Commit e1f91027 authored by Sander Bollen's avatar Sander Bollen
Browse files

remove java dependency

parent 5970e699
Pipeline #2547 passed with stages
in 16 minutes and 45 seconds
......@@ -35,12 +35,6 @@ if not Path(REFERENCE).exists():
raise FileNotFoundError("Reference file {0} "
"does not exist.".format(REFERENCE))
JAVA = config.get("JAVA") # TODO: should be handled by conda?!
if JAVA is None:
raise ValueError("You must set --config JAVA=<path>")
if not Path(JAVA).exists():
raise FileNotFoundError("{0} does not exist".format(JAVA))
GATK = config.get("GATK")
if GATK is None:
raise ValueError("You must set --config GATK=<path>")
......@@ -324,7 +318,6 @@ rule baserecal:
"""Base recalibrated BAM files"""
input:
bam = "{sample}/bams/{sample}.markdup.bam",
java = JAVA,
gatk = GATK,
ref = REFERENCE,
dbsnp = DBSNP,
......@@ -333,7 +326,7 @@ rule baserecal:
output:
grp = "{sample}/bams/{sample}.baserecal.grp"
conda: "envs/gatk.yml"
shell: "{input.java} -XX:ParallelGCThreads=1 -jar {input.gatk} -T "
shell: "java -XX:ParallelGCThreads=1 -jar {input.gatk} -T "
"BaseRecalibrator -I {input.bam} -o {output.grp} -nct 8 "
"-R {input.ref} -cov ReadGroupCovariate -cov QualityScoreCovariate "
"-cov CycleCovariate -cov ContextCovariate -knownSites "
......
......@@ -16,26 +16,6 @@
- "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/
REFERENCE=Snakefile
exit_code: 1
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/
REFERENCE=Snakefile JAVA=/very/unlikely/to/exist
exit_code: 1
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/
......
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