IKIM-Essen · johanneskoester · Oct 12, 2022 · Sep 1, 2022 · Sep 1, 2022 · Sep 1, 2022
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -133,7 +133,6 @@ jobs:
       - name: Test rule ${{ matrix.rule }} on ${{ matrix.technology }} ${{ matrix.seq_method }} data
         uses: snakemake/[email protected]
         with:
-          stagein: mamba env create -f workflow/envs/trinity.yaml -n trinity
           directory: .tests
           snakefile: workflow/Snakefile
           args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"

diff --git a/workflow/envs/abyss.yaml b/workflow/envs/abyss.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - abyss =2.3.1
diff --git a/workflow/envs/bamclipper.yaml b/workflow/envs/bamclipper.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bamclipper =1.0
   - samtools =1.14 # see https://github.com/merenlab/anvio/issues/1479
diff --git a/workflow/envs/bcftools.yaml b/workflow/envs/bcftools.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bcftools =1.10
diff --git a/workflow/envs/bedtools.yaml b/workflow/envs/bedtools.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - bedtools =2.30.0
diff --git a/workflow/envs/canu.yaml b/workflow/envs/canu.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   # do not use canu 2.2 !
   - canu =2.1.1

diff --git a/workflow/envs/delly.yaml b/workflow/envs/delly.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - delly =0.8.7
   - pysam =0.16
diff --git a/workflow/envs/entrez.yaml b/workflow/envs/entrez.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
-  - entrez-direct =13.9
+  - entrez-direct =16.2
diff --git a/workflow/envs/fgbio.yaml b/workflow/envs/fgbio.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - fgbio =1.3
diff --git a/workflow/envs/genometools.yaml b/workflow/envs/genometools.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - genometools-genometools =1.6.2
diff --git a/workflow/envs/gff3sort.yaml b/workflow/envs/gff3sort.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - gff3sort = 0.1
diff --git a/workflow/envs/kraken.yaml b/workflow/envs/kraken.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - kraken2 =2.1.1
   - krona =2.7.1
diff --git a/workflow/envs/longshot.yaml b/workflow/envs/longshot.yaml
@@ -1,4 +1,6 @@
 channels:
+  - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - longshot =0.4
diff --git a/workflow/envs/mason.yaml b/workflow/envs/mason.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - mason =2.0
diff --git a/workflow/envs/medaka.yaml b/workflow/envs/medaka.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - medaka =1.0
   - tensorflow =1.14

diff --git a/workflow/envs/megahit.yaml b/workflow/envs/megahit.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - megahit =1.2
diff --git a/workflow/envs/minimap2.yaml b/workflow/envs/minimap2.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - minimap2 =2.22
diff --git a/workflow/envs/multiqc.yaml b/workflow/envs/multiqc.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - multiqc =1.11
diff --git a/workflow/envs/nanofilt.yaml b/workflow/envs/nanofilt.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - nanofilt =2.8
   - gzip =1.11

diff --git a/workflow/envs/nanoqc.yaml b/workflow/envs/nanoqc.yaml
@@ -1,4 +1,6 @@
 channels:
+  - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - nanoqc =0.9
diff --git a/workflow/envs/notramp.yaml b/workflow/envs/notramp.yaml
@@ -1,7 +1,8 @@
 channels:
   - simakro
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - notramp =1.0.5
   - minimap2 =2.22
diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml
@@ -1,5 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - pangolin =4.1.2
+  - tabulate <0.9 # TODO remove once pangolin 4.1.3 is available in bioconda
diff --git a/workflow/envs/pysam.yaml b/workflow/envs/pysam.yaml
@@ -1,6 +1,7 @@
 channels:
   - conda-forge
   - bioconda
+  - nodefaults
 dependencies:
   - jupyter =1.0
   - pysam =0.16

diff --git a/workflow/envs/python.yaml b/workflow/envs/python.yaml
@@ -2,6 +2,7 @@ channels:
   - conda-forge
   - bioconda
   - anaconda
+  - nodefaults
 dependencies:
   - pandas =1.2
   - jupyter =1.0

diff --git a/workflow/envs/quast.yaml b/workflow/envs/quast.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - quast =5.0
diff --git a/workflow/envs/ragoo.yaml b/workflow/envs/ragoo.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - imperial-college-research-computing
+  - nodefaults
 dependencies:
   - ragoo =1.1
diff --git a/workflow/envs/rbt.yaml b/workflow/envs/rbt.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - rust-bio-tools =0.39
diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - samtools =1.14
diff --git a/workflow/envs/seqtk.yaml b/workflow/envs/seqtk.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - seqtk =1.3
diff --git a/workflow/envs/snakemake.yaml b/workflow/envs/snakemake.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - snakemake =7.0
diff --git a/workflow/envs/sourmash.yaml b/workflow/envs/sourmash.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - sourmash =3.5
diff --git a/workflow/envs/spades.yaml b/workflow/envs/spades.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - spades =3.15
diff --git a/workflow/envs/svn.yaml b/workflow/envs/svn.yaml
@@ -1,4 +1,5 @@
 channels:
   - anaconda
+  - nodefaults
 dependencies:
   - svn =1.10
diff --git a/workflow/envs/tabix.yaml b/workflow/envs/tabix.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - tabix =0.2
   - curl
diff --git a/workflow/envs/trinity.yaml b/workflow/envs/trinity.yaml
@@ -1,7 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
-  - defaults
+  - bioconda
+  - nodefaults
 dependencies:
   - trinity =2.13
   # ensure that we use a bowtie2 that already contains fixed dependency constraints

diff --git a/workflow/envs/ucsc.yaml b/workflow/envs/ucsc.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - ucsc-bigbedtobed =377
diff --git a/workflow/envs/unix.yaml b/workflow/envs/unix.yaml
@@ -1,6 +1,7 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - curl
   - sed
diff --git a/workflow/envs/varlociraptor.yaml b/workflow/envs/varlociraptor.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - varlociraptor =4.9
diff --git a/workflow/envs/velvet.yaml b/workflow/envs/velvet.yaml
@@ -1,5 +1,6 @@
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - nodefaults
 dependencies:
   - velvet =1.2
diff --git a/workflow/notebooks/assembly-benchmark-results.py.ipynb b/workflow/notebooks/assembly-benchmark-results.py.ipynb
@@ -197,5 +197,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/notebooks/call-strains.py.ipynb b/workflow/notebooks/call-strains.py.ipynb
@@ -74,5 +74,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/notebooks/plot-all-strains-kallisto.py.ipynb b/workflow/notebooks/plot-all-strains-kallisto.py.ipynb
@@ -53,5 +53,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/notebooks/plot-all-strains-pangolin.py.ipynb b/workflow/notebooks/plot-all-strains-pangolin.py.ipynb
@@ -46,5 +46,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/notebooks/plot-read-call.py.ipynb b/workflow/notebooks/plot-read-call.py.ipynb
@@ -100,5 +100,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/notebooks/plot-strains-kallisto.py.ipynb b/workflow/notebooks/plot-strains-kallisto.py.ipynb
@@ -60,5 +60,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/notebooks/test-benchmark-results.py.ipynb b/workflow/notebooks/test-benchmark-results.py.ipynb
@@ -52,5 +52,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 4
+ "nbformat_minor": 5
 }
diff --git a/workflow/rules/lineage_variant_calling.smk b/workflow/rules/lineage_variant_calling.smk
@@ -48,6 +48,15 @@ rule generate_lineage_variant_table:
         "../scripts/generate-lineage-variant-table.py"
 
 
+rule get_lineage_variant_table:
+    input:
+        expand(
+            "results/{date}/lineage-variant-report/{sample}.csv",
+            date="2022-05-16",
+            sample=get_samples_for_date("2022-05-16"),
+        ),
+
+
 use rule overview_table_html as generate_lineage_variant_report with:
     input:
         "results/{date}/lineage-variant-report/{sample}.csv",