s Snakefile
--config
REFERENCE=tests/data/ref.fa
GATK=tests/GenomeAnalysisTK.jar
DBSNP=tests/data/database.vcf.gz
ONETHOUSAND=tests/data/database.vcf.gz
HAPMAP=tests/data/database.vcf.gz
SAMPLE_CONFIG=tests/data/sample_config.json
exit_code: 0
stderr:
contains:
- "Job counts"
- "localrule all:"
- "(100%) done"
must_not_contain:
- "rror"
tags:
- functional
- name: test-integration-run
- name: test-integration-no-cluster
command: >-
bash -c '
snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
--cluster "sbatch --parsable" -r -p -s Snakefile
--config REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
DBSNP=tests/data/database.vcf.gz
ONETHOUSAND=tests/data/database.vcf.gz
HAPMAP=tests/data/database.vcf.gz
SAMPLE_CONFIG=tests/data/sample_config.json'
exit_code: 0
stderr:
contains:
- "Job counts"
- "localrule all:"
- "(100%) done"
must_not_contain:
- "rror"
tags:
- integration
- name: test-singularity-integration-no-cluster
command: >-
bash -c '
snakemake --use-singularity --jobs 100 -w 120
snakemake
--use-singularity
--singularity-prefix /tmp/singularity
--singularity-args ' --bind /tmp'
--jobs 10 -w 120
-r -p -s Snakefile
--config REFERENCE=tests/data/ref.fa GATK=tests/data/ref.fa
--config
REFERENCE=tests/data/ref.fa
DBSNP=tests/data/database.vcf.gz
ONETHOUSAND=tests/data/database.vcf.gz
HAPMAP=tests/data/database.vcf.gz
SAMPLE_CONFIG=tests/data/sample_config.json'
KNOWN_SITES=tests/data/database.vcf.gz
SAMPLE_CONFIG=tests/data/sample_config.json
exit_code: 0
stderr:
contains:
......@@ -37,4 +20,4 @@
must_not_contain:
- "rror"
tags:
- singularity-integration
\ No newline at end of file
- integration
......@@ -16,90 +16,6 @@
- "Reference file /very/unlikely/to/exist does not exist"
tags:
- sanity
- name: test-no-gatk
command: >
snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=/test/
REFERENCE=Snakefile JAVA=Snakefile
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=/very/unlikely/to/exist
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile
DBSNP=/very/unlikely/to/exist
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=/very/unlikely/to/exist
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=Snakefile
exit_code: 1
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/
REFERENCE=Snakefile JAVA=Snakefile GATK=Snakefile DBSNP=Snakefile
ONETHOUSAND=Snakefile HAPMAP=/very/unlikely/to/exist
exit_code: 1
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/
......
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