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cluster.yaml
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cluster.yaml
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__default__:
time: 5:00:00
threads: 5
vmem: 10G
#stderr: logs/snakejob.{rule}.{wildcards.sample}.{jobid}.err
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.library}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
make_mt_gmap_db:
time: 3:00:00
threads: 1
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.ref_genome_mt}.out
make_mt_n_gmap_db:
time: 3:00:00
threads: 1
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
fastqc_raw:
time: 1:00:00
threads: 2
vmem: 4G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.library}.out
fastqc_filtered:
time: 1:00:00
threads: 3
vmem: 4G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.library}.out
trimmomatic:
time: 2:00:00
threads: 4
vmem: 4G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.library}.out
map_nuclear_MT_PE:
time: 3:00:00
threads: 4
map_nuclear_MT_SE:
time: 3:00:00
threads: 4
sam2fastq:
time: 3:00:00
threads: 1
filtering_mt_alignments:
time: 5:00:00
threads: 1
vmem: 10G
sam2bam:
time: 3:00:00
threads: 1
vmem: 3G
sort_bam:
time: 3:00:00
threads: 1
vmem: 3G
mark_duplicates:
time: 3:00:00
threads: 1
vmem: 3G
merge_bam:
time: 3:00:00
threads: 1
vmem: 3G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
left_align_merged_bam:
time: 3:00:00
threads: 1
vmem: 4G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
clip_bam:
time: 3:00:00
threads: 1
vmem: 3G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
clip_bam_recalculate_MD:
time: 3:00:00
threads: 1
vmem: 3G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
bam2cov:
time: 3:00:00
threads: 1
vmem: 3G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
make_single_VCF:
time: 3:00:00
threads: 1
vmem: 3G
stdout: logs/cluster_jobs/snakejob.{rule}.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out
variant_calling:
time: 3:00:00
threads: 1
vmem: 4G
stdout: logs/cluster_jobs/snakejob.variant_calling.out
#stdout: logs/cluster_jobs/snakejob.variant_calling.{wildcards.sample}.{wildcards.ref_genome_mt}.{wildcards.ref_genome_n}.out