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cluster.yaml
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# Values specified under __default__ will be inherited by other rules unless they are overridden.
# See https://snakemake.readthedocs.io/en/v7.32.3/snakefiles/configuration.html.
__default__:
time: "12:00:00"
mem: 10g
cpus: "{threads}"
nodes: 1
output: "{DIR_LOGS_CLUSTER}/{rule}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.err"
split_fastq:
time: "48:00:00"
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.err"
compress_fastq:
time: "48:00:00"
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
adaptor_trimming:
mem: 50g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
barcode_id:
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
barcode_identification_efficiency:
time: "05:00:00"
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
split_bpm_dpm:
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
cutadapt_dpm:
mem: 50g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
cutadapt_oligo:
mem: 50g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
bowtie2_align:
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
rename_and_filter_chr:
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
repeat_mask:
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
merge_dna:
time: "24:00:00"
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.err"
fastq_to_bam:
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
merge_beads:
time: "24:00:00"
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.err"
make_clusters:
mem: 50g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.{wildcards.splitid}.err"
merge_clusters:
time: "24:00:00"
mem: 100g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.err"
clusters_all:
time: "24:00:00"
pipeline_counts:
mem: 50g
threshold_tag_and_split:
time: "24:00:00"
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.sample}.err"
index_splitbams:
time: "04:00:00"
mem: 4g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.file}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.file}.err"
generate_splitbam_statistics:
time: "24:00:00"
splitbams_merged:
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.target}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.target}.err"
generate_bigwigs:
mem: 20g
output: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.file}.out"
error: "{DIR_LOGS_CLUSTER}/{rule}.{wildcards.file}.err"