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feat: add cram support to applybsqr (#563)
* add cram support to applybsqr * reference is 'ref' in input, cram support in spark * fix test config * cram output in tests, not input * added pipe symbol * wrapper path wrong * more parameters in snakefile for spark
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Original file line number | Diff line number | Diff line change |
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|
@@ -6,3 +6,4 @@ dependencies: | |
- gatk4 =4.2 | ||
- openjdk =8 | ||
- snakemake-wrapper-utils =0.3 | ||
- samtools =1.16 |
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@@ -0,0 +1,18 @@ | ||
rule gatk_applybqsr: | ||
input: | ||
bam="mapped/{sample}.bam", | ||
ref="genome.fasta", | ||
dict="genome.dict", | ||
recal_table="recal/{sample}.grp", | ||
output: | ||
bam="recal/{sample}.cram", | ||
log: | ||
"logs/gatk/gatk_applybqsr/{sample}.log", | ||
params: | ||
extra="", # optional | ||
java_opts="", # optional | ||
embed_ref=True, # embed the reference in cram output | ||
resources: | ||
mem_mb=1024, | ||
wrapper: | ||
"master/bio/gatk/applybqsr" |
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -6,3 +6,4 @@ dependencies: | |
- gatk4 =4.2 | ||
- openjdk =8 | ||
- snakemake-wrapper-utils =0.3 | ||
- samtools =1.16 |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,22 @@ | ||
rule gatk_applybqsr_spark: | ||
input: | ||
bam="mapped/{sample}.bam", | ||
ref="genome.fasta", | ||
dict="genome.dict", | ||
recal_table="recal/{sample}.grp", | ||
output: | ||
bam="recal/{sample}.cram", | ||
log: | ||
"logs/gatk/gatk_applybqsr_spark/{sample}.log", | ||
params: | ||
extra="", # optional | ||
java_opts="", # optional | ||
#spark_runner="", # optional, local by default | ||
#spark_master="", # optional | ||
#spark_extra="", # optional | ||
embed_ref=True, # embed reference in cram output | ||
exceed_thread_limit=True, # samtools is also parallized | ||
resources: | ||
mem_mb=1024, | ||
wrapper: | ||
"master/bio/gatk/applybqsrspark" |
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