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cluster.yaml
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---
__default__:
time: '06:00:00'
nodes: 1
partition: exacloud
job-name: "{rule}.{wildcards.sample}"
output: logs/{rule}/{wildcards.sample}_%j.out
error: logs/{rule}/{wildcards.sample}_%j.err
cpus-per-task: 4
mem: 8G
trim_galore_pe:
error: logs/trim_galore/{wildcards.sample}_%j.err
output: logs/trim_galore/{wildcards.sample}_%j.out
fastq_screen:
cpus-per-task: 8
error: logs/fastq_screen/{wildcards.sample}.err
output: logs/fastq_screen/{wildcards.sample}.out
bowtie2:
time: '12:00:00'
output: logs/bowtie2/{rule}_%j.out
error: logs/bowtie2/{rule}_%j.err
cpus-per-task: 12
mem: 64G
fragment_length_plot:
job-name: "frag_len"
output: logs/fragment_length_plot/fragment_length_plot.out
error: logs/fragment_length_plot/fragment_length_plot.err
# when and after merging replicates, start using 'cond' wildcards.
merge_bams:
job-name: merge.{wildcards.cond}
output: logs/merge_bams/{wildcards.cond}_%j.out
error: logs/merge_bams/{wildcards.cond}_%j.err
bigwig:
job-name: bw.{wildcards.cond}
output: logs/bigwig/{wildcards.cond}_%j.out
error: logs/bigwig/{wildcards.cond}_%j.err
cpus-per-task: 16
call_peaks:
job-name: peak.{wildcards.cond}
output: logs/call_peaks/{wildcards.cond}_%j.out
error: logs/call_peaks/{wildcards.cond}_%j.err
filter_peaks:
job-name: filter_peaks.{wildcards.cond}
output: logs/filter_peaks/{wildcards.cond}_%j.out
error: logs/filter_peaks/{wildcards.cond}_%j.err
consensus_interval:
job-name: consensus
output: logs/consensus_intervals/consensus_intervals_%j.out
error: logs/consensus_intervals/consensus_intervals_%j.err
cpus-per-task: 2
footprinting:
job-name: foot.{wildcards.cond}
output: logs/footprinting/{wildcards.cond}_%j.out
error: logs/footprinting/{wildcards.cond}_%j.err
cpus-per-task: 16
mem: 32G
diff_motifs:
job-name: diff_motifs
output: logs/diff_motifs/diff_motifs_%j.out
error: logs/diff_motifs/diff_motifs_%j.err
footprint_tracks:
job-name: tracks.{wildcards.cond}
output: logs/footprint_tracks/{wildcards.cond}_%j.out
error: logs/footprint_tracks/{wildcards.cond}_%j.err
differential:
job-name: diff.{wildcards.case}
output: logs/differential/diff_{wildcards.control}_{wildcards.case}_%j.out
error: logs/differential/diff_{wildcards.control}_{wildcards.case}_%j.err
cpus-per-task: 24
mem: 32G
time: '24:00:00'
sort_stats:
job-name: sort_stats
output: logs/sort_stats/sort_stats_%j.out
error: logs/sort_stats/sort_stats_%j.err
chip_screen:
job-name: "{wildcards.cond}.{wildcards.chip}"
output: "logs/chip_screen/{wildcards.cond}_{wildcards.chip}_%j.out"
error: "logs/chip_screen/{wildcards.cond}_{wildcards.chip}_%j.err"