change resources

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