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Add configurable rules for additional variant callers #75

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126 changes: 126 additions & 0 deletions config/day_profiles/local/templates/rule_config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -371,6 +371,132 @@ lofreq2:
b37_lofreq_chrms: "19~1-50000000,19~50000001-59128983,21~1-48129895" # 1~1-50000000,1~50000001-100000000,1~100000001-150000000,1~150000001-200000000,1~200000001-249250621,2~1-50000000,2~50000001-100000000,2~100000001-150000000,2~150000001-200000000,2~200000001-243199373,3~1-50000000,3~50000001-100000000,3~100000001-150000000,3~150000001-198022430,4~1-50000000,4~50000001-100000000,4~100000001-150000000,4~150000001-191154276,5~1-50000000,5~50000001-100000000,5~100000001-150000000,5~150000001-180915260,6~1-50000000,6~50000001-100000000,6~100000001-150000000,6~150000001-171115067,7~1-50000000,7~50000001-100000000,7~100000001-150000000,7~150000001-159138663,8~1-50000000,8~50000001-100000000,8~100000001-146364022,9~1-50000000,9~50000001-100000000,9~100000001-141213431,10~1-50000000,10~50000001-100000000,10~100000001-135534747,11~1-50000000,11~50000001-100000000,11~100000001-135006516,12~1-50000000,12~50000001-100000000,12~100000001-133851895,13~1-50000000,13~50000001-100000000,13~100000001-115169878,14~1-50000000,14~50000001-100000000,14~100000001-107349540,15~1-50000000,15~50000001-100000000,15~100000001-102531392,16~1-50000000,16~50000001-90354753,17~1-50000000,17~50000001-81195210,18~1-50000000,18~50000001-78077248,19~1-50000000,19~50000001-59128983,20~1-50000000,20~50000001-63025520,21~1-48129895,22~1-50000000,22~50000001-51304566,23~1-50000000,23~50000001-100000000,23~100000001-150000000,23~150000001-155270560,24~1-50000000,24~50000001-59373566"
numa: " OMP_THREADS=64 OMP_PROC_BIND=close OMP_PLACES=threads OMP_PROC_BIND=TRUE OMP_DYNAMIC=TRUE OMP_MAX_ACTIVE_LEVELS=1 OMP_SCHEDULE=dynamic OMP_WAIT_POLICY=ACTIVE "

ascat:
threads: 8
partition: "i8"
mem_mb: 48000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

cnvkit:
threads: 8
partition: "i8"
mem_mb: 48000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

control_freec:
threads: 8
partition: "i8"
mem_mb: 48000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

freebayes:
threads: 8
partition: "i8"
mem_mb: 24000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

gatk_haplotypecaller:
threads: 8
partition: "i8"
mem_mb: 32000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

gatk_mutect2:
threads: 16
partition: "i8"
mem_mb: 64000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

indexcov:
threads: 4
partition: "i8"
mem_mb: 16000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

mpileup:
threads: 4
partition: "i8"
mem_mb: 16000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

msisensor2:
threads: 8
partition: "i8"
mem_mb: 24000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

msisensor_pro:
threads: 8
partition: "i8"
mem_mb: 24000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

muse:
threads: 12
partition: "i8"
mem_mb: 48000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

strelka:
threads: 12
partition: "i8"
mem_mb: 48000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

parascopy:
threads: 4
partition: "i8"
Expand Down
126 changes: 126 additions & 0 deletions config/day_profiles/slurm/templates/rule_config.yaml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -309,6 +309,132 @@ lofreq2:
b37_lofreq_chrms: "1~1-50000000,1~50000001-100000000,1~100000001-150000000,1~150000001-200000000,1~200000001-249250621,2~1-50000000,2~50000001-100000000,2~100000001-150000000,2~150000001-200000000,2~200000001-243199373,3~1-50000000,3~50000001-100000000,3~100000001-150000000,3~150000001-198022430,4~1-50000000,4~50000001-100000000,4~100000001-150000000,4~150000001-191154276,5~1-50000000,5~50000001-100000000,5~100000001-150000000,5~150000001-180915260,6~1-50000000,6~50000001-100000000,6~100000001-150000000,6~150000001-171115067,7~1-50000000,7~50000001-100000000,7~100000001-150000000,7~150000001-159138663,8~1-50000000,8~50000001-100000000,8~100000001-146364022,9~1-50000000,9~50000001-100000000,9~100000001-141213431,10~1-50000000,10~50000001-100000000,10~100000001-135534747,11~1-50000000,11~50000001-100000000,11~100000001-135006516,12~1-50000000,12~50000001-100000000,12~100000001-133851895,13~1-50000000,13~50000001-100000000,13~100000001-115169878,14~1-50000000,14~50000001-100000000,14~100000001-107349540,15~1-50000000,15~50000001-100000000,15~100000001-102531392,16~1-50000000,16~50000001-90354753,17~1-50000000,17~50000001-81195210,18~1-50000000,18~50000001-78077248,19~1-50000000,19~50000001-59128983,20~1-50000000,20~50000001-63025520,21~1-48129895,22~1-50000000,22~50000001-51304566,23~1-50000000,23~50000001-100000000,23~100000001-150000000,23~150000001-155270560,24~1-50000000,24~50000001-59373566"
numa: " OMP_THREADS=1 OMP_PROC_BIND=close OMP_PLACES=threads OMP_DYNAMIC=true OMP_MAX_ACTIVE_LEVELS=1 OMP_SCHEDULE=dynamic OMP_WAIT_POLICY=ACTIVE "

ascat:
threads: 24
partition: "i192,i128,i192mem"
mem_mb: 96000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

cnvkit:
threads: 24
partition: "i192,i128,i192mem"
mem_mb: 96000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

control_freec:
threads: 24
partition: "i192,i128,i192mem"
mem_mb: 96000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

freebayes:
threads: 16
partition: "i192,i128,i192mem"
mem_mb: 64000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

gatk_haplotypecaller:
threads: 24
partition: "i192,i128,i192mem"
mem_mb: 96000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

gatk_mutect2:
threads: 48
partition: "i192,i128,i192mem"
mem_mb: 128000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

indexcov:
threads: 8
partition: "i192,i128,i192mem"
mem_mb: 32000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

mpileup:
threads: 8
partition: "i192,i128,i192mem"
mem_mb: 32000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

msisensor2:
threads: 16
partition: "i192,i128,i192mem"
mem_mb: 64000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

msisensor_pro:
threads: 16
partition: "i192,i128,i192mem"
mem_mb: 64000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

muse:
threads: 32
partition: "i192,i128,i192mem"
mem_mb: 128000
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

strelka:
threads: 32
partition: "i192,i128,i192mem"
mem_mb: 128000
use_normal: true
env_yaml: "../envs/vanilla_v0.1.yaml"
reference: ""
extra_inputs: {}
extra_args: ""
command_template: ""

parascopy:
threads: 8
partition: "i192,i128,i192mem"
Expand Down
1 change: 1 addition & 0 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -283,6 +283,7 @@ include: "rules/varnet.smk"
include: "rules/manta.smk"
include: "rules/merge_all_bams.smk"
include: "rules/mosdepth.smk"
include: "rules/additional_variant_callers.smk"
include: "rules/quickmer2.smk"
include: "rules/multiqc_cov_aln.smk"
include: "rules/multiqc_final_wgs.smk"
Expand Down
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