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R2915/example_pipelines/MelArray/pipeline/subworkflows/AnaCovar.snake
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AnaCovar.snake
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################################################
## MelArray - Analyze Covariates sub-pipeline ##
################################################
#
# @author: Phil Cheng, USZ (for original pipeline)
# @author: Balazs Laurenczy, ETHZ (for Snakemake pipeline)
# @date: 2017-2018
########
# INIT #
########
# if this Snakefile runs as a subworkflow
if "subw_outputs_dict" in locals() and "IDs" in locals():
# specify the final required outputs by expanding the final output with some existing IDs
subw_outputs_dict['AnaCovar'] = expand(paths['recal_plots'], id = IDs)
#########
# RULES #
#########
# post recalibration step
rule postrecal:
input:
fixmate_bam = paths['fixmate_bam'],
fixmate_bai = paths['fixmate_bai'],
base_recal_table = paths['base_recal_table']
output:
postrecal_table = paths['postrecal_table']
log:
postrecal_out = paths['postrecal_out']
shell:
# wrap the whole command in one string
(
# append the Singularity container call (if needed)
SINGULARITY_CMD +
# create the command for GATK with the amount of memory specified in the config
'gatk --java-options "-Xmx{memory}G" '.format(**soft['gatk']) +
# specify the GATK JAR path, the GATK command and the reference genome
'BaseRecalibrator -R {ref_genome} '.format(**rule_paths) +
# specify the reference files
'-known-sites {dbsnp} -known-sites {mills} -known-sites {1000G} -known-sites {gnomAD} -L {bed} '.format(**rule_paths) +
# specify the inputs and output path
'--input {fixmate_bam} -bqsr {base_recal_table} --output {postrecal_table} '.format(**rule_paths) +
# specify the interval padding
'--interval-padding {interval_padding} '.format(**soft['postrecal']) +
# dump all standard and error output to the log file
'&> {postrecal_out}'.format(**paths)
# replace all instances of '{id}' with '{wildcards.id}'
).replace('{id}', '{wildcards.id}')
# analyze covariates step
rule analyze_covariates:
input:
base_recal_table = paths['base_recal_table'],
postrecal_table = paths['postrecal_table']
output:
recal_plots = paths['recal_plots']
log:
recal_plots_out = paths['recal_plots_out']
shell:
# wrap the whole command in one string
(
# append the Singularity container call (if needed)
SINGULARITY_CMD +
# create the command for GATK with the amount of memory specified in the config
'gatk --java-options "-Xmx{memory}G" '.format(**soft['gatk']) +
# specify the GATK JAR path, the GATK command and the reference genome
'AnalyzeCovariates -R {ref_genome} '.format(**rule_paths) +
# specify the inputs and outputs
'-before {base_recal_table} -after {postrecal_table} -plots {recal_plots} '.format(**rule_paths) +
# dump all standard and error output to the log file
'&> {recal_plots_out}'.format(**paths)
# replace all instances of '{id}' with '{wildcards.id}'
).replace('{id}', '{wildcards.id}')
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