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Commit 7791c651 authored by james94's avatar james94
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memory

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configuration/define_resources.yaml
+ 92
− 97
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......@@ -10,25 +10,25 @@
unzipHiC_R1:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 12000
time: "00:30:05"
threads: 8
mem_mb: 500
time: "01:30:05"
threads: 4
# symlinkUnzippedHiC_R1:
# jobname: GEP.{rule}.{wildcards.asmID}
# memory: 10
# mem_mb: 10
# time: "00:05:00"
# threads: 1
unzipHiC_R2:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 12000
time: "00:30:05"
threads: 8
mem_mb: 500
time: "01:30:05"
threads: 4
# symlinkUnzippedHiC_R2:
# jobname: GEP.{rule}.{wildcards.asmID}
# memory: 10
# mem_mb: 10
# time: "00:05:00"
# threads: 1
......@@ -36,98 +36,98 @@ unzipHiC_R2:
pretext_index_PRI_asm:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 72000
mem_mb: 72000
time: "02:30:00"
threads: 2
threads: 1
pretext_fastq2bam_R1:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 32000
mem_mb: 32000
time: "08:00:00"
threads: 12
pretext_fastq2bam_R2:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 32000
mem_mb: 32000
time: "08:00:00"
threads: 12
pretext_filter_5primeEnd_R1:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 200
mem_mb: 200
time: "08:00:00"
threads: 4
pretext_filter_5primeEnd_R2:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 200
mem_mb: 200
time: "08:00:00"
threads: 4
pretext_filtered_combine:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 9500
mem_mb: 9500
time: "08:30:00"
threads: 12
pretext_map:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 32000
mem_mb: 32000
time: "08:30:00"
threads: 12
pretext_snapshot:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
mem_mb: 500
time: "00:10:00"
threads: 1
pretextMaps2md:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:10:00"
threads: 1
# pretextMaps2md:
# jobname: GEP.{rule}.{wildcards.asmID}
# mem_mb: 500
# time: "00:10:00"
# threads: 1
unzipFasta_PRI:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:05:00"
mem_mb: 500
time: "00:15:00"
threads: 4
# symlinkUnzippedFasta_PRI:
# jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500
# time: "00:05:00"
# threads:
# mem_mb: 500
# time: "00:15:00"
# threads: 1
unzipFasta_ALT:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:05:00"
threads: 14
mem_mb: 500
time: "00:15:00"
threads: 4
#
# symlinkUnzippedFasta_ALT:
# jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
merqury:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 40000
mem_mb: 40000
time: "08:00:00"
threads: 12
threads: 8
busco5:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 150000
mem_mb: 150000
time: "1-00:00:00"
threads: 16
......@@ -135,7 +135,7 @@ busco5:
# moveBuscoOutputs:
# jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
......@@ -148,60 +148,60 @@ busco5:
genomescope2:
jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
memory: 500
time: "00:05:00"
mem_mb: 500
time: "00:15:00"
threads: 1
assemblyStats:
jobname: GEP.{rule}.{wildcards.asmID}
memory: 500
time: "00:05:00"
mem_mb: 500
time: "00:15:00"
threads: 1
# saveConfiguration_and_getKeyValues_kmer:
# jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
# memory: 500
# mem_mb: 500
# time: "00:05:00"
# threads: 1
#
#
# saveConfiguration_and_getKeyValues:
# jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
#
#
# aggregateAllAssemblies:
# jobname: GEP.{rule}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
#
# makeReport:
# jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
#
#
# addFullTable:
# jobname: GEP.{rule}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
#
# aggregateReport:
# jobname: GEP.{rule}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# threads: 1
makePDF:
jobname: GEP.{rule}
memory: 1000
mem_mb: 1000
time: "00:10:05"
threads: 1
......@@ -209,26 +209,26 @@ makePDF:
unzipFastq_R1:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
memory: 96000
time: "00:30:05"
threads: 2
mem_mb: 96000
time: "01:45:05"
threads: 4
unzipFastq_R2:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
memory: 96000
time: "00:30:05"
mem_mb: 96000
time: "01:45:05"
threads: 4
# symlinkUnzippedFastq_R1:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
# memory: 500
# mem_mb: 500
# time: "00:01:35"
# threads: 1
#
# symlinkUnzippedFastq_R2:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
# memory: 500
# mem_mb: 500
# time: "00:01:35"
# threads: 1
......@@ -237,75 +237,75 @@ unzipFastq_R2:
# symLink_trim10xbarcodes_notrimAdapt:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500
# mem_mb: 500
# time: "00:01:35"
# threads: 1
#
# symlinks_no10xOrAdaptTrim:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500
# mem_mb: 500
# time: "00:01:35"
# threads: 1
#
#
# symlinks_no10xwithAdaptTrim:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500
# mem_mb: 500
# time: "00:01:35"
# threads: 1
#
#
# symlink_trim10xbarcodesR2:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}
# memory: 500
# mem_mb: 500
# time: "00:01:35"
# threads: 1
trim10xbarcodes:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}
memory: 500
time: "04:00:05"
mem_mb: 500
time: "02:30:05"
threads: 4
trimAdapters:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}
memory: 500
time: "04:00:05"
mem_mb: 500
time: "02:30:05"
threads: 8
fastqc_Illumina:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}
memory: 1000
mem_mb: 1000
time: "04:00:05"
threads: 4
# multiqc_hifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}
# memory: 500
# mem_mb: 500
# time: "01:00:05"
# threads: 1
meryl_R1:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
memory: 20000
time: "01:00:05"
threads: 8
mem_mb: 20000
time: "01:30:05"
threads: 12
meryl_R2:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
memory: 20000
time: "01:00:05"
threads: 8
mem_mb: 20000
time: "01:30:05"
threads: 12
meryl_illumina_build:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
memory: 30000
time: "00:45:05"
threads: 8
mem_mb: 30000
time: "02:45:05"
threads: 12
......@@ -313,48 +313,43 @@ meryl_illumina_build:
###### HIFI BUILD #######
unzipHifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
memory: 128000
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
mem_mb: 128000
time: "00:30:05"
threads: 4
# symlinkUnzippedHifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
# symlinkfornotSmartTrimmed:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500
# mem_mb: 500
# time: "00:05:05"
fastqc_hifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
memory: 12000
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
mem_mb: 12000
time: "04:00:05"
threads: 4
# multiqc_hifi:
# # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
# memory: 4000
# time: "01:15:05"
multiqc_hifi:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
mem_mb: 4000
time: "01:15:05"
meryl_hifi_count:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}.{wildcards.kmer}
memory: 96000
time: "04:30:05"
threads: 16
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}.{wildcards.kmer}
mem_mb: 96000
time: "02:30:05"
meryl_hifi_build:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.smrtornot}.{wildcards.kmer}
memory: 96000
time: "04:30:05"
threads: 16
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.smrtornot}.{wildcards.kmer}
mem_mb: 96000
time: "01:30:05"
trimSMRTbell:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
memory: 96000
time: "04:30:05"
threads: 8
mem_mb: 96000
time: "01:30:05"
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