Update modules

tests/csv/3.0/tumor_mutational_burden.csv

@@ -0,0 +1,2 @@
+patient,sample,vcf,tbi,variantcaller,annotation
+hcc1395,hcc1395,/Users/monarchy/Projects/Coding/sarek/HCC1395T_vs_HCC1395N.mutect2.filtered_VEP.ann.vcf.gz,/Users/monarchy/Projects/Coding/sarek/HCC1395T_vs_HCC1395N.mutect2.filtered_VEP.ann.vcf.gz.tbi,mutect2,vep

tests/test_markduplicates_from_cram.yml

@@ -66,7 +66,7 @@
     - path: results/preprocessing/recalibrated/test/test.recal.cram
     # binary changes md5sums on reruns.
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-      md5sum: adac39d7845f64f6b35b766751393b06
+      md5sum: feb197ae262a1f95ea54a118e949342e
     - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
       md5sum: bdb8f185c35dd1eec7ce2f69bce57972
     - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt

tests/test_tiddit.yml

@@ -25,7 +25,7 @@
     - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.TsTv.qual
       md5sum: bc68ae4e688e9fb772b457069e604883
     - path: results/variant_calling/tiddit/sample3/sample3.tiddit.ploidies.tab
-      md5sum: d65f8aa5bb136f77c23264640481f047
+      md5sum: fcfd2ecf6e7eef532e072757354c8a90
     - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz
     # conda changes md5sums for test.
     - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz.tbi
@@ -63,7 +63,7 @@
     - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.TsTv.qual
       md5sum: bc68ae4e688e9fb772b457069e604883
     - path: results/variant_calling/tiddit/sample1/sample1.tiddit.ploidies.tab
-      md5sum: d65f8aa5bb136f77c23264640481f047
+      md5sum: fcfd2ecf6e7eef532e072757354c8a90
     - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz
     # conda changes md5sums for test.
     - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz.tbi
@@ -89,7 +89,7 @@
     - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.TsTv.qual
       md5sum: bc68ae4e688e9fb772b457069e604883
     - path: results/variant_calling/tiddit/sample2/sample2.tiddit.ploidies.tab
-      md5sum: 0f01874e20df10ecc7418d4537c7aa82
+      md5sum: 5c5d70295c3957990502cb692e07a965
     - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz
     # conda changes md5sums for test.
     - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz.tbi

tests/test_umi.yml

@@ -47,9 +47,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: d0713716f63ac573f4a3385733e9a537
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 9c424aaae1d200f67a1ecc3e55ad5a6a
+      md5sum: f8a2f99e2bf353b8691c1f252a8ef30e
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: e64175125c512651b2819ced400bc846
+      md5sum: 44cb4ed98f9b18f8522c537264bb69d0
 # - name: Run UMI TSO test
 #   command: nextflow run main.nf -profile test,umi_tso
 #   tags: