Merge pull request #5 from projectoriented/master

Remove methylink script and plug in package instead

.gitignore

@@ -4,5 +4,6 @@ alignments/**
 log/**
 tmp/**
 **.code-workspace
+.idea
 Clair3
-workflow/scripts/longphase
+workflow/scripts/longphase

workflow/envs/methylink.yaml

@@ -4,3 +4,5 @@ channels:
   - defaults
 dependencies:
   - pysam
+  - pip:
+      - methylink==0.4.0

workflow/rules/methylink.smk

@@ -10,9 +10,22 @@ rule link_bam:
         hrs=24,
         disk_free=250,
     threads: 16
+    envmodules:
+        "modules",
+        "modules-init",
+        "modules-gs/prod",
+        "modules-eichler/prod",
+        "methylink/0.4.0",
     conda:
         "../envs/methylink.yaml"
     log:
         "log/{sample}.{phase}.methlylink.log",
-    script:
-        "../scripts/append_mod_tags.py"
+    shell:
+        """
+        methylink \
+            --threads {threads} \
+            --aln {input.aln_bam} \
+            --sample {wildcards.sample}_{wildcards.phase} \
+            --methyl_bams "$(echo {input.methyl_bam})" \
+            --output {output.linked_bam} 2>&1 | tee {log}
+        """

workflow/rules/variant_calling.smk

@@ -170,6 +170,5 @@ rule bgzip_vcf:
     threads: 1
     shell:
         """
-        bcftools sort -o /dev/stdout -O v {input.vcf} | bgzip -c > {output.zipped}
-        tabix {output.zipped}
+        bcftools sort -o /dev/stdout -O v {input.vcf} | bgzip -c > {output.zipped} && tabix {output.zipped}
         """