Merge pull request #38 from broadinstitute/ct-update-viral-core

update viral-core 2.3.0 -> 2.3.1

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.3.0
+FROM quay.io/broadinstitute/viral-core:2.3.1
 
 LABEL maintainer "[email protected]"
 

assembly.py

@@ -478,7 +478,7 @@ def order_and_orient(inFasta, inReference, outFasta,
             assert r==0
 
         scaffolds = [tuple(Bio.SeqIO.parse(scaffolds_fasta[ref_num], 'fasta')) for ref_num in range(n_refs)]
-        base_counts = [sum([len(seg.seq.ungap('N')) for seg in scaffold]) \
+        base_counts = [sum([len(seg.seq.replace("N","")) for seg in scaffold]) \
             if len(scaffold)==n_genome_segments else 0 for scaffold in scaffolds]
         best_ref_num = numpy.argmax(base_counts)
         if (len(scaffolds[best_ref_num]) != n_genome_segments) and not allow_incomplete_output:

docs/requirements.txt

@@ -2,7 +2,7 @@ jinja2==3.1.2 # https://github.com/readthedocs/readthedocs.org/issues/9037#issue
 Sphinx==5.3.0 #override sphinx pinning done by RTD: https://docs.readthedocs.io/en/stable/build-default-versions.html#external-dependencies
 sphinx-argparse
 sphinx-rtd-theme==1.1.1
-matplotlib==2.2.4
+matplotlib>=2.2.4
 PyYAML==6.0
 mock==5.0.1
 recommonmark

requirements-conda.txt

@@ -5,8 +5,8 @@ muscle=3.8.1551
 spades>=3.15.5
 fastani>=1.34
 mashtree>=1.4.6
-#sourmash-minimal>=4.8.6 ## see below
-#sourmash_plugin_branchwater>=0.9.1  ## running into resolver problems at least with our current version of python
+sourmash-minimal>=4.8.6 ## see below
+sourmash_plugin_branchwater>=0.9.1  ## running into resolver problems at least with our current version of python
 skani>=0.2.1
-kwip>=0.2.0
+#kwip>=0.2.0 ## relies on khmer, which as of 2024-03-12 does not support python 3.10
 # Python packages below