From fc7d38fa6439aa56b90e29cdc25a0c96935a9d1e Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Mon, 8 Aug 2022 11:56:11 +0200
Subject: [PATCH] change resources
---
configuration/define_resources.yaml | 79 ++++++++++++++---------------
1 file changed, 38 insertions(+), 41 deletions(-)
diff --git a/configuration/define_resources.yaml b/configuration/define_resources.yaml
index e422569..47a48bb 100644
--- a/configuration/define_resources.yaml
+++ b/configuration/define_resources.yaml
@@ -8,63 +8,62 @@
#### PRETEXT ####
-unzipHiC_R1:
- mem_mb: 500
+unzipFastq_R1_HiC:
+ mem_mb: 5000
time: "01:30:05"
threads: 4
-unzipHiC_R2:
- mem_mb: 500
+unzipFastq_R2_HiC:
+ mem_mb: 5000
time: "01:30:05"
threads: 4
-pretext_index_PRI_asm:
+indexFasta_PRI:
mem_mb: 72000
time: "02:30:00"
threads: 1
-pretext_fastq2bam_R1:
+convertFastqTObam_R1_HiC:
mem_mb: 32000
time: "08:00:00"
threads: 12
-pretext_fastq2bam_R2:
+convertFastqTObam_R2_HiC:
mem_mb: 32000
time: "08:00:00"
threads: 12
-pretext_filter_5primeEnd_R1:
- mem_mb: 200
+filter5PrimeEnd_R1_HiC:
+ mem_mb: 2000
time: "08:00:00"
threads: 4
-pretext_filter_5primeEnd_R2:
- mem_mb: 200
+filter5PrimeEnd_R2_HiC:
+ mem_mb: 2000
time: "08:00:00"
threads: 4
-pretext_filtered_combine:
+pairAndCombineFiltered_HiC:
mem_mb: 9500
time: "08:30:00"
threads: 12
-pretext_map:
+pretextMap:
mem_mb: 32000
time: "08:30:00"
threads: 12
-pretext_snapshot:
+pretextSnapshot:
mem_mb: 500
time: "00:10:00"
threads: 1
-
unzipFasta_PRI:
mem_mb: 500
time: "00:15:00"
@@ -90,7 +89,7 @@ busco5:
threads: 16
-genomescope2:
+GenomeScope2Profiles:
mem_mb: 500
time: "00:15:00"
threads: 1
@@ -102,20 +101,20 @@ assemblyStats:
threads: 1
-makePDF:
- mem_mb: 1000
- time: "00:10:05"
- threads: 1
+# ReportWithoutComparisonTables_createPDF:
+# mem_mb: 1000
+# time: "00:10:05"
+# threads: 1
###### Rules for illuminadb building ##########
-unzipFastq_R1:
+unzipFastq_R1_illumina:
mem_mb: 96000
time: "01:45:05"
threads: 4
-unzipFastq_R2:
+unzipFastq_R2_illumina:
mem_mb: 96000
time: "01:45:05"
threads: 4
@@ -123,36 +122,36 @@ unzipFastq_R2:
-trim10xbarcodes:
- mem_mb: 500
+trim10xBarcodes_illumina:
+ mem_mb: 5000
time: "02:30:05"
threads: 4
-trimAdapters:
- mem_mb: 500
+trimSequencingAdapters_illumina:
+ mem_mb: 5000
time: "02:30:05"
threads: 8
-fastqc_Illumina:
+fastQC_illumina:
mem_mb: 1000
time: "04:00:05"
threads: 4
-meryl_R1:
+merylCount_R1_illumina:
mem_mb: 20000
time: "01:30:05"
threads: 12
-meryl_R2:
+merylCount_R2_illumina:
mem_mb: 20000
time: "01:30:05"
threads: 12
-meryl_illumina_build:
+merylUnion_illumina:
mem_mb: 30000
time: "02:45:05"
threads: 12
@@ -162,35 +161,33 @@ meryl_illumina_build:
###### HIFI BUILD #######
-unzipHifi:
+unzipFastq_hifi:
mem_mb: 128000
time: "01:30:05"
threads: 4
+trimSMRTBellAdapters_hifi:
+ mem_mb: 96000
+ time: "01:30:05"
+ threads: 4
-fastqc_hifi:
+fastQC_hifi:
mem_mb: 12000
time: "04:00:05"
threads: 2
-multiqc_hifi:
+multiQC_hifi:
mem_mb: 4000
time: "01:15:05"
threads: 2
-meryl_hifi_count:
+merylCount_hifi:
mem_mb: 96000
time: "02:30:05"
threads: 12
-meryl_hifi_build:
+merylUnion_hifi:
mem_mb: 96000
time: "01:30:05"
threads: 12
-
-
-trimSMRTbell:
- mem_mb: 96000
- time: "01:30:05"
- threads: 4
--
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