fix: rename-contigs to include target bed intersection and add mapping files to resources

.test/config/config.yaml

@@ -1,7 +1,7 @@
 variant-calls:
-  dummy-giab: 
-    path: "resources/variants/na12878/all.truth.bcf"
-    benchmark: "giab-na12878-exome"
+  # dummy-giab: 
+  #   path: "resources/variants/na12878/all.truth.bcf"
+  #   benchmark: "giab-na12878-exome"
   dummy-chm: 
     path: "resources/variants/chm-eval/all.truth.bcf"
     benchmark: "chm-eval"

workflow/resources/rename-contigs/README.md

@@ -0,0 +1,13 @@
+# rename-contigs
+The reference is denoted in Ensembl notation. If the caller is using USCS notation, the contigs need to be renamed like 
+```
+chr12 
+```
+becomes
+```
+12
+```
+
+Two files are provided: One for GRCh38 as reference genome and one for GRCh37. The path to those files needs to be denoted in the user config to enable the `rename_contigs` rule.
+
+The files were taken from [dpryan79/ChromosomeMappings](https://github.com/dpryan79/ChromosomeMappings).

workflow/resources/rename-contigs/grch37_ucsc2ensembl.txt

@@ -0,0 +1,93 @@
+chr1	1
+chr2	2
+chr3	3
+chr4	4
+chr5	5
+chr6	6
+chr7	7
+chr8	8
+chr9	9
+chr10	10
+chr11	11
+chr12	12
+chr13	13
+chr14	14
+chr15	15
+chr16	16
+chr17	17
+chr18	18
+chr19	19
+chr20	20
+chr21	21
+chr22	22
+chrX	X
+chrY	Y
+chrM	MT
+chr1_gl000191_random	GL000191.1
+chr1_gl000192_random	GL000192.1
+chr4_gl000193_random	GL000193.1
+chr4_gl000194_random	GL000194.1
+chr7_gl000195_random	GL000195.1
+chr8_gl000196_random	GL000196.1
+chr8_gl000197_random	GL000197.1
+chr9_gl000198_random	GL000198.1
+chr9_gl000199_random	GL000199.1
+chr9_gl000200_random	GL000200.1
+chr9_gl000201_random	GL000201.1
+chr11_gl000202_random	GL000202.1
+chr17_gl000203_random	GL000203.1
+chr17_gl000204_random	GL000204.1
+chr17_gl000205_random	GL000205.1
+chr17_gl000206_random	GL000206.1
+chr18_gl000207_random	GL000207.1
+chr19_gl000208_random	GL000208.1
+chr19_gl000209_random	GL000209.1
+chr21_gl000210_random	GL000210.1
+chrUn_gl000211	GL000211.1
+chrUn_gl000212	GL000212.1
+chrUn_gl000213	GL000213.1
+chrUn_gl000214	GL000214.1
+chrUn_gl000215	GL000215.1
+chrUn_gl000216	GL000216.1
+chrUn_gl000217	GL000217.1
+chrUn_gl000218	GL000218.1
+chrUn_gl000219	GL000219.1
+chrUn_gl000220	GL000220.1
+chrUn_gl000221	GL000221.1
+chrUn_gl000222	GL000222.1
+chrUn_gl000223	GL000223.1
+chrUn_gl000224	GL000224.1
+chrUn_gl000225	GL000225.1
+chrUn_gl000226	GL000226.1
+chrUn_gl000227	GL000227.1
+chrUn_gl000228	GL000228.1
+chrUn_gl000229	GL000229.1
+chrUn_gl000230	GL000230.1
+chrUn_gl000231	GL000231.1
+chrUn_gl000232	GL000232.1
+chrUn_gl000233	GL000233.1
+chrUn_gl000234	GL000234.1
+chrUn_gl000235	GL000235.1
+chrUn_gl000236	GL000236.1
+chrUn_gl000237	GL000237.1
+chrUn_gl000238	GL000238.1
+chrUn_gl000239	GL000239.1
+chrUn_gl000240	GL000240.1
+chrUn_gl000241	GL000241.1
+chrUn_gl000242	GL000242.1
+chrUn_gl000243	GL000243.1
+chrUn_gl000244	GL000244.1
+chrUn_gl000245	GL000245.1
+chrUn_gl000246	GL000246.1
+chrUn_gl000247	GL000247.1
+chrUn_gl000248	GL000248.1
+chrUn_gl000249	GL000249.1
+chr4_ctg9_hap1	HSCHR4_1
+chr6_apd_hap1	HSCHR6_MHC_APD
+chr6_cox_hap2	HSCHR6_MHC_COX
+chr6_dbb_hap3	HSCHR6_MHC_DBB
+chr6_mann_hap4	HSCHR6_MHC_MANN
+chr6_mcf_hap5	HSCHR6_MHC_MCF
+chr6_qbl_hap6	HSCHR6_MHC_QBL
+chr6_ssto_hap7	HSCHR6_MHC_SSTO
+chr17_ctg5_hap1	HSCHR17_1