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.

tests/test_functional_run.yml

-- 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

tests/test_integration_run.yml

-- 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

tests/test_sanity_checks.yml

@@ -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/