Automate nf-core/pacsomatic tumor-normal workflows with Python scripts.
npx skills add https://github.com/tassiovale/claude-code-kit --skill pacsomatic-tassiovale
Please help me install this Agent Skill. Skill: pacsomatic Source: https://github.com/tassiovale/claude-code-kit/tree/main/skills/pacsomatic Command: npx skills add https://github.com/tassiovale/claude-code-kit --skill pacsomatic-tassiovale
This Skill simplifies the process of running tumor-normal analysis workflows using nf-core/pacsomatic, automating the validation of inputs, generation of samplesheets, and execution on various platforms.
Run the pacsomatic skill with the provided BAM files, patient IDs, and output directory. For example:
python scripts/run_pacsomatic.py \
--tumor-bam /path/to/tumor.bam \
--normal-bam /path/to/normal.bam \
--patient-id P001 \
--tumor-sample-id P001_T \
--normal-sample-id P001_N \
--outdir /path/to/output \
--genome GRCh38 \
--profile singularity,sanger \
--executor local \
--run
High-intent search queries and answers about installing and using this skill.
To run a matched tumor-normal workflow automatically, use this Skill to execute nf-core/pacsomatic. It validates your inputs, generates the required samplesheets, and orchestrates the workflow execution locally or on a scheduler.
Yes, you can submit tumor-normal analysis jobs to schedulers. The workflow supports submission to LSF, Slurm, PBS, and SGE, alongside local execution for running analysis directly on your current machine.
For nf-core/pacsomatic tumor-normal analysis, you need matched tumor and normal BAM files, patient IDs, tumor and normal sample IDs, an output directory, and a reference genome like GRCh38 to validate inputs and generate samplesheets.
Yes, the pacsomatic workflow supports Singularity for containerized execution. You can specify the singularity profile alongside others, like sanger, when launching the workflow to ensure reproducible bioinformatics analysis.
You need Python to execute the nf-core/pacsomatic workflow because the Skill relies on Python scripts to validate inputs, generate samplesheets, and handle the workflow orchestration before launching the actual bioinformatics pipeline.
dralkhGenerate validated nf-core/pacsomatic samplesheets and launch scripts from tumor-normal BAM inputs.
SheshiyerGenerate and schedule pre-launch announcement and reminder emails with JSON handoff.
Lord1EgyptValidate and execute nf-core/pacsomatic pipelines for tumor-normal BAM analysis.
Estrella-231Generate pacsomatic samplesheets and Nextflow launch artifacts from tumor-normal BAM inputs.