update readme in progress

uclahs-cds · Aug 2, 2023 · 5eb6aa7 · 5eb6aa7
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/docs/mutect2_flowchart.puml b/docs/mutect2_flowchart.puml
@@ -21,8 +21,8 @@ $intermediate_process(gatk_mergeVcfs, 'GATK MergeVcfs', 'Output: unfiltered VCF'
 $intermediate_process(mutect2_mergeStats, 'GATK MergeMutectStats', 'Output: Mutect2 stats')
 $intermediate_process(gatk_learnReadOrientation, 'GATK LearnReadOrientationModel', 'Output: orientation bias artifacts table')
 $intermediate_process(mutect2_filterCalls, 'GATK FilterMutectCalls', 'Output: VCF with non-PASSing variants tagged %newline()Optional output: filtering stats')
-$output_process(bcftools_filterVCF, 'remove non-PASS variants', 'Output: VCF including only variants that passed above filters')
-$output_process(bcftools_splitVCF, 'split by variant type', 'Output: %newline()pass-snvs.vcf.gz %newline()pass-mnvs.vcf.gz %newline()pass-indels.vcf.gz')
+$intermediate_process(bcftools_filterVCF, 'remove non-PASS variants', 'Output: VCF including only variants that passed above filters')
+$output_process(bcftools_splitVCF, 'split by variant type', 'Output: %newline()SNV.vcf.gz %newline()MNV.vcf.gz %newline()Indel.vcf.gz')
 $qc_process(gatk_filteringStats, 'Optional', 'Output: filteringStats.tsv')
 
 reference_genome -d-> gatk_splitIntervals
@@ -47,7 +47,7 @@ reference_genome -d-> mutect2_filterCalls
 contamination_table -d-> mutect2_filterCalls
 mutect2_filterCalls -d-> gatk_filteringStats
 mutect2_filterCalls -d-> bcftools_filterVCF : // filtered.vcf.gz //
-bcftools_filterVCF -d-> bcftools_splitVCF : // pass.vcf.gz //
+bcftools_filterVCF -d-> bcftools_splitVCF : // all-pass.vcf.gz //
 
 $add_legend('left')
 

diff --git a/test/config/a_mini-all-tools.config b/test/config/a_mini-all-tools.config
@@ -17,7 +17,7 @@ params {
     dataset_id = 'TWGSAMIN'
      // setting params.exome to TRUE will add the '--exome' option when running manta and strelka2 and the -E option when running MuSE
     exome = false
-    save_intermediate_files = false
+    save_intermediate_files = true
 
     // module options
     bgzip_extra_args = ''