Merge pull request #100 from jts/1.9-rc

1.9 rc

README.md

@@ -226,6 +226,20 @@ Variant annotation output can be found in `qc_annotation` and the recurrent
 amino acid change heatmap can be found in `plots/<prefix>_aa_mutation_heatmap.pdf`.
 
 
+## Pangolin Version 4
+Pangolin version 4 included several changes which required updates
+to the `ncov-tools` environment.  By default, `ncov-tools` will run pangolin
+4 and will require changes to `ncov-parser` version 1.9 to parse the output
+and populate the summary QC file.
+
+Backward compability with Pangolin 3 is available and will require the following
+parameter addition in the `config.yaml` file:
+```
+pangolin_version: "3"
+```
+Note that the specific version is not required, only if it is "3" or "4".
+
+
 ## Credit and Acknowledgements
 
 * The tree-with-SNPs plot was inspired by a plot shared by Mads Albertsen.

VERSION.txt

@@ -1 +1 @@
-v.1.8.0
+v.1.9.0

workflow/envs/environment.yml

@@ -30,11 +30,10 @@ dependencies:
   - usher
   - pip:
       - dendropy>=4.4.0
-      - pyvcf
+      - pyvcf3
       - ncov-parser
-      - git+https://github.com/hCoV-2019/lineages.git
-      - git+https://github.com/hCoV-2019/pangolin.git
+      - git+https://github.com/cov-lineages/pangolin.git
+      - git+https://github.com/cov-lineages/pangolin-data.git
       - git+https://github.com/cov-lineages/constellations.git
       - git+https://github.com/cov-lineages/scorpio.git
-      - git+https://github.com/cov-lineages/pangolin-data.git
       - git+https://github.com/jts/ncov-watch.git

workflow/rules/analysis.smk

@@ -152,7 +152,8 @@ rule make_sample_qc_summary:
         py_script="get_qc.py",
         metadata_opt=get_qc_summary_metadata_opt,
         platform_opt=get_platform_opt,
-        run_name_opt=get_run_name_opt
+        run_name_opt=get_run_name_opt,
+        pangolin_version_opt=get_pangolin_version_opt
     shell:
         "{params.py_script} --alleles {input.alleles} \
                             --coverage {input.samplecoverage} \
@@ -162,7 +163,7 @@ rule make_sample_qc_summary:
                             --sample {wildcards.sample} \
                             --lineage {input.lineagereport} \
                             --aa_table {input.aa_table} \
-                            --mutations {input.watch} \
+                            --mutations {input.watch} {params.pangolin_version_opt} \
                             --run_name {params.run_name_opt} > {output}"
 
 # merge the per-sample summary files into the run-level report

workflow/rules/common.smk

@@ -235,6 +235,15 @@ def get_annotated_variants(wildcards):
 def get_all_masked_consensus(wildcards):
     return ["masked_fasta/{sample}.masked_consensus.fasta".format(sample=s) for s in get_sample_names()]
 
+def get_pangolin_version_opt(wildcards):
+    if "pangolin_version" in config:
+        return "--pangolin_ver %s" % (config['pangolin_version'])
+    else:
+        return ""
+
+
+
+
 
 # generate the amplicon-level bed file from the input primer bed
 rule make_amplicon_bed: