Merge pull request #10 from LUMC/develop

Full rewrite of the pipeline

tests/data/reference/target_genes.bed

+chrM	7444	7515

tests/data/sample_config.json

-{
-  "samples": {
-    "micro": {
-      "libraries": {
-        "lib_01": {
-        "R1": "tests/data/micro_R1.fq.gz",
-        "R2": "tests/data/micro_R2.fq.gz"
-      }
-      }
-    }
-  }
-}
\ No newline at end of file

tests/test_dry_run.yml

-- name: test-dry-run
-  command: >-
-    snakemake -n -r -p -s Snakefile --config OUTPUT_DIR=teststtest/
-    JAVA=README.md REFERENCE=tests/data/ref.fa GATK=README.md
-    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
+- name: dry-run-vanilla
+  tags:
+    - dry-run
+  command: >
+    snakemake -n -r -p -s Snakefile --configfile
+    tests/data/config/sample_config.json
   exit_code: 0
   stdout:
     contains:
-      - "Job counts"
-      - "localrule all:"
+      - Job counts
+      - 'localrule all:'
+      - 'output: micro/vcf/micro.vcf.gz'
+      - 'output: micro/vcf/micro.g.vcf.gz'
+      - multiple_metrics
+      - 'output: stats.tsv'
+      - micro/bams/micro.alignment_summary_metrics
+      - micro/bams/micro.insert_size_metrics
     must_not_contain:
-      - "rror"
+      - rror
+      - rule multisample_vcf
   stderr:
     must_not_contain:
-      - "rror"
+      - rror
+
+- name: dry-run-target-baits
   tags:
     - dry-run
+  command: >
+    snakemake -n -r -p -s Snakefile --configfile
+    tests/data/config/sample_config_target_baits.json
+  exit_code: 0
+  stdout:
+    contains:
+      - Job counts
+      - 'localrule all:'
+      - hs_metrics
+      - micro.hs_metrics.txt
+    must_not_contain:
+      - rror
+  stderr:
+    must_not_contain:
+      - rror
+
+- name: dry-run-bed-coverage
+  tags:
+    - dry-run
+  command: >
+    snakemake -s Snakefile -n --configfile
+    tests/data/config/sample_config_bed_coverage.json
+  stdout:
+    contains:
+    - 'output: micro/vcf/micro_10.bed'
+    - 'output: micro/vcf/micro_60.bed'
+    - 'output: micro/vcf/micro_120.bed'
+    - 'output: micro/vcf/micro_196.bed'
+
+- name: dry-run-multisample
+  tags:
+    - dry-run
+  command: >
+    snakemake -s Snakefile -n --configfile
+    tests/data/config/sample_config_multisample.json
+  exit_code: 0
+  stdout:
+    contains:
+      - Job counts
+      - rule multisample_vcf

tests/test_functional_run.yml

-- name: test-integration-run
-  command: >-
-    bash -c '
-    snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
-    --cluster "sbatch --parsable"
-    --cluster-status "${PWD}/cluster/slurm-cluster-status/slurm-cluster-status.py"
-    -r -p -s Snakefile
-    --config JAVA=$(which java)
-    REFERENCE=${FUNCTIONAL_REF} GATK=${GATK_JAR}
-    DBSNP=${FUNCTIONAL_DBSNP}
-    ONETHOUSAND=${FUNCTIONAL_ONETHOUSAND}
-    HAPMAP=${FUNCTIONAL_HAPMAP}
-    SAMPLE_CONFIG=${FUNCTIONAL_SAMPLE_CONFIG}'
-  exit_code: 0
-  stderr:
-    contains:
-      - "Job counts"
-      - "localrule all:"
-      - "(100%) done"
-    must_not_contain:
-      - "rror"
-  tags:
-    - functional

tests/test_sanity.yml

+- name: sanity-no-reference
+  tags:
+    - sanity
+  command: >
+    snakemake -n -r -p -s Snakefile --configfile
+    tests/data/config/invalid_config_no_ref.json
+  exit_code: 1
+  stdout:
+    contains:
+      - 'Invalid --configfile: ''reference'' is a required property'
+
+- name: sanity-reference-does-not-exist
+  tags:
+    - sanity
+  command: >
+    snakemake -n -r -p -s Snakefile --configfile
+    tests/data/config/invalid_config_fake_ref.json
+  exit_code: 1
+  stdout:
+    contains:
+      - Missing input files for rule align
+      - /this/file/is/not/there
+
+- name: sanity-snakemake
+  tags:
+    - sanity
+  command: |
+    snakemake --version
+
+- name: sanity-singularity
+  tags:
+    - sanity
+  command: |
+    singularity --version
+  stdout:
+    contains:
+      - singularity version 3
+
+- name: sanity-baits-only
+  tags:
+    - sanity
+  command: >
+    snakemake -s Snakefile -n --configfile
+    tests/data/config/invalid_config_baitsfile_only.json
+  exit_code: 1
+  stdout:
+    contains:
+      - 'Invalid --configfile: "baitsfile" specified without "targetsfile"'
+
+- name: sanity-targets-only
+  tags:
+    - sanity
+  command: >
+    snakemake -s Snakefile -n --configfile
+    tests/data/config/sample_config_targets_only.json
+  stdout:
+    contains:
+      - rule hs_metrics
+
+- name: sanity-samples-overlapping-name
+  tags:
+    - sanity
+  command: >
+    snakemake -s Snakefile -n --configfile
+    tests/data/config/invalid_config_two_samples.json
+  exit_code: 1
+  stdout:
+    contains:
+      - 'Invalid --configfile: sample names should not overlap ("micro1" is contained in "micro12")'
+
+- name: sanity-multisample
+  tags:
+    - sanity
+  command: >
+    snakemake -s Snakefile -n --configfile
+    tests/data/config/sample_config_multisample.json
+
+- name: sanity-snakemake-lint
+  tags:
+    - sanity
+  command: >
+    snakemake --lint --configfile tests/data/config/sample_config.json