specified python version to ensure wheel is working when create env

ylab-hi · Mar 2, 2024 · 5c03fcb · 5c03fcb
1 parent ee8eb42
commit 5c03fcb
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Showing 2 changed files with 10 additions and 12 deletions.
diff --git a/workflow/envs/spladder.yml b/workflow/envs/spladder.yml
@@ -1,11 +1,9 @@
 channels:
  - anaconda
  - bioconda
- - conda-forge
 dependencies:
-- configargparse
-- pip
-- pip:
-  - spladder==3.0.4
-  - vcfpy==0.13.6
-
+ - python=3.6
+ - pysam
+ - pip
+ - pip:
+   - spladder==3.0.4
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -177,11 +177,11 @@ def get_input_hlatyping_PE(wildcards):
     return dict(
         zip(
           ["fwd", "rev"],
-          expand("results/{sample}/{seqtype}/reads/{group}_{readtype}_preproc.fq.gz",
-                  sample = wildcards.sample,
-                  seqtype = "dnaseq" if wildcards.nartype == "DNA" else "rnaseq",
-                  group = wildcards.group,
-                  readtype = wildcards.readtype)
+          expand("results/{sample}/{seqtype}/reads/{group}_{pair}_preproc.fq.gz",
+                 sample=wildcards.sample,
+                 seqtype = "dnaseq" if wildcards.nartype == "DNA" else "rnaseq",
+                 group=wildcards.group,
+                 pair=["R1","R2"])
           )
     )