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hw6_1.smk
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hw6_1.smk
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SAMPLES = [ "A" ]
print ( "Reading file phase.. #start" )
@workflow.rule(name='all', lineno=5, snakefile='/Users/mikhaillebedev/study/snakemake_tutorial/Snakefile')
@workflow.input(
"plot.svg" ,
expand ( "peaks/{sample}.bed" , sample = SAMPLES )
)
@workflow.norun()
@workflow.run
def __rule_all(input, output, params, wildcards, threads, resources, log, version, rule, conda_env, container_img, singularity_args, use_singularity, env_modules, bench_record, jobid, is_shell, bench_iteration, cleanup_scripts, shadow_dir):
pass
@workflow.rule(name='align', lineno=16, snakefile='/Users/mikhaillebedev/study/snakemake_tutorial/Snakefile')
@workflow.input( "reads/{sample}.fq.gz"
)
@workflow.output( "bams/{sample}.bam"
)
@workflow.run
def __rule_align(input, output, params, wildcards, threads, resources, log, version, rule, conda_env, container_img, singularity_args, use_singularity, env_modules, bench_record, jobid, is_shell, bench_iteration, cleanup_scripts, shadow_dir):
print ( "Executing 'align' rule.." )
@workflow.rule(name='call_peaks', lineno=29, snakefile='/Users/mikhaillebedev/study/snakemake_tutorial/Snakefile')
@workflow.input( "bams/{sample}.bam"
)
@workflow.output( "peaks/{sample}.bed"
)
@workflow.script ( "scripts/call_peaks.py"
)
@workflow.run
def __rule_call_peaks(input, output, params, wildcards, threads, resources, log, version, rule, conda_env, container_img, singularity_args, use_singularity, env_modules, bench_record, jobid, is_shell, bench_iteration, cleanup_scripts, shadow_dir):
script ( "scripts/call_peaks.py" , '/Users/mikhaillebedev/study/snakemake_tutorial/Snakefile' , input, output, params, wildcards, threads, resources, log, config, rule, conda_env, container_img, singularity_args, env_modules, bench_record, jobid, bench_iteration, cleanup_scripts, shadow_dir
)
@workflow.rule(name='plot', lineno=45, snakefile='/Users/mikhaillebedev/study/snakemake_tutorial/Snakefile')
@workflow.input(
expand ( "peaks/{sample}.bed" , sample = SAMPLES )
)
@workflow.output( "plot.svg"
)
@workflow.shellcmd ( "echo TODO"
)
@workflow.run
def __rule_plot(input, output, params, wildcards, threads, resources, log, version, rule, conda_env, container_img, singularity_args, use_singularity, env_modules, bench_record, jobid, is_shell, bench_iteration, cleanup_scripts, shadow_dir):
shell ( "echo TODO" , bench_record=bench_record, bench_iteration=bench_iteration
)
print ( "Reading file phase.. #end" )
Reading file phase.. #start
Reading file phase.. #end