Merge pull request #70 from iqbal-lab-org/anno_fixes

Fix bugs in annotation workflow, and remove defaults channel from environment configurations
iqbal-lab-org · Aug 14, 2024 · 87d42c2 · 87d42c2
2 parents 9199e41 + e4551ad
commit 87d42c2
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Showing 10 changed files with 3 additions and 11 deletions.
diff --git a/pling/anno_snakemake/Snakefile b/pling/anno_snakemake/Snakefile
@@ -67,7 +67,7 @@ rule panaroo:
     params:
         files = lambda wildcards: [f"{OUTPUTPATH}/annotation/{wildcards.community}/bakta/{genome}/{genome}.gff3" for genome in COMMUNITY_TO_PLASMID[wildcards.community]]
     shell:
-        "panaroo -i {params.files} -o {output.pangenome} --clean-mode moderate -a pan --merge_paralogs -t {threads}"
+        "panaroo -i {params.files} -o {output.pangenome} --clean-mode moderate -a pan --merge_paralogs -t {threads} --remove-invalid-genes"
 
 rule gen_minimap_input:
     input:

diff --git a/pling/envs/bakta.yaml b/pling/envs/bakta.yaml
@@ -1,7 +1,6 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python =3.9
-  - bakta =1.8.2
+  - bakta =1.9.3
diff --git a/pling/envs/blocks.yaml b/pling/envs/blocks.yaml
@@ -1,7 +1,6 @@
 channels:
  - conda-forge
  - bioconda
- - defaults
 dependencies:
  - python =3.8
  - pandas =1.4.3

diff --git a/pling/envs/ding_and_glpk.yaml b/pling/envs/ding_and_glpk.yaml
@@ -1,6 +1,5 @@
 channels:
  - conda-forge
- - defaults
  - gurobi
 dependencies:
  - python =3.8

diff --git a/pling/envs/env.yaml b/pling/envs/env.yaml
@@ -1,6 +1,5 @@
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - python =3.8
   - pandas =1.5.3

diff --git a/pling/envs/integerise.yaml b/pling/envs/integerise.yaml
@@ -2,7 +2,6 @@ name: integerise
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
  - python =3.8
  - intervaltree =3.0.2

diff --git a/pling/envs/minimap_input.yaml b/pling/envs/minimap_input.yaml
@@ -1,4 +1,4 @@
 channels:
   - bioconda
 dependencies:
- - biopython =1.78
+ - biopython
diff --git a/pling/envs/panaroo.yaml b/pling/envs/panaroo.yaml
@@ -1,7 +1,6 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python =3.9
   - panaroo >=1.3
diff --git a/pling/envs/plasnet.yaml b/pling/envs/plasnet.yaml
@@ -1,7 +1,6 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python =3.9
   - pip

diff --git a/pling/envs/smash.yaml b/pling/envs/smash.yaml
@@ -1,7 +1,6 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python =3.10
   - sourmash =4.4.0