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Commit 7791c651 authored by james94's avatar james94
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configuration/define_resources.yaml
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...@@ -10,25 +10,25 @@ ...@@ -10,25 +10,25 @@
unzipHiC_R1: unzipHiC_R1:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 12000 mem_mb: 500
time: "00:30:05" time: "01:30:05"
threads: 8 threads: 4
# symlinkUnzippedHiC_R1: # symlinkUnzippedHiC_R1:
# jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
# memory: 10 # mem_mb: 10
# time: "00:05:00" # time: "00:05:00"
# threads: 1 # threads: 1
unzipHiC_R2: unzipHiC_R2:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 12000 mem_mb: 500
time: "00:30:05" time: "01:30:05"
threads: 8 threads: 4
# symlinkUnzippedHiC_R2: # symlinkUnzippedHiC_R2:
# jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
# memory: 10 # mem_mb: 10
# time: "00:05:00" # time: "00:05:00"
# threads: 1 # threads: 1
...@@ -36,98 +36,98 @@ unzipHiC_R2: ...@@ -36,98 +36,98 @@ unzipHiC_R2:
pretext_index_PRI_asm: pretext_index_PRI_asm:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 72000 mem_mb: 72000
time: "02:30:00" time: "02:30:00"
threads: 2 threads: 1
pretext_fastq2bam_R1: pretext_fastq2bam_R1:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 32000 mem_mb: 32000
time: "08:00:00" time: "08:00:00"
threads: 12 threads: 12
pretext_fastq2bam_R2: pretext_fastq2bam_R2:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 32000 mem_mb: 32000
time: "08:00:00" time: "08:00:00"
threads: 12 threads: 12
pretext_filter_5primeEnd_R1: pretext_filter_5primeEnd_R1:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 200 mem_mb: 200
time: "08:00:00" time: "08:00:00"
threads: 4 threads: 4
pretext_filter_5primeEnd_R2: pretext_filter_5primeEnd_R2:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 200 mem_mb: 200
time: "08:00:00" time: "08:00:00"
threads: 4 threads: 4
pretext_filtered_combine: pretext_filtered_combine:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 9500 mem_mb: 9500
time: "08:30:00" time: "08:30:00"
threads: 12 threads: 12
pretext_map: pretext_map:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 32000 mem_mb: 32000
time: "08:30:00" time: "08:30:00"
threads: 12 threads: 12
pretext_snapshot: pretext_snapshot:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 500 mem_mb: 500
time: "00:10:00" time: "00:10:00"
threads: 1 threads: 1
pretextMaps2md: # pretextMaps2md:
jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
memory: 500 # mem_mb: 500
time: "00:10:00" # time: "00:10:00"
threads: 1 # threads: 1
unzipFasta_PRI: unzipFasta_PRI:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 500 mem_mb: 500
time: "00:05:00" time: "00:15:00"
threads: 4 threads: 4
# symlinkUnzippedFasta_PRI: # symlinkUnzippedFasta_PRI:
# jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500 # mem_mb: 500
# time: "00:05:00" # time: "00:15:00"
# threads: # threads: 1
unzipFasta_ALT: unzipFasta_ALT:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 500 mem_mb: 500
time: "00:05:00" time: "00:15:00"
threads: 14 threads: 4
#
# symlinkUnzippedFasta_ALT: # symlinkUnzippedFasta_ALT:
# jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
merqury: merqury:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 40000 mem_mb: 40000
time: "08:00:00" time: "08:00:00"
threads: 12 threads: 8
busco5: busco5:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 150000 mem_mb: 150000
time: "1-00:00:00" time: "1-00:00:00"
threads: 16 threads: 16
...@@ -135,7 +135,7 @@ busco5: ...@@ -135,7 +135,7 @@ busco5:
# moveBuscoOutputs: # moveBuscoOutputs:
# jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
...@@ -148,60 +148,60 @@ busco5: ...@@ -148,60 +148,60 @@ busco5:
genomescope2: genomescope2:
jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer} jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
memory: 500 mem_mb: 500
time: "00:05:00" time: "00:15:00"
threads: 1 threads: 1
assemblyStats: assemblyStats:
jobname: GEP.{rule}.{wildcards.asmID} jobname: GEP.{rule}.{wildcards.asmID}
memory: 500 mem_mb: 500
time: "00:05:00" time: "00:15:00"
threads: 1 threads: 1
# saveConfiguration_and_getKeyValues_kmer: # saveConfiguration_and_getKeyValues_kmer:
# jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer} # jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
# memory: 500 # mem_mb: 500
# time: "00:05:00" # time: "00:05:00"
# threads: 1 # threads: 1
# #
# #
# saveConfiguration_and_getKeyValues: # saveConfiguration_and_getKeyValues:
# jobname: GEP.{rule}.{wildcards.asmID} # jobname: GEP.{rule}.{wildcards.asmID}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
# #
# #
# aggregateAllAssemblies: # aggregateAllAssemblies:
# jobname: GEP.{rule} # jobname: GEP.{rule}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
#
# makeReport: # makeReport:
# jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer} # jobname: GEP.{rule}.{wildcards.asmID}.{wildcards.kmer}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
# #
# #
# addFullTable: # addFullTable:
# jobname: GEP.{rule} # jobname: GEP.{rule}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
# #
# aggregateReport: # aggregateReport:
# jobname: GEP.{rule} # jobname: GEP.{rule}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# threads: 1 # threads: 1
makePDF: makePDF:
jobname: GEP.{rule} jobname: GEP.{rule}
memory: 1000 mem_mb: 1000
time: "00:10:05" time: "00:10:05"
threads: 1 threads: 1
...@@ -209,26 +209,26 @@ makePDF: ...@@ -209,26 +209,26 @@ makePDF:
unzipFastq_R1: unzipFastq_R1:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
memory: 96000 mem_mb: 96000
time: "00:30:05" time: "01:45:05"
threads: 2 threads: 4
unzipFastq_R2: unzipFastq_R2:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
memory: 96000 mem_mb: 96000
time: "00:30:05" time: "01:45:05"
threads: 4 threads: 4
# symlinkUnzippedFastq_R1: # symlinkUnzippedFastq_R1:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
# memory: 500 # mem_mb: 500
# time: "00:01:35" # time: "00:01:35"
# threads: 1 # threads: 1
# #
# symlinkUnzippedFastq_R2: # symlinkUnzippedFastq_R2:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}.{wildcards.trimAdapters}
# memory: 500 # mem_mb: 500
# time: "00:01:35" # time: "00:01:35"
# threads: 1 # threads: 1
...@@ -237,75 +237,75 @@ unzipFastq_R2: ...@@ -237,75 +237,75 @@ unzipFastq_R2:
# symLink_trim10xbarcodes_notrimAdapt: # symLink_trim10xbarcodes_notrimAdapt:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500 # mem_mb: 500
# time: "00:01:35" # time: "00:01:35"
# threads: 1 # threads: 1
# #
# symlinks_no10xOrAdaptTrim: # symlinks_no10xOrAdaptTrim:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500 # mem_mb: 500
# time: "00:01:35" # time: "00:01:35"
# threads: 1 # threads: 1
# #
# #
# symlinks_no10xwithAdaptTrim: # symlinks_no10xwithAdaptTrim:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500 # mem_mb: 500
# time: "00:01:35" # time: "00:01:35"
# threads: 1 # threads: 1
# #
# #
# symlink_trim10xbarcodesR2: # symlink_trim10xbarcodesR2:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}
# memory: 500 # mem_mb: 500
# time: "00:01:35" # time: "00:01:35"
# threads: 1 # threads: 1
trim10xbarcodes: trim10xbarcodes:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}
memory: 500 mem_mb: 500
time: "04:00:05" time: "02:30:05"
threads: 4 threads: 4
trimAdapters: trimAdapters:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trim10x}
memory: 500 mem_mb: 500
time: "04:00:05" time: "02:30:05"
threads: 8 threads: 8
fastqc_Illumina: fastqc_Illumina:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}
memory: 1000 mem_mb: 1000
time: "04:00:05" time: "04:00:05"
threads: 4 threads: 4
# multiqc_hifi: # multiqc_hifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}
# memory: 500 # mem_mb: 500
# time: "01:00:05" # time: "01:00:05"
# threads: 1 # threads: 1
meryl_R1: meryl_R1:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
memory: 20000 mem_mb: 20000
time: "01:00:05" time: "01:30:05"
threads: 8 threads: 12
meryl_R2: meryl_R2:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
memory: 20000 mem_mb: 20000
time: "01:00:05" time: "01:30:05"
threads: 8 threads: 12
meryl_illumina_build: meryl_illumina_build:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.trimAdapters}.{wildcards.trim10x}.{wildcards.kmer}
memory: 30000 mem_mb: 30000
time: "00:45:05" time: "02:45:05"
threads: 8 threads: 12
...@@ -313,48 +313,43 @@ meryl_illumina_build: ...@@ -313,48 +313,43 @@ meryl_illumina_build:
###### HIFI BUILD ####### ###### HIFI BUILD #######
unzipHifi: unzipHifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
memory: 128000 mem_mb: 128000
time: "00:30:05" time: "00:30:05"
threads: 4
# symlinkUnzippedHifi: # symlinkUnzippedHifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
# symlinkfornotSmartTrimmed: # symlinkfornotSmartTrimmed:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter} # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
# memory: 500 # mem_mb: 500
# time: "00:05:05" # time: "00:05:05"
fastqc_hifi: fastqc_hifi:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
memory: 12000 mem_mb: 12000
time: "04:00:05" time: "04:00:05"
threads: 4
# multiqc_hifi: multiqc_hifi:
# # jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
# memory: 4000 mem_mb: 4000
# time: "01:15:05" time: "01:15:05"
meryl_hifi_count: meryl_hifi_count:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}.{wildcards.kmer} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}.{wildcards.kmer}
memory: 96000 mem_mb: 96000
time: "04:30:05" time: "02:30:05"
threads: 16
meryl_hifi_build: meryl_hifi_build:
# jobname: GEP.{rule}.{wildcards.sample}.{wildcards.smrtornot}.{wildcards.kmer} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.smrtornot}.{wildcards.kmer}
memory: 96000 mem_mb: 96000
time: "04:30:05" time: "01:30:05"
threads: 16
trimSMRTbell: trimSMRTbell:
jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter} jobname: GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}
memory: 96000 mem_mb: 96000
time: "04:30:05" time: "01:30:05"
threads: 8
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