From 2d09737209836293004c3da6e14eac53c5f86511 Mon Sep 17 00:00:00 2001
From: Thomas Weber <thomas.weber@embl.de>
Date: Thu, 20 Jun 2024 19:23:23 +0000
Subject: [PATCH] Updating GH actions, small fixes for v8 upgrade

---
 workflow/envs/mc_base.yaml      | 2 ++
 workflow/rules/plots.smk        | 7 +++----
 workflow/rules/strandphaser.smk | 5 ++++-
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/workflow/envs/mc_base.yaml b/workflow/envs/mc_base.yaml
index 7c4dd81c..f4eda90b 100644
--- a/workflow/envs/mc_base.yaml
+++ b/workflow/envs/mc_base.yaml
@@ -20,3 +20,5 @@ dependencies:
   # ArbiGent Hufsah deps
   - pytables
   - xopen
+  # Fix jbrowse tracks generation
+  - pybigwig
\ No newline at end of file
diff --git a/workflow/rules/plots.smk b/workflow/rules/plots.smk
index 41fa28de..a64d7248 100644
--- a/workflow/rules/plots.smk
+++ b/workflow/rules/plots.smk
@@ -345,10 +345,9 @@ rule jbrowse_genome_browser_file:
     log:
         "{folder}/log/JBROWSE/{sample}.log",
     conda:
-        "/g/korbel2/weber/miniconda3/envs/genome_browsing"
-        # "../envs/genome_browsing.yaml"
-    container:
-        None
+        "../envs/mc_base.yaml"
+    # container:
+    #     None
     resources:
         mem_mb=get_mem_mb,
     shell:
diff --git a/workflow/rules/strandphaser.smk b/workflow/rules/strandphaser.smk
index 2ff58e84..4a345e1c 100644
--- a/workflow/rules/strandphaser.smk
+++ b/workflow/rules/strandphaser.smk
@@ -75,11 +75,14 @@ rule run_strandphaser_per_chrom:
         """
 
 
+ruleorder: summarise_ploidy > merge_strandphaser_vcfs
+
+
 rule merge_strandphaser_vcfs:
     input:
         vcfs=aggregate_vcf_gz,
         tbis=aggregate_vcf_gz_tbi,
-        ploidy_summary="{folder}/{sample}/ploidy/ploidy_summary.txt",
+        summary="{folder}/{sample}/ploidy/ploidy_summary.txt",
     output:
         vcfgz="{folder}/{sample}/strandphaser/phased-snvs/{sample}.vcf.gz",
     log: