Reformat sample_calc

[dltamayo]

Moving towards de-hardcoding of metadata fields

[Copilot]

Pull Request Overview

Refactors sample calculation workflow to produce per-sample CSVs with richer metadata, then aggregates them for plotting, moving away from hard‑coded column definitions. Introduces a new SAMPLE_AGGREGATE process and updates downstream notebook to align with renamed metadata fields; also adds dynamic CPU allocation to TCRDIST3.

• Introduce per-sample output file naming (stats/, vdj/) and new aggregation step replacing prior collectFile usage.
• Update analysis notebook to rely on CSV headers instead of hard-coded column name lists and rename metadata fields (patient_id -> subject_id, sample_id -> sample).
• Add dynamic CPU allocation logic to TCRDIST3 process.

Reviewed Changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
subworkflows/local/sample.nf	Replaces collectFile outputs with collection + aggregation processes; updates inputs to plotting step.
notebooks/sample_stats_template.qmd	Changes CSV reading strategy and metadata field names; adjusts plotting hover fields and grouping.
modules/local/sample/tcrdist3.nf	Adds dynamic cpus directive based on task.memory.
modules/local/sample/sample_calc.nf	Changes output file paths/name patterns and serializes sample metadata as JSON.
modules/local/sample/sample_aggregate.nf	New process to concatenate multiple per-sample CSVs into aggregated files.

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[Copilot]

The cpus directive depends on task.memory, which itself is derived later by the memory block; this circular dependency can result in task.memory being undefined or default when cpus is evaluated. Derive both cpu and memory from the same underlying metric (e.g., count_table.size()) or compute memory first in a variable and base cpus on that variable instead of task.memory.

Suggested change

	if (task.memory > 256.GB)
	return 16 * task.attempt
	else if (task.memory > 64.GB)
	return 8 * task.attempt
	else if (task.memory > 4.GB)
	return 4 * task.attempt
	else
	return 2 * task.attempt
	}
	def sz = count_table.size()
	def mb = 1024 * 1024
	if (sz > 26 * mb)
	return 16 * task.attempt
	else if (sz > 20 * mb)
	return 8 * task.attempt
	else if (sz > 10 * mb)
	return 4 * task.attempt
	else
	return 2 * task.attempt
	}

[dimalvovs]

• setting to 'Request changes' avoid being unnoticed, but feel free to create additional issues to address if we need it merged now;
• nf-test test minimal example runs without errors, nice!
• nextflow lint main.nf returns "❌ 4 files had 21 errors", most errors are really simple to fix, the benefit besides having better code formatting and standardization are beautiful flow charts such as below. Can be done now or if preferred, with a dedicated refactoring feature.
  
• in the same refactoring category, I could not find the versions.yml output in the minimal example test results;
• skimmed through Copilot comments and left mine where applicable
• regarding the resource allocation, it does seem to work, run this gist https://gist.github.com/dimalvovs/3b1853effe9105c96ca40ac3e8886332
  that produces these outputs:

 N E X T F L O W   ~  version 25.04.8

Launching `main.nf` [loquacious_kare] DSL2 - revision: 39f7d81a10

executor >  local (12)
[d4/613c6c] MAKE_TEST_FILES (3) [100%] 6 of 6 ✔
[47/10b6db] TCRDIST3_MATRIX (6) [100%] 6 of 6 ✔
cpus:8 memory:1.3 GB size:20480
cpus:2 memory:163.8 MB size:4096
cpus:4 memory:655.4 MB size:10240
cpus:8 memory:5.1 GB size:30720
cpus:2 memory:409.6 MB size:2048
cpus:4 memory:655.4 MB size:6144

and also is susceptible to restricting resources from the nextflow.config:

 N E X T F L O W   ~  version 25.04.8
Launching `main.nf` [friendly_angela] DSL2 - revision: 39f7d81a10

[17/8f8b22] MAKE_TEST_FILES (6) [100%] 6 of 6 ✔
[77/703366] TCRDIST3_MATRIX (6) [100%] 6 of 6 ✔
cpus:1 memory:409.6 MB size:2048
cpus:1 memory:1 GB size:20480
cpus:1 memory:1 GB size:30720
cpus:1 memory:163.8 MB size:4096
cpus:1 memory:655.4 MB size:10240
cpus:1 memory:655.4 MB size:6144