amend

cmkobel · Jul 23, 2024 · d26cd71 · d26cd71
1 parent 8f75111
commit d26cd71
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diff --git a/.github/workflows/dry-run.yaml b/.github/workflows/dry-run.yaml
@@ -47,3 +47,9 @@ jobs:
         run: |
           unzip tests/E._faecium/fna.zip
           ./comparem2 --config input_genomes="*.fna" --dry-run
+          ./comparem2 --config input_genomes="*.fna" --until fast --dry-run
+          ./comparem2 --config input_genomes="*.fna" --until isolate --dry-run
+          ./comparem2 --config input_genomes="*.fna" --until meta --dry-run
+          ./comparem2 --config input_genomes="*.fna" --until downloads --dry-run
+          
+          
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,6 @@
 FROM condaforge/mambaforge:latest
 LABEL io.github.snakemake.containerized="true"
-LABEL io.github.snakemake.conda_env_hash="f29d4934eea74bbc8f2df01cd3a17987e59aa0b52a1a046e6b42b2761a635ccf"
+LABEL io.github.snakemake.conda_env_hash="cf476c6668d24302993f66463f385bf746ac4a653744220814b23a7cdc2e54e1"
 
 # Step 1: Retrieve conda environments
 
@@ -68,21 +68,6 @@ COPY workflow/envs/any2fasta.yaml /conda-envs/55f257b7a2d5325550dfe5652bd53c22/e
 RUN mkdir -p /conda-envs/5c39a05942fff213bbc045e0d6dc61a3
 COPY workflow/envs/assembly-stats.yaml /conda-envs/5c39a05942fff213bbc045e0d6dc61a3/environment.yaml
 
-# Conda environment:
-#   source: workflow/envs/bakta.yaml
-#   prefix: /conda-envs/349bbcba5bdfd7faab9097a8a3f7f6d2
-#   name: bakta
-#   channels:
-#     - conda-forge
-#     - bioconda
-#   dependencies:
-#     - bakta=1
-#   
-#   # https://github.com/oschwengers/bakta?tab=readme-ov-file#bioconda
-#   # conda install -c conda-forge -c bioconda bakta
-RUN mkdir -p /conda-envs/349bbcba5bdfd7faab9097a8a3f7f6d2
-COPY workflow/envs/bakta.yaml /conda-envs/349bbcba5bdfd7faab9097a8a3f7f6d2/environment.yaml
-
 # Conda environment:
 #   source: workflow/envs/busco.yaml
 #   prefix: /conda-envs/29ddfde03b648d05bcbe1b488c9d275e
@@ -124,22 +109,19 @@ COPY workflow/envs/dbcan.yaml /conda-envs/8fd5cba1a415e69056b71dd889a203b8/envir
 
 # Conda environment:
 #   source: workflow/envs/eggnog.yaml
-#   prefix: /conda-envs/c9417166084cc9d781efd6970419263f
+#   prefix: /conda-envs/5ab146b4f8a224935ba7154dde2d9065
 #   name: eggnog
 #   channels:
-#     - anaconda
 #     - conda-forge
 #     - bioconda
 #   dependencies:
-#     - bioconda::diamond
-#     - anaconda::biopython
-#     - bioconda::eggnog-mapper
+#     - bioconda::eggnog-mapper=2.1.12
 #   
 #   
 #   # https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.12#user-content-Installation
 #   # conda install -c bioconda -c conda-forge eggnog-mapper
-RUN mkdir -p /conda-envs/c9417166084cc9d781efd6970419263f
-COPY workflow/envs/eggnog.yaml /conda-envs/c9417166084cc9d781efd6970419263f/environment.yaml
+RUN mkdir -p /conda-envs/5ab146b4f8a224935ba7154dde2d9065
+COPY workflow/envs/eggnog.yaml /conda-envs/5ab146b4f8a224935ba7154dde2d9065/environment.yaml
 
 # Conda environment:
 #   source: workflow/envs/fasttree.yaml
@@ -310,11 +292,10 @@ RUN mamba env create --prefix /conda-envs/b06d3784eaabfc8abcf62a294f54bad9 --fil
     mamba env create --prefix /conda-envs/a77979bb28302ba15eb49ca8f93197f7 --file /conda-envs/a77979bb28302ba15eb49ca8f93197f7/environment.yaml && \
     mamba env create --prefix /conda-envs/55f257b7a2d5325550dfe5652bd53c22 --file /conda-envs/55f257b7a2d5325550dfe5652bd53c22/environment.yaml && \
     mamba env create --prefix /conda-envs/5c39a05942fff213bbc045e0d6dc61a3 --file /conda-envs/5c39a05942fff213bbc045e0d6dc61a3/environment.yaml && \
-    mamba env create --prefix /conda-envs/349bbcba5bdfd7faab9097a8a3f7f6d2 --file /conda-envs/349bbcba5bdfd7faab9097a8a3f7f6d2/environment.yaml && \
     mamba env create --prefix /conda-envs/29ddfde03b648d05bcbe1b488c9d275e --file /conda-envs/29ddfde03b648d05bcbe1b488c9d275e/environment.yaml && \
     mamba env create --prefix /conda-envs/cc9543e16cbf71e94c901e40623c2b25 --file /conda-envs/cc9543e16cbf71e94c901e40623c2b25/environment.yaml && \
     mamba env create --prefix /conda-envs/8fd5cba1a415e69056b71dd889a203b8 --file /conda-envs/8fd5cba1a415e69056b71dd889a203b8/environment.yaml && \
-    mamba env create --prefix /conda-envs/c9417166084cc9d781efd6970419263f --file /conda-envs/c9417166084cc9d781efd6970419263f/environment.yaml && \
+    mamba env create --prefix /conda-envs/5ab146b4f8a224935ba7154dde2d9065 --file /conda-envs/5ab146b4f8a224935ba7154dde2d9065/environment.yaml && \
     mamba env create --prefix /conda-envs/785d03a6b41f3872cfe5d325544fd5a7 --file /conda-envs/785d03a6b41f3872cfe5d325544fd5a7/environment.yaml && \
     mamba env create --prefix /conda-envs/df2a53a81d11717a831dda8590f53cd5 --file /conda-envs/df2a53a81d11717a831dda8590f53cd5/environment.yaml && \
     mamba env create --prefix /conda-envs/8614b56b87888c570d4ed7d9eda3b5be --file /conda-envs/8614b56b87888c570d4ed7d9eda3b5be/environment.yaml && \

diff --git a/comparem2 b/comparem2
@@ -4,7 +4,7 @@ __author__ = "Carl M. Kobel"
 
 
 # --- Development: Versioning ---------------------------------------
-__version__ = "2.9.1"
+__version__ = "2.10.1"
 # Places to bump
 #  - here
 #  - workflow/Snakefile, because the snakefile can possibly be run without the ./comparem2 binary. Report gets from here.
@@ -25,8 +25,8 @@ __version__ = "2.9.1"
 
 # --- Development: Update Dockerfile --------------------------------
 # Update Dockerfile:
-# export COMPAREM2_BASE="$(pwd -P)"; export COMPAREM2_PROFILE="profiles/apptainer/default"; snakemake --snakefile "${COMPAREM2_BASE}/workflow/Snakefile" --configfile "${COMPAREM2_BASE}/config/config.yaml" --containerize > Dockerfile 
-# And then remove the header text (comparem2 logo).
+# export COMPAREM2_BASE="$(pwd -P)"; export COMPAREM2_PROFILE="profiles/apptainer/default"; snakemake --snakefile "${COMPAREM2_BASE}/workflow/Snakefile" --configfile "${COMPAREM2_BASE}/config/config.yaml" --containerize | grep -A 10000 "FROM condaforge" > Dockerfile
+# And then remove the header text (comparem2 logo, etc.) if necessary
 # In the future I will make my docker images myself:
 # sudo docker build -t cmkobel/comparem2:v2.8.1 . && sudo docker push cmkobel/comparem2:v2.8.1
 

diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -4,7 +4,7 @@
 
 __author__ = "Carl M. Kobel"
 
-__version__ = "2.9.1" # Haven't yet found a neat way of passing the version from the comparem2 executable, so for now it has to be defined here as well.
+__version__ = "2.10.1" # Haven't yet found a neat way of passing the version from the comparem2 executable, so for now it has to be defined here as well.
 
 # https://semver.org/
 version_major = ".".join(__version__.split(".")[:1])
@@ -376,6 +376,7 @@ rule fast:
 
 
 # Rules designed for bins of metagenomic origin
+# Could be cool to find a way of setting command line arguments like panaroo thresholds and stuff.
 rule meta:
     input: expand(\
         ["{output_directory}/metadata.tsv", \
@@ -384,12 +385,11 @@ rule meta:
         "{output_directory}/samples/{sample}/sequence_lengths/{sample}_seqlen.tsv", \
         "{output_directory}/samples/{sample}/busco/short_summary_extract.tsv", \
         "{output_directory}/checkm2/quality_report.tsv", \
-        "{output_directory}/samples/{sample}/diamond_kegg/{sample}_diamond_kegg.tsv", \
+        "{output_directory}/samples/{sample}/eggnog/{sample}.emapper.genepred.gff", \
         "{output_directory}/kegg_pathway/kegg_pathway_enrichment_analysis.tsv", \
         "{output_directory}/samples/{sample}/dbcan/overview.txt", \
         "{output_directory}/samples/{sample}/interproscan/{sample}_interproscan.tsv", \
         "{output_directory}/gtdbtk/gtdbtk.summary.tsv", \
-        "{output_directory}/mlst/mlst.tsv", \
         "{output_directory}/samples/{sample}/.annotation/{sample}.gff", \
         "{output_directory}/mashtree/mashtree.newick"], \
         output_directory = output_directory, \
@@ -403,12 +403,12 @@ rule isolate:
         "{output_directory}/.install_report_environment_aot.flag", \
         "{output_directory}/assembly-stats/assembly-stats.tsv", \
         "{output_directory}/samples/{sample}/sequence_lengths/{sample}_seqlen.tsv", \
-        "{output_directory}/samples/{sample}/diamond_kegg/{sample}_diamond_kegg.tsv", \
+        "{output_directory}/samples/{sample}/.annotation/{sample}.gff", \
+        "{output_directory}/samples/{sample}/eggnog/{sample}.emapper.genepred.gff", \
         "{output_directory}/kegg_pathway/kegg_pathway_enrichment_analysis.tsv", \
         "{output_directory}/gtdbtk/gtdbtk.summary.tsv", \
         "{output_directory}/mlst/mlst.tsv", \
         "{output_directory}/abricate/card_detailed.tsv", \
-        "{output_directory}/samples/{sample}/.annotation/{sample}.gff", \
         "{output_directory}/panaroo/summary_statistics.txt", \
         "{output_directory}/fasttree/fasttree.newick", \
         "{output_directory}/snp-dists/snp-dists.tsv", \
@@ -417,7 +417,6 @@ rule isolate:
 
 
 
-
 # --- Dynamic report ------------------------------------------------
 # For calling the report subpipeline we need some variables. The easiest way to communicate these from the main pipeline to the report pipeline, is to write a config.yaml.