From 811b1a5439ae6c00b9bea9161c63a68f4c24d697 Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Mon, 21 Mar 2022 11:54:25 +0100
Subject: [PATCH] cluster config pretext
---
SUBMIT_CONFIG/slurm/cluster.yaml | 82 ++++++++++++++++++++++++++++++--
1 file changed, 77 insertions(+), 5 deletions(-)
diff --git a/SUBMIT_CONFIG/slurm/cluster.yaml b/SUBMIT_CONFIG/slurm/cluster.yaml
index d50e4df..69b8e28 100644
--- a/SUBMIT_CONFIG/slurm/cluster.yaml
+++ b/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"
--
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