Commit 724315d0 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

removed dup

parent e562158a
"__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" :
......@@ -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}",
......
"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" :
"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" :
"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" :
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