Add support for CellRanger ARC - #15

Draft

arteymix wants to merge 55 commits into

feature-cellranger-arc

Commits on Oct 22, 2025

Improve sratools support
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92f82ba
Add support for Cell Ranger
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ccc61a5
Add an option to DynamicTaskWithOutputMixin to not unpack singleton output
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01439e2
Add a task namespace for CellRangerCount
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04f9e76
Disable singleton unpacking by default for DynamicTaskWithOutputMixin
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e8521a1
Revert "Disable singleton unpacking by default for DynamicTaskWithOutputMixin"
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8e9d493
Add Python 3.14 to the CI
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adcb7b7
Add cellranger.BamToFastq
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ea59d20
Write CellRanger to a temporary output directory
arteymix
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4a5b71b
Cap the length of Slurm job names to 100 characters
arteymix
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b7d3ef1
Fix typo in walltime description
arteymix
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f799b81
Write cutadapt output atomatically
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da39ee4
Make multiqc task atomic
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b683caa
Add a resources for running Cell Ranger count and bamtofastq
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e5ae23c
Add a resource for cutadapt jobs
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fcf2795
Add an io_jobs resource for I/O intensive jobs
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f4005f3
Cleanups cutadapt optional parameter defaults
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22e75d8
Use Luigi's builtin temporary output for fastq-dump
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41649db
More work...
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785441a
Improvements for scheduled external programs
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0363b8d
Make fastqc.GenerateReport atomic
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2db27ca
Add a .fastq.gz to the temporary output files of cutadapt
arteymix
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bad7b8e
cutadapt: Use the patched temporary_path() implementation to preserve file extension
arteymix
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d63187f
Add io_jobs to the default resources
arteymix
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fd975bb
Add fastqc_jobs and mark prefetch consume an io_jobs resource
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248d38a
bcftools: Make all output atomic
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6c59b7f
Drop empty gatk module
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8f69622
vep: Make vep.Annotate atomic
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0b4bfc8
sratoolkit: Fix formatting
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ef7699f
Formatting and minor cleanups
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568455f
Defer checks for task parameters
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f524a11
Add a local and ssh scheduler definitions
arteymix
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ca5886c
Add testspaths to pytest.ini
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370af87
fixup! Add a local and ssh scheduler definitions
arteymix
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66b60ee
Fix various typing issues
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cd94527
Migrate to pyproject.toml
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00dcaac
Allow schedulers to provide task status and progress updates
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17531bd

Commits on Oct 23, 2025

Add development dependencies
arteymix
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efed7c7
schedulers: Few improvements to task status tracking with Slurm
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f5a05ec
Add missing bioluigi.tasks package
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101e8fa
schedulers: Do not set cwd for srun, --chdir already takes care of it
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0243d77
Add dev dependencies for building docs
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6573466
Ignore build directories
arteymix
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6d1dda4

Commits on Oct 25, 2025

Commits on Oct 26, 2025

fixup! Delete temporary Luigi files/directories when task fail
arteymix
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9ce7b59

Commits on Oct 27, 2025

Rename bioluigi to BioluigiConfig
arteymix
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8e4083c
Make samtools executable configurable
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1f6e29f
Update README.md
arteymix
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c756e22
Use ABC on ScheduledExternalProgramTask and ScheduledTask
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4d276bd
Add support fo rcellranger arc
arteymix
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153f526