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adjusted memory & time requirements #78

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adjusted memory & time requirements #78

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48 changes: 27 additions & 21 deletions config/sbatch.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,92 +6,98 @@ __default__:
queue: "debug"
error: "logs/%x_%j_%N.err"
output: "logs/%x_%j_%N.log"

##################
### ASSIGNMENT ###
##################

assignment_getInputs:
time: "0-10:00"
queue: medium

assignment_merge:
time: "0-08:00"
queue: medium

assignment_fastq_split:
time: "0-02:00"
threads: 1
mem: 10G
queue: medium

assignment_mapping:
time: "0-02:00"
threads: 10
mem: 10G
queue: medium

assignment_collect:
time: "1-12:00"
threads: 30
mem: 10G
queue: medium

assignment_getBCs:
time: "0-04:00"
threads: 1
queue: short

assignment_statistic_totalCounts:
time: "0-01:00"
threads: 1
queue: medium
mem: 60G

assignment_statistic_assignedCounts:
time: "0-01:00"
threads: 1
queue: medium
mem: 10G

assignment_statistic_assignment:
time: "0-01:00"
threads: 1
queue: medium
mem: 20G

##############
### COUNTS ###
##############

counts_demultiplexed_BAM_umi:
time: "4-00:00"
mem: 22G
queue: "medium"

counts_mergeTrimReads_demultiplexed_BAM_umi:
time: "4-00:00"
mem: 12G
queue: "medium"

counts_create_BAM_umi:
time: "4-00:00"
mem: 12G
time: "2-00:00"
queue: "medium"

counts_raw_counts_umi:
time: "0-22:00"
mem: 6G
time: "0-12:00"
queue: "medium"

counts_final_counts_umi_samplerer:
mem: 20G
queue: medium
#########################
### (ASSIGNED) COUNTS ###
#########################


counts_dna_rna_merge_counts:
time: "0-10:00"
time: "0-06:00"
queue: "medium"

#######################
### ASSIGNED COUNTS ###
#######################

assigned_counts_dna_rna_merge:
time: "4-00:00"
time: "0-12:00"
mem: 20G
queue: "medium"

assigned_counts_assignBarcodes:
time: "4-00:00"
time: "0-12:00"
queue: "medium"
mem: 10G
mem: 20G

assigned_counts_createAssignmentPickleFile:
mem: 10G
Expand All @@ -114,7 +120,7 @@ statistic_counts_frequent_umis:
queue: "medium"

statistic_counts_barcode_base_composition:
time: "1-00:00"
time: "0-12:00"
queue: "medium"
mem: 20G

Expand All @@ -128,8 +134,8 @@ statistic_correlation_bc_counts:
queue: "medium"

statistic_correlation_calculate:
time: "2-00:00"
mem: 120G
time: "1-00:00"
mem: 20G
queue: "medium"

############################
Expand All @@ -138,5 +144,5 @@ statistic_correlation_calculate:

statistic_bc_overlap_run:
time: "0-05:00"
mem: 10G
mem: 20G
queue: "medium"