Claude Skill Nextflow
Claude is adding Nextflow Development to the skill, so I give that a test.
It currently supports 3 pipelines (rnaseq, sark, and atacseq), but I try to make it to run rnavar to see how good it can extend the jobs.
Claimed Features:
Download public datasets from GEO/SRA: this could be done with nextflow fetchngs too. Auto-detect data types and suggest appropriate pipelines: this only works for current 3 pipeines by calculating confidence scores for each pipelin, but it is extendable. Generate pipeline-compatible samplesheets: this is helpful, I can see the benefit for non-coding experimentalist. Environment validation and troubleshooting guidance: I have to tell it to load the nextflow module on HPC, but it can load the non-default newer version, so I gave that a point.
The sareck testing went smoothly, since nextflow have good test profile.
Then I asked it to create a samplesheet for rnavar pipeine, and of course it lied to say there is no rnavar pipeline. However, when I point that out, it clearly correct itself, and start to generate pipeline for rnavar. But, it was trying to run rnavar/1.0.0, which is 4 years old. And also it missed the cached references genome in the config file. Then I asked it to run rnavar/1.2.2, but it was not able to start due to some proxy issue to pull the pipeline. I have to exit the claude code, and manually pull down the pipeline, which seems no issue. Then restart claude to resume the pipeline, which can run. The most impressive part is it was able to modify the commands due to some errors in the references settings, so that can save sometime. But it also did not use the config file that are composed for the cluster, only use the singularity profile instead.
Money talks, how much does it cost? That’s
❯ /cost ⎿ Total cost: $0.1155 Total duration (API): 26s Total duration (wall): 14m 1s Total code changes: 0 lines added, 0 lines removed Usage by model: claude-haiku: 13.5k input, 222 output, 0 cache read, 0 cache write ($0.0146) claude-sonnet: 38 input, 1.2k output, 51.1k cache read, 17.9k cache write ($0.1008)