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Merged
merged 21 commits into from
Oct 28, 2025
Merged

feat: Add Alignoth wrapper #4676

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065fd31
feat: Add Alignoth wrapper
fxwiegand Oct 27, 2025
d292e54
Add env pinnings
fxwiegand Oct 27, 2025
a2700f7
Update alignoth output dir and add test for output-dir
fxwiegand Oct 27, 2025
9af6c87
Format
fxwiegand Oct 27, 2025
29eb0f2
Add log file output to alignoth test rules
fxwiegand Oct 27, 2025
8e128a1
Refactor parameter handling for clarity and consistency
fxwiegand Oct 27, 2025
2613460
Replace hasattr checks with attribute access for snakemake.output
fxwiegand Oct 27, 2025
30ffc1b
Use dict get instead of hasattr for input checks
fxwiegand Oct 27, 2025
f72a669
Fix input checks to use default empty string with get()
fxwiegand Oct 27, 2025
e287754
Update test_wrappers.py
fxwiegand Oct 27, 2025
2ec4b61
Simplify parameter handling and command construction
fxwiegand Oct 27, 2025
fb5ae99
Update meta.yaml
fxwiegand Oct 27, 2025
d8c090c
Simplify ValueError formatting in wrapper.py
fxwiegand Oct 27, 2025
4c64cc5
Simplify output handling for Alignoth wrapper
fxwiegand Oct 27, 2025
76c65e0
Use directory() for output-dir in alignoth_output_dir rule
fxwiegand Oct 27, 2025
a647d3a
Improve output handling and error checking in wrapper
fxwiegand Oct 27, 2025
4ce79d5
Remove ValueError for non-standard output paths
fxwiegand Oct 27, 2025
5abbc0d
Update envs
fxwiegand Oct 27, 2025
671a5d7
Rename rule from alignoth_tsv to alignoth_html
fxwiegand Oct 27, 2025
959ee33
Dont redirect stdout
fxwiegand Oct 27, 2025
2300aa3
Remove os import
fxwiegand Oct 27, 2025
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31 changes: 31 additions & 0 deletions bio/alignoth/environment.linux-64.pin.txt
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# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
# created-by: conda 25.9.1
@EXPLICIT
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.10.5-hbd8a1cb_0.conda#f9e5fbc24009179e8b0409624691758a
https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-h767d61c_7.conda#f7b4d76975aac7e5d9e6ad13845f92fe
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-h767d61c_7.conda#c0374badb3a5d4b1372db28d19462c53
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda#f7f0d6cc2dc986d42ac2689ec88192be
https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda#b38117a3c920364aff79f870c984b4a3
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda#280ea6eee9e2ddefde25ff799c4f0363
https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-15.2.0-hcd61629_7.conda#f116940d825ffc9104400f0d7f1a4551
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-15.2.0-h8f9b012_7.conda#5b767048b1b3ee9a954b06f4084f93dc
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda#47e340acb35de30501a76c7c799c41d7
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.5.4-h26f9b46_0.conda#14edad12b59ccbfa3910d42c72adc2a0
https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda#c277e0a4d549b03ac1e9d6cbbe3d017b
https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
https://conda.anaconda.org/conda-forge/linux-64/libgfortran-15.2.0-h69a702a_7.conda#8621a450add4e231f676646880703f49
https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.1-hcf80075_0.conda#eecce068c7e4eddeb169591baac20ac4
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-15.2.0-h4852527_7.conda#f627678cf829bd70bccf141a19c3ad3e
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda#6432cb5d4ac0046c3ac0a8a0f95842f9
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.67.0-had1ee68_0.conda#b499ce4b026493a13774bcf0f4c33849
https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.30-pthreads_h94d23a6_2.conda#dfc5aae7b043d9f56ba99514d5e60625
https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-37_h4a7cf45_openblas.conda#8bc098f29d8a7e3517bac5b25aab39b1
https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.16.0-h4e3cde8_0.conda#a401aa9329350320c7d3809a7a5a1640
https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-37_h0358290_openblas.conda#3794858d4d6910a7fc3c181519e0b77a
https://conda.anaconda.org/bioconda/linux-64/alignoth-1.1.3-h1520f10_0.conda#2be85e366db3bf6f0d302158330d4668
6 changes: 6 additions & 0 deletions bio/alignoth/environment.yaml
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channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- alignoth =1.1.3
18 changes: 18 additions & 0 deletions bio/alignoth/meta.yaml
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name: alignoth
description: |
Alignoth generates alignment plots from BAM files.
This wrapper allows specifying BAMs, reference FASTA, VCFs,
highlight regions, auxiliary tags, and output options.
url: https://github.com/alignoth/alignoth
input:
- bam: Path to indexed BAM file
- reference: Path to indexed reference FASTA file
- vcf: Path to indexed VCF file (Optional)
- bed: Path to BED file (Optional)
output: "HTML, JSON or directory path"
authors:
- Felix Wiegand
params:
- extra: "Extra command line arguments to pass directly to alignoth."
notes: |
Output needs to end with .html, .json or a directory path.
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41 changes: 41 additions & 0 deletions bio/alignoth/test/Snakefile
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rule alignoth_json:
input:
bam="NA12878.bam",
reference="ref.fa",
vcf="1257A.vcf.gz"
output:
"out/json_plot.vl.json"
params:
extra="-g 1:50-280 -h coolregion:200-210"
log:
"logs/log.txt"
wrapper:
"master/bio/alignoth"

rule alignoth_html:
input:
bam="NA12878.bam",
reference="ref.fa",
vcf="1257A.vcf.gz"
output:
"out/plot.html"
params:
extra="-g 1:50-280 -h coolregion:200-210"
log:
"logs/log.txt"
wrapper:
"master/bio/alignoth"

rule alignoth_output_dir:
input:
bam="NA12878.bam",
reference="ref.fa",
vcf="1257A.vcf.gz"
output:
directory("output-dir/")
params:
extra="-g 1:50-280 -h coolregion:200-210"
log:
"logs/log.txt"
wrapper:
"master/bio/alignoth"
2 changes: 2 additions & 0 deletions bio/alignoth/test/ref.fa
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>1
TGTGCACCCAGGCTAATTAATGTTCATGGGAACTAATTAGAGCTGACATGTACAGCCAGCCTTTTGCTTACTCTGCGGGATCTTGTTCTGTGTGATTTCTCTAGGGGGAGCCTGCTCACTTTGAGTATTTGATGTATCCATTGCACTCAGCACCCATCACCGGTCTAGCTACCTGCATCCGCAAACCCCTTATAGCCACCTGTTCTCTGGATCGATCCATCCGCCTTTGGAATTATGAAACAAAGTAAGGAATGAAAGGCTTGCCTACTTTATTATGCAAGACCCCAGTTGTGAATTTATGTGAATTATTTTAATTACAGTGTTCCAAACTTTAATTATTTAGAAGCTTTCAGTTGGAAAAGATTTTTAAAAAATCAAGTCAGTCAACCTACCTGTTTCTCACTCTTGCGTGGGCTAGAAAACTACTTTGTGGTTTATTTAATGCTTACCACATGCTAGACACTGGGGACATGAAGAGATGAAGACAACACCTCAGTCTCTCACCTTCTTACATAAACTCCTGGGTCCCTCCAGCTCTCCTATCCCCTTGTTTCCCACAGGAACTGCTCTTTGCTTCAGGGAGCTCTCCAGACCCTTTCTTCCTCATCTTTCTCCCAGGACATCACTATCTCAACCACCCCCAACTCCCTCCTGACTTTACCTTCCAGCACAGCTTCCCTGGGAAGCTCCAACCCTAGGTGGACCCCCACCCCCTACTGTTTTCTTTGTTCTTATGTACAACTTCTGGGGCTTCTGGGGAAAAAATACTTGGACAATACTCATGAATTTTGGAATATAAACAGAGCTATGTCTTCAGCATCGCTAGACCACACCTTGACCAGTCTCCCTATCTACCATGCTCCACGCTGGACATTATCCCCTAATAACCAAGATCTAGAAAAGAGAGGAACCAACAATTGCAAACAGTAGTGTGTCTCAAATACGATGATAACAATATATATCAGATACAGTAGATGACTGGAAGGATTTAGTGAGCTAAGCTTACAATTCAGTAATTGATCTTTTTCACAGCACCCTGGAACTATTTAAGGAATACCAAGAAGAGGCATATTCCATCAGCCTTCATCCATCTGGACACTTCATTGTAGTAGGGTTTGCTGACAAACTACGCCTCATGAATCTACTCATTGATGATATACGTTCTTTCAAAGAATACTCTGTTAGAGGATGCGGAGAGGTAAAAAAAAAACTGCTGAAGACAAAAGTCCAGTTTCTTAGAAAGCCACGGCTGAAATATCAGGAACTAACATGATCTGGGGAGGTGGGACCAAAATCTGTCTTGGAGAACTACAGTGGCTTAAAAAAAGGGGGAAGGAGGAAATCCAGTTATTTTCCCAGCAACCTTATTGAGTATATGGTTCCATCCCCATATTCTTATGTCCACCAGACTATTTCATTGAACCTAAAACCTTGTGAGATCCCCGCTATGATAAGTCCTGTCTGTAATTGTGGAATATTAACAAATATTTTAAAAGAAAAGTAATCTCAGAATCAGAGTCACAGCTAAGAAGGTGAGGTTGGAGACGGAGGAGCCAGGGAAAAATAAGCATCAATGGTGAGAGGTAATAAAGAGCGCATCAGCTTTCCCTGAGGTGTCTTGCAGAAACAAGGCAATGATTTCAGGAATTACTTCCCCGGCTCTGAAACATGCTTCTACAGGCAAAATGATTGCTTGTGGTCCCAACGGCTTAATGATTTGTGGGCCTGACAGTGTCAGCATCTGGCCACTATGAGTTACAGGAATAATGAAAGTGTCTGAAAATGTCAGCCACTCCTCAGTCTCATTTGCACCTTCCCCCCACTCCCACCCTCACACGTAGTTTCAGTCTGAACTCGTTGGGAAAAGCACCTCTTGACTGTAACCTCTAATTAGACTGCTCACTTCCTGCTTGCTTGCTCTCTTGCTGTCTTTCCCTATAGTGTTCCTTTAGCAATGGAGGTCACCTGTTTGCTGCAGTCAATGGAAATGTGATTCACGTTTACACCACCACGAGCCTAGAGAACATCTCAAGCCTGAAAGGACACACAGGGAAGGTAAGTGAGTGAACAGTCTCTGGGGAAACAAGGGGCACGGAGCCAAGTATGCCGCCAGCCAGTGGGATACAGGTGAACAAAAGAGAGATGGTTCCTTTCCTCATGGGTTCACTGTCTACTTGGGGAAAGAGACAATAAAACAAATGCACAGACAAATGTAGTTACTAATTGCAGTTCCACTGAAAGAAAAACATGGTGTTGTTGTGAGAGAAATAATGAAGGGGGCGGCATAATTTAGGTGGCTGTATTTGCAAAGGCTTGGTCCTATAAGAGTGAGTAGGAGTTAATCAGACACAACTGGTGGGGATAATCACTGCAGATAGGGATCCAAAGGCCAGAGATGGGAGACTCATAGG
1 change: 1 addition & 0 deletions bio/alignoth/test/ref.fa.fai
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1 2411 3 2411 2412
3 changes: 3 additions & 0 deletions bio/alignoth/test/test.bed
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1 260 300 MVSTP1
1 400 450 LH44
1 600 650 GR63
46 changes: 46 additions & 0 deletions bio/alignoth/wrapper.py
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__author__ = "Felix Wiegand"
__copyright__ = "Copyright 2025, Felix Wiegand"
__email__ = "[email protected]"
__license__ = "MIT"

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)
extra = snakemake.params.get("extra", "")
output = snakemake.output[0]

cmd = ["alignoth"]

# BAM input
if snakemake.input.get("bam", ""):
cmd.append(f"-b {snakemake.input.bam}")
else:
raise ValueError("BAM input required")

# Reference
if snakemake.input.get("reference", ""):
cmd.append(f"-r {snakemake.input.reference}")
else:
raise ValueError("Reference input required")

# Optional VCF
if snakemake.input.get("vcf", ""):
cmd.append(f"-v {snakemake.input.vcf}")

# Optional BED
if snakemake.input.get("bed", ""):
cmd.append(f"--bed {snakemake.input.bed}")

cmd.append(f"{extra}")
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⚠️ Potential issue | 🟡 Minor

Avoid appending empty extra parameter.

Line 35 appends extra even when it's an empty string (the default). This adds an unnecessary empty element to the command list. Additionally, if extra contains multiple space-separated arguments, appending it as a single string means it will be treated as one argument when the list is joined.

Apply this diff to fix both issues:

-cmd.append(f"{extra}")
+if extra:
+    import shlex
+    cmd.extend(shlex.split(extra))

This ensures:

  • Empty extra is not appended
  • Multiple arguments in extra are properly split and added as separate list elements
🤖 Prompt for AI Agents 
In bio/alignoth/wrapper.py around line 35, the code unconditionally appends the
extra string which can add an empty element or treat multiple space-separated
args as one; change it so that you only add extra when non-empty and split it
into separate arguments (use shlex.split or equivalent) and extend the cmd list
with the resulting tokens instead of appending the raw string.


# HTML output
if output.endswith(".html"):
cmd.append("--html")
shell(f"{' '.join(cmd)} > {output} {log}")
# Default: JSON output to single file via stdout
elif output.endswith(".json"):
shell(f"{' '.join(cmd)} > {output} {log}")
# Assume output is directory
else:
cmd.append(f"-o {output}")
shell(f"{' '.join(cmd)} {log}")
7 changes: 7 additions & 0 deletions test_wrappers.py
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Expand Up @@ -250,6 +250,13 @@ def test_agat(run):
)


def test_alignoth(run):
run(
"bio/alignoth",
["snakemake", "--cores", "1", "--use-conda", "-F", "out/json_plot.vl.json", "out/plot.html", "output-dir/"],
)


def test_miller(run):
run(
"utils/miller",
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