diff --git a/configuration/define_resources.yaml b/configuration/define_resources.yaml
index 1243261d9fed40d264571cd6d3ec5be7991d8687..3098c7c861d3e624bcdaf70add41c16cc0f2b8a1 100644
--- a/configuration/define_resources.yaml
+++ b/configuration/define_resources.yaml
@@ -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"