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A comprehensive, opinionated plant variant calling pipeline in Snakemake

License: Mozilla Public License 2.0

Python 21.70% Dockerfile 0.47% Shell 11.28% TeX 66.55%

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acanthophis's Issues

Included Dockerfile does not build

Running docker build -t acanthophis . from root of repository and throws following error. It seems Dockerfile is outdated.

16.77 INFO: pip is looking at multiple versions of acanthophis to determine which version is compatible with other requirements. This could take a while.
16.77 ERROR: Ignored the following versions that require a different python version: 8.0.0 Requires-Python >=3.11; 8.0.1 Requires-Python >=3.11; 8.1.0 Requires-Python >=3.11; 8.1.1 Requires-Python >=3.11; 8.1.2 Requires-Python >=3.11; 8.1.3 Requires-Python >=3.11; 8.2.0 Requires-Python >=3.11; 8.2.1 Requires-Python >=3.11; 8.2.2 Requires-Python >=3.11; 8.2.3 Requires-Python >=3.11
16.77 ERROR: Could not find a version that satisfies the requirement snakemake>=8 (from acanthophis) (from versions: 1.0, 1.0.1, 1.0.2, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.2, 1.2.1, 1.2.3, 2.0, 2.1, 2.1.1, 2.2, 2.2.1, 2.2.2, 2.3, 2.4, 2.4.1, 2.4.2, 2.4.3, 2.4.4, 2.4.5, 2.4.6, 2.4.7, 2.4.7.1, 2.4.8, 2.4.9, 2.5, 2.5.1, 2.5.2, 2.5.2.1, 2.5.2.2, 3.0b1, 3.0, 3.1, 3.1.1, 3.2, 3.2.1, 3.2.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.5.0, 3.5.1, 3.5.2, 3.5.3, 3.5.4, 3.5.5, 3.6.0, 3.6.1, 3.7.0, 3.7.1, 3.8.0, 3.8.1, 3.8.2, 3.9.0, 3.9.1, 3.10.0, 3.10.1, 3.10.2, 3.11.0, 3.11.1, 3.11.2, 3.12.0, 3.13.0, 3.13.1, 3.13.2, 3.13.3, 4.0.0, 4.1.0, 4.2.0, 4.3.0, 4.3.1, 4.4.0, 4.5.0, 4.5.1, 4.6.0, 4.7.0, 4.8.0, 4.8.1, 5.0.0, 5.1.1, 5.1.2, 5.1.3, 5.1.4, 5.1.5, 5.2.0, 5.2.1, 5.2.2, 5.2.3, 5.2.4, 5.3.0, 5.3.1, 5.4.0, 5.4.1, 5.4.2, 5.4.3, 5.4.4, 5.4.5, 5.5.0, 5.5.1, 5.5.2, 5.5.3, 5.5.4, 5.6.0, 5.7.0, 5.7.1, 5.7.4, 5.8.0, 5.8.1, 5.8.2, 5.9.0, 5.9.1, 5.10.0, 5.11.0, 5.11.1, 5.11.2, 5.12.0, 5.12.1, 5.12.2, 5.12.3, 5.13.0, 5.14.0, 5.15.0, 5.16.0, 5.17.0, 5.18.0, 5.18.1, 5.19.0, 5.19.1, 5.19.2, 5.19.3, 5.20.0, 5.20.1, 5.21.0, 5.22.0, 5.22.1, 5.23.0, 5.24.0, 5.24.1, 5.24.2, 5.25.0, 5.26.0, 5.26.1, 5.27.2, 5.27.3, 5.27.4, 5.28.0, 5.29.0, 5.30.0, 5.30.1, 5.30.2, 5.31.0, 5.31.1, 5.32.0, 5.32.1, 5.32.2, 6.0.0, 6.0.1, 6.0.2, 6.0.3, 6.0.4, 6.0.5, 6.1.0, 6.1.1, 6.1.2, 6.2.0, 6.2.1, 6.3.0, 6.4.0, 6.4.1, 6.5.0, 6.5.1, 6.5.2, 6.5.3, 6.5.5, 6.6.0, 6.6.1, 6.7.0, 6.8.0, 6.8.1, 6.8.2, 6.9.0, 6.9.1, 6.10.0, 6.11.0, 6.11.1, 6.12.0, 6.12.1, 6.12.2, 6.12.3, 6.13.0, 6.13.1, 6.14.0, 6.15.0, 6.15.1, 6.15.2, 6.15.3, 6.15.4, 6.15.5, 7.0.0, 7.0.1, 7.0.2, 7.0.3, 7.0.4, 7.1.0, 7.1.1, 7.2.0, 7.2.1, 7.3.0, 7.3.1, 7.3.2, 7.3.3, 7.3.4, 7.3.5, 7.3.6, 7.3.7, 7.3.8, 7.4.0, 7.5.0, 7.6.0, 7.6.1, 7.6.2, 7.7.0, 7.8.0, 7.8.1, 7.8.2, 7.8.3, 7.8.5, 7.9.0, 7.10.0, 7.11.0, 7.12.0, 7.12.1, 7.13.0, 7.14.0, 7.14.1, 7.14.2, 7.15.0, 7.15.1, 7.15.2, 7.16.0, 7.16.1, 7.16.2, 7.17.0, 7.17.1, 7.18.0, 7.18.1, 7.18.2, 7.19.0, 7.19.1, 7.20.0, 7.21.0, 7.22.0, 7.23.0, 7.23.1, 7.24.0, 7.24.1, 7.24.2, 7.25.0, 7.25.1, 7.25.2, 7.25.3, 7.25.4, 7.26.0, 7.28.0, 7.28.1, 7.28.2, 7.28.3, 7.29.0, 7.30.0, 7.30.1, 7.30.2, 7.31.0, 7.31.1, 7.32.0, 7.32.1, 7.32.2, 7.32.3, 7.32.4)
16.77 ERROR: No matching distribution found for snakemake>=8
------
Dockerfile:5
--------------------
   3 |     WORKDIR /usr/local/src/acanthophis
   4 |     COPY . .
   5 | >>> RUN conda config --add channels bioconda &&  mamba install --yes --all snakemake && pip install -e .
   6 |     
--------------------
ERROR: failed to solve: process "/bin/sh -c conda config --add channels bioconda &&  mamba install --yes --all snakemake && pip install -e ." did not complete successfully: exit code: 1

For JOSS Review

Unable to run tests: missing 'populate_metadata' in module 'acanthophis'

(Part of review thread openjournals/joss-reviews#6062)

Hello! I tried running the tests for this repo by following the instructions here and found the following minor issues:

  • The conda environment file is currently not conda.yml as per the README, but environment-setup.yml
  • In that environment-setup.yml, installing msprime from pip failed - see attached log file
    failed_pip_install_msprime.txt. I found that simply installing msprime from conda-forge worked instead, as per instructions here.
    --> Update the .yml accordingly?
  • The last part of the README in the tests directory should be updated to reflect the current status of Acanthophis - i.e.,
    using the instructions from here in the main README, or just link to that.
    Same for the comment '# once I put this on PyPI:' - I see acanthophis is on PyPI

And here is a more major issue:

  • Running snakemake --snakefile Snakefile.generate-rawdata -j 8 --use-conda completed fine and produced the rawdata. However, for actually running acanthophis on the generated
    test dataset, snakemake --snakefile Snakefile -j 8 --use-conda, Snakefile and config.yml are missing.
    I saw that inside the script test.sh there are instructions to generate them, using acanthophis-init. Please either
    tell the user to run setup.sh and test.sh, or acanthophis-init, in the README code block.
  • Having done as above, command snakemake --snakefile Snakefile -j 8 --use-conda gives the following error: 
    AttributeError in file /home/adminbrice/Desktop/research/writing/reviewing_exernal/JOSS/Acanthophis/test_tool/Acanthophis/tests/Snakefile, line 4:
  module 'acanthophis' has no attribute 'populate_metadata'
File "/home/adminbrice/Desktop/research/writing/reviewing_exernal/JOSS/Acanthophis/test_tool/Acanthophis/tests/Snakefile", line 4, in <module>

[JOSS Review] Errors with Mac Installation

Re openjournals/joss-reviews#6062

On my Macbook M1 I tried this:

git clone https://github.com/kdm9/Acanthophis.git
mamba env create -f environment-setup.yml -n acanthophis-demo
conda activate acanthophis-demo
pip install -U acanthophis # confirmed v0.3.0 was installed 
cd Acanthophis/tests
 
acanthophis-init .
 
snakemake --snakefile Snakefile.generate-rawdata -j 8 --use-conda

This all ran no problems at all.

I then ran

snakemake snakemake -j 8 --use-conda --conda-frontend mamba

which errored:

Traceback (most recent call last):
  File "/Users/a1667917/mambaforge/envs/acanthophis-demo/lib/python3.11/site-packages/snakemake/cli.py", line 1886, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/acanthophis-demo/lib/python3.11/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/Users/a1667917/mambaforge/envs/acanthophis-demo/lib/python3.11/site-packages/snakemake/api.py", line 425, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/acanthophis-demo/lib/python3.11/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/Users/a1667917/mambaforge/envs/acanthophis-demo/lib/python3.11/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/Users/a1667917/Documents/Reviews/acanthophis/Acanthophis/tests/Snakefile", line 6, in <module>
AttributeError: module 'acanthophis' has no attribute 'populate_metadata'

George

[JOSS Review] Improve `tests` docs

Re openjournals/joss-reviews#6062

After running

snakemake --snakefile Snakefile.generate-rawdata -j 8 --use-conda

which completed perfectly, the instructions say:

"To initialise your own workflow, copy ./Snakefile and ./config.yml to a new directory"

However, there isn't a Snakefile or config.yml file in the tests directory. I assume that you need to start a new project as per the main documentation - it would be good to make this clearer.

George

Review comments on the JOSS software paper

(Part of review thread openjournals/joss-reviews#6062)

Overall, the paper reads well, and I am convinced of your pipeline's value both in terms of
need for the community, functionality and level of configurability. For the software paper to fully convey this,
and to clarify certain points/features, I've provided the following comments below. They mostly relate to
providing definitions, more details on the pipeline and use cases, and discussions of design choices and limitations.

In two comments I refer to adding a possible 'Discussion' section to the paper. I'm not sure if this is
something that JOSS does or not - if not, it's fine to address the comments directly on lines they refer to.

  • For clarity the term 'Hologenomics' should be defined at the very beginning of the paper (currently 'hologenome' is defined only on Line 38).
    E.g. in the paper you could tag it after the first sentence of the 'Summary' section:
    '...joint discovery of both plant genetic variation and variation [...] of plant-associated microbiomes. We refer to this as hologenomics.'

    Please also define this term in the repo README or documentation.md.

  • Line 29: 'has attracted many users' do you have a metric for this (e.g. number of git clones, or PyPI downloads)? Otherwise, I would leave this statement out;
    it's already obvious in my opinion that this pipeline is valuable, and you have studies that use it (see below).

  • Lines 30-31: It seems that Ahrens et al. (2021) discusses using the pipeline only through referring to Murray et al. (2019), in which parts of an earlier version of this pipeline are discussed.
    Perhaps state as such: 'this pipeline was first developed in Murray et al. (2019) for use in [x and y], and subsequently used
    in Ahrens et al. (2021) for analysing species [x' and y']'.
    Also, what are the improvements in the pipeline since Murray et al. (2019)? (I'm not saying there are none)
    I believe you've added taxonomic identification since then - it would be good to state this.

  • Relating to use cases: has Acanthophis been used already in a hologenomics context - i.e. identifying microbial species present on/near
    focal plant species? If so, please give an example - it's not clear to me that Ahrens et al. (2021) or Murray et al. (2019) do this.
    If not, can you discuss how for example Karasov et al. (2022) did 'hologenomics', did they build their own pipeline?

  • Relating to hologenomics: I don't think your pipeline does host x microbe genetic association tests, perhaps add one sentence in a 'Discussion' section
    about how a user could then seek to do this, after running Acanthophis?

  • Line 29: Related to comment above, can you discuss Taxprofiler a little bit more - can Taxprofiler perform taxonomic assignment for plant
    reads? If not, say that explicitly. Then, you could state that Acanthophis does both variant calling and taxonomic identification, and so
    performs functionality of both Snakemake's variant calling pipeline and the nf-core Taxprofiler pipelines.
    Does Acanthophis do anything that they don't? (perhaps genetic distances?) And (being devil's advocate) in what
    cases is running Acanthophis better than running those two pipelines independently?
    (I guess one obvious answer is analysing plant genomes; can Taxprofiler do hologenomics?)

  • Line 36: Why can't your pipeline be run on long-read data (PacBio, ONT)? It is already valuable
    for the pipeline to target short-read datasets, but it would be nice for the reader to understand
    what prevents Acanthophis processing/being useful for long-read data.
    This could be stated in a 'Discussion' section of the paper.

  • Line 59: why should input reference genomes be uncompressed fasta files? I'm pretty sure that for at least
    bwa-mem and minimap2, the fasta can be gzipped.

  • Line 64: what does 'combines filter-passing alleles back into unique sites' mean? Two clauses back you say that before this filtering
    you split multi-allelic variants, so I assume it's not related to that process?

  • Lines 66-69: very nice paralellisation strategies!

  • Lines 71-74: This sentence is v. hard to understand. I think it'd be clearer to say 'Acanthophis creates taxonomic profiles using any of Kraken2 [etc...],
    or using other public sequence databases'. + Give examples of public sequence databases, and also whether the databases are automatically downloaded during execution.

  • Line 77: For 'Stage 5: De novo Estimates of Genetic Dissimilarity', you provide means to compute genetic dissimilarity measures from the
    reads themselves - i.e. alignment and variant-calling free, which is nice. Does Acanthopis also compute VCF-based dissimilarity measures?
    If not, please state why not.

  • Lines 81-84: please explicitly mention at least some of the tools/stages that MultiQC can run on, to get a sense of what the user can visualise and assess at the end.

  • Perhaps after Line 84, state how independent the stages are: e.g. 'the user can perform all of variant calling, genetic distance estimation and taxonomic profiling isolation', if that's correct

[JOSS Review] Error with Linux Tests - `init` and also Freebayes

Re openjournals/joss-reviews#6062

I ran the same code for #15 on a Linux box (Ubuntu 20.04).

git clone https://github.com/kdm9/Acanthophis.git
mamba env create -f environment-setup.yml -n acanthophis-demo
conda activate acanthophis-demo
pip install -U acanthophis # v0.3.0 was installed

cd Acanthophis/tests
acanthophis-init .
snakemake --snakefile Snakefile.generate-rawdata -j 8 --use-conda
snakemake snakemake -j 8 --use-conda --conda-frontend mamba

Unlike #15 on the Mac, the command acanthophis-init . did not work as designed - it created a structure like:

config.yml
environment.yml
rawdata/
workflow/

with the Snakefile and rules subdirectory in the workflow directory. I'm not really sure why.

In any case, once I copied the Snakefile, rules directory and config.schema.yml file into the correct location, acanthophis did indeed run as expected (the required conda envs were created, almost every rule ran well).

Specifically I ran:

snakemake -j 8 --use-conda --conda-frontend mamba --keep-going

However, there was an error:

Error in rule freebayes:
    jobid: 277
    input: rawdata/reference/genome.fa, output/variants/raw_split/bwa~lambda~all_samples.bamlist, output/variants/raw_split/bwa~lambda~all_samples.fosn
    output: tmp/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:16385-32768.bcf
    log: output/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:16385-32768.bcf.log (check log file(s) for error details)
    conda-env: /data/Acanthophis/tests/l/.snakemake/conda/bd7a1f75aa6d5405df665da7e2521080_
    shell:
        ( freebayes   --theta 0.01   --ploidy 2   --use-best-n-alleles 4      --min-mapping-quality 30   --min-base-quality 15   --read-max-mismatch-fraction 0.1   --skip-coverage 4000   --prob-contamination 0.05   --strict-vcf   --region 'NC_001416:16385-32768'   --fasta-reference rawdata/reference/genome.fa   --bam-list output/variants/raw_split/bwa~lambda~all_samples.bamlist   --samples output/variants/raw_split/bwa~lambda~all_samples.fosn | bcftools view   -O b6   -o tmp/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:16385-32768.bcf ) >output/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:16385-32768.bcf.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[Tue Jan 16 02:32:33 2024]
Error in rule freebayes:
    jobid: 275
    input: rawdata/reference/genome.fa, output/variants/raw_split/bwa~lambda~all_samples.bamlist, output/variants/raw_split/bwa~lambda~all_samples.fosn
    output: tmp/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:1-16384.bcf
    log: output/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:1-16384.bcf.log (check log file(s) for error details)
    conda-env: /data/Acanthophis/tests/l/.snakemake/conda/bd7a1f75aa6d5405df665da7e2521080_
    shell:
        ( freebayes   --theta 0.01   --ploidy 2   --use-best-n-alleles 4      --min-mapping-quality 30   --min-base-quality 15   --read-max-mismatch-fraction 0.1   --skip-coverage 4000   --prob-contamination 0.05   --strict-vcf   --region 'NC_001416:1-16384'   --fasta-reference rawdata/reference/genome.fa   --bam-list output/variants/raw_split/bwa~lambda~all_samples.bamlist   --samples output/variants/raw_split/bwa~lambda~all_samples.fosn | bcftools view   -O b6   -o tmp/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:1-16384.bcf ) >output/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416:1-16384.bcf.log 2>&1
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message

When I examined the log output/variants/raw_split/freebayes~bwa~lambda~all_samples/NC_001416\:1-16384.bcf.log it said

Failed to read from standard input: unknown file type

If it helps, the remaining DAG jobs are:

job                   count
------------------  -------
all                       1
bcffilter                 2
bcfmerge                  1
bcfmerge2group            1
finalvariantidx           1
freebayes                 2
premergevariantidx        2
vcfstats                  1
total                    11

Select jobs to execute...

I've inspected the rule's input files, they look as expected (I assume).

George

Missing contribution/community guidelines

(Part of review thread openjournals/joss-reviews#6062)

The three following guidelines are missing, on how to: 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

(Presumably points 2 and 3 can just be raising issues on the repo)
Please provide these either in a section in the main README or in a separate CONTRIBUTING.md file linked to in the README

[JOSS Review] tab/space bug

Re openjournals/joss-reviews#6062

After #11 copying the Snakefile, I ran:

snakemake --snakefile Snakefile -j 8 --use-conda

which yielded an error (at the bottom of this issue).

It can be fixed by replacing tab with spaces in the line

" --prob-contamination 1e-3"

in the freebayes rule in the varcall.rules file.

Traceback (most recent call last):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/Users/a1667917/Documents/Reviews/acanthophis/Acanthophis/tests/Snakefile", line 18, in <module>
    rules.varcall.input,
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1347, in include
    code, linemap, rulecount = parse(
                               ^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 1307, in parse
    for t, orig_token in automaton.consume():
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 110, in consume
    for t, orig in self.state(token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 1212, in python
    for t in self.subautomaton(token.string, token=token).consume():
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 110, in consume
    for t, orig in self.state(token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 784, in block_content
    for t in self.block(e.token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 784, in block_content
    for t in self.block(e.token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 784, in block_content
    for t in self.block(e.token):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 199, in block
    yield from self.block_content(token)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 773, in block_content
    for t in self.subautomaton(
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 107, in consume
    for token in self.snakefile:
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/parser.py", line 1238, in __next__
    return next(self.tokens)
           ^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/tokenize.py", line 541, in _generate_tokens_from_c_tokenizer
    raise e from None
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/tokenize.py", line 537, in _generate_tokens_from_c_tokenizer
    for info in it:
  File "<string>", line 101
    	"   --skip-coverage 100000"
    	                           ^
TabError: inconsistent use of tabs and spaces in indentation

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1371, in include
    e = update_lineno(e, self.linemaps)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/exceptions.py", line 165, in update_lineno
    ex.lineno = linemaps[ex.filename][ex.lineno]
                ~~~~~~~~^^^^^^^^^^^^^
KeyError: '<string>'

[JOSS Review] kraken.rules error

After fixing #12, I ran into this bug.

I tried to fix it, but it seems as though kraken.rules doesn't exist in the source code.

I had v0.2.0 of acanthophis installed via pip

pip install acanthophis 

  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/cli.py", line 1887, in args_to_api
    dag_api = workflow_api.dag(
              ^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 326, in dag
    return DAGApi(
           ^^^^^^^
  File "<string>", line 6, in __init__
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 421, in __post_init__
    self.workflow_api._workflow.dag_settings = self.dag_settings
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/api.py", line 372, in _workflow
    workflow.include(
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/Users/a1667917/Documents/Reviews/acanthophis/Acanthophis/tests/Snakefile", line 24, in <module>
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/snakemake/workflow.py", line 1369, in include
    exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
  File "/Users/a1667917/mambaforge/envs/someproject/lib/python3.12/site-packages/acanthophis/rules/kraken.rules", line 53, in <module>
KeyError: 'all'

[JOSS Review] Source install v1.0.0rc4.dev6 error on OSX

Re openjournals/joss-reviews#6062

After #13 , I instead proceeded with a source install instead of pip

i.e.


mamba create -n someproject python snakemake pip natsort
mamba activate someproject
git clone https://github.com/kdm9/Acanthophis.git

cd Acanthophis 
pip install -e .

which worked

Installing collected packages: acanthophis
Successfully installed acanthophis-1.0.0rc4.dev6

Then I tried to run acanthophis-init, which did not:

cd ..
acanthophis-init some_project

Traceback (most recent call last):
  File "/Users/a1667917/mambaforge/envs/someproject/bin/acanthophis-init", line 8, in <module>
    sys.exit(init())
             ^^^^^^
  File "/Users/a1667917/Documents/Reviews/acanthophis/Acanthophis/acanthophis/cmd.py", line 64, in init
    template_dir = acanthophis.get_resource("template/")
                   ^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'acanthophis' has no attribute 'get_resource'

George

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