removed dup

allmine

+    "__default__" :
+    "alternative_proteins" :
+    "annovar" :
+    "bams_list" :
+    "bwa_index" :
+    "bwa_pe" :
+    "bwa_se" :
+    "cov_track" :
+    "fastp_pe"  :
+    "fastqc_pe" :
+    "fastqc_se" :
+    "freebayes" :
+    "make_markdown" :
+    "make_report" :
+    "merge_bams" :
+    "multiqc_bam" :
+    "parse_bam_with_bed" :
+    "pe_trim_and_merge" :
+    "varscan" :
+    "vcf4_to_avinput" :
+    "whatshap" :

cluster.json

@@ -298,6 +298,26 @@
         "mem"       : "2g"
     },
 
+
+    "MarkDuplicates" :
+    {
+        "jobname"   : "{rule}_{wildcards.sample}",
+        "time"      : "36:00:00",
+        "cores"     : 1,
+        "mem"       : "7g",
+        "out"       : "{rule}_{wildcards.sample}.out"
+    },
+
+    "SplitNCigarReads" :
+    {
+        "jobname"   : "{rule}_{wildcards.sample}",
+        "time"      : "36:00:00",
+        "cores"     : 1,
+        "mem"       : "7g",
+        "out"       : "{rule}_{wildcards.sample}.out"
+    },
+
+
     "gatk4_hc" :
     {
         "jobname"   : "{rule}_{wildcards.sample}-{wildcards.mychr}",

pe

+    "MarkDuplicates" :
+    "SplitNCigarReads" :
+    "__default__" :
+    "alternative_proteins" :
+    "annovar" :
+    "bam_stats" :
+    "bams_list" :
+    "bowtie2_index" :
+    "bowtie2_pe" :
+    "bowtie2_se" :
+    "bwa_index" :
+    "bwa_pe" :
+    "bwa_se" :
+    "combinevcf" :
+    "cov_track" :
+    "cutadapt_pe"  :
+    "fastp_pe"  :
+    "fastp_se"  :
+    "fastqc_pe" :
+    "fastqc_se" :
+    "freebayes" :
+    "freebayes_parallel" :
+    "gatk4_combine_calls" :
+    "gatk4_filterIndels" :
+    "gatk4_filterSnps" :
+    "gatk4_gc" :
+    "gatk4_gdb" :
+    "gatk4_gvcf_map_file" :
+    "gatk4_hc" :
+    "gatk4_indels_quality_graphe_pdf" :
+    "gatk4_select_indels_variants" :
+    "gatk4_select_snps_variants" :
+    "gatk4_snps_quality_graphe_pdf" :
+    "keep_duplicates" :
+    "make_markdown" :
+    "make_report" :
+    "mergePE" :
+    "merge_bams" :
+    "multiqc_bam" :
+    "multiqc_fastqc" :
+    "parse_bam_with_bed" :
+    "remove_duplicates" :
+    "star_index" :
+    "star_index2" :
+    "star_pass1" :
+    "star_pass2" :
+    "trim_and_merge_pe" :
+    "varscan" :
+    "vcf4_to_avinput" :
+    "whatshap" :

rna

+    "MarkDuplicates" :
+    "SplitNCigarReads" :
+    "__default__" :
+    "alternative_proteins" :
+    "annovar" :
+    "bam_stats" :
+    "bams_list" :
+    "bowtie2_index" :
+    "bowtie2_pe" :
+    "bowtie2_se" :
+    "bwa_index" :
+    "bwa_pe" :
+    "bwa_se" :
+    "combinevcf" :
+    "cov_track" :
+    "cutadapt_pe"  :
+    "fastp_pe"  :
+    "fastp_se"  :
+    "fastqc_pe" :
+    "fastqc_se" :
+    "freebayes" :
+    "freebayes_parallel" :
+    "gatk4_combine_calls" :
+    "gatk4_filterIndels" :
+    "gatk4_filterSnps" :
+    "gatk4_gc" :
+    "gatk4_gdb" :
+    "gatk4_gvcf_map_file" :
+    "gatk4_hc" :
+    "gatk4_indels_quality_graphe_pdf" :
+    "gatk4_select_indels_variants" :
+    "gatk4_select_snps_variants" :
+    "gatk4_snps_quality_graphe_pdf" :
+    "keep_duplicates" :
+    "make_markdown" :
+    "make_report" :
+    "mergePE" :
+    "merge_bams" :
+    "multiqc_bam" :
+    "multiqc_fastqc" :
+    "parse_bam_with_bed" :
+    "remove_duplicates" :
+    "star_index" :
+    "star_index2" :
+    "star_pass1" :
+    "star_pass2" :
+    "trim_and_merge_pe" :
+    "varscan" :
+    "vcf4_to_avinput" :
+    "whatshap" :

se

+    "MarkDuplicates" :
+    "SplitNCigarReads" :
+    "__default__" :
+    "alternative_proteins" :
+    "annovar" :
+    "bam_stats" :
+    "bams_list" :
+    "bowtie2_index" :
+    "bowtie2_pe" :
+    "bowtie2_se" :
+    "bwa_index" :
+    "bwa_pe" :
+    "bwa_se" :
+    "combinevcf" :
+    "cov_track" :
+    "cutadapt_pe"  :
+    "fastp_pe"  :
+    "fastp_se"  :
+    "fastqc_pe" :
+    "fastqc_se" :
+    "freebayes" :
+    "freebayes_parallel" :
+    "gatk4_combine_calls" :
+    "gatk4_filterIndels" :
+    "gatk4_filterSnps" :
+    "gatk4_gc" :
+    "gatk4_gdb" :
+    "gatk4_gvcf_map_file" :
+    "gatk4_hc" :
+    "gatk4_indels_quality_graphe_pdf" :
+    "gatk4_select_indels_variants" :
+    "gatk4_select_snps_variants" :
+    "gatk4_snps_quality_graphe_pdf" :
+    "keep_duplicates" :
+    "make_markdown" :
+    "make_report" :
+    "mergePE" :
+    "merge_bams" :
+    "multiqc_bam" :
+    "multiqc_fastqc" :
+    "parse_bam_with_bed" :
+    "remove_duplicates" :
+    "star_index" :
+    "star_index2" :
+    "star_pass1" :
+    "star_pass2" :
+    "trim_and_merge_pe" :
+    "varscan" :
+    "vcf4_to_avinput" :
+    "whatshap" :