feat(rna): add ENA parallel processor for 10x faster FASTQ downloads

- New process_apis_mellifera_ena.py downloads pre-extracted FASTQs directly from ENA
- Uses ENA Portal API for reliable URL discovery
- 20 workers safe since no extraction bottleneck
- Observed: 19-42 sec/sample vs 50+ min via NCBI
- Reduce NCBI fallback pipeline to 10 workers

Author: docxology

output/amalgkit/apis_mellifera_all/work/quant/DRR129208/run_info.json

@@ -0,0 +1,14 @@
+{
+	"n_targets": 28355,
+	"n_bootstraps": 0,
+	"n_processed": 772651,
+	"n_pseudoaligned": 636494,
+	"n_unique": 349326,
+	"p_pseudoaligned": 82.4,
+	"p_unique": 45.2,
+	"kallisto_version": "0.51.1",
+	"index_version": 13,
+	"k-mer length": 31,
+	"start_time": "Thu Feb  5 06:10:14 2026",
+	"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/DRR129208 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/DRR129208/DRR129208.fastq.gz"
+}

output/amalgkit/apis_mellifera_all/work/quant/SRR12584229/run_info.json

@@ -0,0 +1,14 @@
+{
+	"n_targets": 28355,
+	"n_bootstraps": 0,
+	"n_processed": 2068189,
+	"n_pseudoaligned": 375947,
+	"n_unique": 184261,
+	"p_pseudoaligned": 18.2,
+	"p_unique": 8.9,
+	"kallisto_version": "0.51.1",
+	"index_version": 13,
+	"k-mer length": 31,
+	"start_time": "Thu Feb  5 06:04:09 2026",
+	"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR12584229 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR12584229/SRR12584229.fastq.gz"
+}

output/amalgkit/apis_mellifera_all/work/quant/SRR21601887/run_info.json

@@ -0,0 +1,14 @@
+{
+	"n_targets": 28355,
+	"n_bootstraps": 0,
+	"n_processed": 3746640,
+	"n_pseudoaligned": 0,
+	"n_unique": 0,
+	"p_pseudoaligned": 0.0,
+	"p_unique": 0.0,
+	"kallisto_version": "0.51.1",
+	"index_version": 13,
+	"k-mer length": 31,
+	"start_time": "Thu Feb  5 06:09:47 2026",
+	"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR21601887 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR21601887/SRR21601887.fastq.gz"
+}

output/amalgkit/apis_mellifera_all/work/quant/SRR7412464/run_info.json

@@ -0,0 +1,14 @@
+{
+	"n_targets": 28355,
+	"n_bootstraps": 0,
+	"n_processed": 108758,
+	"n_pseudoaligned": 5,
+	"n_unique": 1,
+	"p_pseudoaligned": 0.0,
+	"p_unique": 0.0,
+	"kallisto_version": "0.51.1",
+	"index_version": 13,
+	"k-mer length": 31,
+	"start_time": "Thu Feb  5 06:09:56 2026",
+	"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR7412464 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR7412464/SRR7412464.fastq.gz"
+}

output/amalgkit/apis_mellifera_all/work/quant/SRR7412489/run_info.json

@@ -0,0 +1,14 @@
+{
+	"n_targets": 28355,
+	"n_bootstraps": 0,
+	"n_processed": 77570,
+	"n_pseudoaligned": 7,
+	"n_unique": 2,
+	"p_pseudoaligned": 0.0,
+	"p_unique": 0.0,
+	"kallisto_version": "0.51.1",
+	"index_version": 13,
+	"k-mer length": 31,
+	"start_time": "Thu Feb  5 06:09:51 2026",
+	"call": "kallisto quant -i output/amalgkit/apis_mellifera_all/work/index/Apis_mellifera_transcripts.idx -o output/amalgkit/apis_mellifera_all/work/quant/SRR7412489 -t 2 --single -l 200 -s 30 /Volumes/blue/data/apis_mellifera/SRR7412489/SRR7412489.fastq.gz"
+}