fix test

AnimalGenomicsETH · Apr 28, 2022 · cc645c6 · cc645c6
1 parent 9cc7ee3
commit cc645c6
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Showing 3 changed files with 4 additions and 5 deletions.
diff --git a/.test/config/run_parameters.yaml b/.test/config/run_parameters.yaml
@@ -27,7 +27,6 @@ split_size:
   SR: 100000000
 winnow_threshold: 0.9998
 haplotypes:
-  - 'asm'
   - 'trio'
   - 'parents'
 assemblers:
@@ -49,7 +48,7 @@ target_metrics:
     - 'mm2.vcf'
     - 'wm2.vcf'
   primary:
-    - 'telo.txt'
+    - 'telo.100.txt'
     - 'repeats.csv'
     - 'repeats.tbl'
     - 'merqury.full.stats'

diff --git a/Snakefile b/Snakefile
@@ -66,7 +66,7 @@ wildcard_constraints:
     data = r'[^\W_]+',
     modifier = r'\w+',
     read_t  = r'hifi|SR',
-    mapper = r'mm2|wm'
+    mapper = r'mm2|wm2'
 
 #------------#
 #DEFINE RULES#

diff --git a/snakepit/variant_calling.smk b/snakepit/variant_calling.smk
@@ -45,9 +45,9 @@ rule mumandco_summarise:
 
 rule paf_variants:
     input:
-        WORK_PATH + '{haplotype}_scaffolds_ref.{mapper}.paf'
+        get_dir('work','{haplotype}_scaffolds_ref.{mapper}.paf')
     output:
-        RESULT_PATH + '.{mapper}.vcf'
+        get_dir('result','.{mapper}.vcf')
     shell:
         'sort {input} -k6,6 -k8,8n | paftools.js call -f {config[ref_genome]} - > {output}'