cluster config pretext

SUBMIT_CONFIG/slurm/cluster.yaml

@@ -5,6 +5,78 @@ __default__:
     qos:        'standard'
 
 
+
+#### PRETEXT ####
+
+unzipHiC_R1:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     96000
+    time:       "00:30:05"
+
+symlinkUnzippedHiC_R1:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     500
+    time:       "00:05:00"
+
+unzipHiC_R2:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     96000
+    time:       "00:30:05"
+
+symlinkUnzippedHiC_R2:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     500
+    time:       "00:05:00"
+
+
+
+pretext_index_PRI_asm:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+pretext_fastq2bam_R1:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+pretext_fastq2bam_R2:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+pretext_filter_5primeEnd_R1:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+pretext_filter_5primeEnd_R2:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+
+pretext_filtered_combine:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+pretext_map:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     9500
+    time:       "02:30:00"
+
+pretext_snapshot:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     500
+    time:       "00:10:00"
+
+pretextMaps2md:
+    jobname:    GEP.{rule}.{wildcards.asmID}
+    memory:     500
+    time:       "00:10:00"
+
+
 unzipFasta_PRI:
     jobname:    GEP.{rule}.{wildcards.asmID}
     memory:     500
@@ -100,8 +172,8 @@ aggregateReport:
 
 makePDF:
     jobname:    GEP.{rule}
-    memory:     500
-    time:       "00:05:05"
+    memory:     1000
+    time:       "00:10:05"
 
 ###### Rules for illuminadb building ##########
 
@@ -211,17 +283,17 @@ symlinkfornotSmartTrimmed:
     time:       "00:05:05"
 
 
-fastqc_hifi_SMRT_removed:
+fastqc_hifi:
     jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
     memory:     12000
     time:       "00:45:05"
 
-multiqc_hifi_SMRTremoved:
+multiqc_hifi:
     jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}
     memory:     4000
     time:       "00:15:05"
 
-meryl_hifi_trimmed_count:
+meryl_hifi_count:
     jobname:    GEP.{rule}.{wildcards.sample}.{wildcards.readCounter}.{wildcards.smrtornot}.{wildcards.kmer}
     memory:     96000
     time:       "02:30:05"