refactor: standardize output directory structure to nested sample paths

All output paths now consistently use {sample}/{sample}.ext pattern:
- fq/{sample}/{sample}.fq.gz
- bam/charging/{sample}/{sample}.charging.bam
- bam/classified/{sample}/{sample}.bam
- bam/final/{sample}/{sample}.bam
- demux/read_ids/{sample}/{sample}.txt
- demux/pod5/{sample}/{sample}.pod5

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: jayhesselberth

CLAUDE.md

@@ -263,4 +263,4 @@ Outputs go to directory specified by `output_dir` in config. Test outputs: `.tes
 Key outputs per sample:
 - `summary/tables/{sample}/{sample}.charging.cpm.tsv.gz` - CPM-normalized charging counts
 - `summary/tables/{sample}/{sample}.charging_prob.tsv.gz` - Per-read charging probabilities
-- `bam/final/{sample}.bam` - Final BAM with CL/CM charging tags
+- `bam/final/{sample}/{sample}.bam` - Final BAM with CL/CM charging tags

workflow/rules/aatrnaseq-process.smk

@@ -57,7 +57,7 @@ rule ubam_to_fastq:
     input:
         rules.rebasecall.output,
     output:
-        os.path.join(outdir, "fq", "{sample}.fq.gz"),
+        os.path.join(outdir, "fq", "{sample}", "{sample}.fq.gz"),
     log:
         os.path.join(outdir, "logs", "ubam_to_fastq", "{sample}"),
     shell:
@@ -120,12 +120,16 @@ rule classify_charging:
         pod5=get_sample_pod5,
         bam=rules.bwa_align.output.bam,
     output:
-        charging_bam=os.path.join(outdir, "bam", "charging", "{sample}.charging.bam"),
+        charging_bam=os.path.join(
+            outdir, "bam", "charging", "{sample}", "{sample}.charging.bam"
+        ),
         charging_bam_bai=os.path.join(
-            outdir, "bam", "charging", "{sample}.charging.bam.bai"
+            outdir, "bam", "charging", "{sample}", "{sample}.charging.bam.bai"
         ),
         temp_sorted_bam=temp(
-            os.path.join(outdir, "bam", "charging", "{sample}.charging.bam.tmp")
+            os.path.join(
+                outdir, "bam", "charging", "{sample}", "{sample}.charging.bam.tmp"
+            )
         ),
     log:
         os.path.join(outdir, "logs", "classify_charging", "{sample}"),
@@ -164,8 +168,12 @@ rule transfer_bam_tags:
         source_bam=rules.classify_charging.output.charging_bam,
         target_bam=rules.bwa_align.output.bam,
     output:
-        classified_bam=os.path.join(outdir, "bam", "classified", "{sample}.bam"),
-        classified_bam_bai=os.path.join(outdir, "bam", "classified", "{sample}.bam.bai"),
+        classified_bam=os.path.join(
+            outdir, "bam", "classified", "{sample}", "{sample}.bam"
+        ),
+        classified_bam_bai=os.path.join(
+            outdir, "bam", "classified", "{sample}", "{sample}.bam.bai"
+        ),
     log:
         os.path.join(outdir, "logs", "transfer_bam_tags", "{sample}"),
     params:
@@ -197,8 +205,8 @@ rule add_adapter_tags:
         bam=rules.transfer_bam_tags.output.classified_bam,
         bai=rules.transfer_bam_tags.output.classified_bam_bai,
     output:
-        bam=os.path.join(outdir, "bam", "final", "{sample}.bam"),
-        bai=os.path.join(outdir, "bam", "final", "{sample}.bam.bai"),
+        bam=os.path.join(outdir, "bam", "final", "{sample}", "{sample}.bam"),
+        bai=os.path.join(outdir, "bam", "final", "{sample}", "{sample}.bam.bai"),
     log:
         os.path.join(outdir, "logs", "add_adapter_tags", "{sample}"),
     params:

workflow/rules/common.smk

@@ -284,7 +284,9 @@ def get_sample_pod5(wildcards):
     Otherwise, use merged POD5 from merge_pods rule.
     """
     if sample_needs_demux(wildcards.sample):
-        return os.path.join(outdir, "demux", "pod5", f"{wildcards.sample}.pod5")
+        return os.path.join(
+            outdir, "demux", "pod5", wildcards.sample, f"{wildcards.sample}.pod5"
+        )
     else:
         return os.path.join(
             outdir, "pod5", wildcards.sample, f"{wildcards.sample}.pod5"

workflow/rules/warpdemux.smk

@@ -198,7 +198,7 @@ rule extract_sample_reads:
     input:
         mapping=get_sample_barcode_mapping,
     output:
-        read_ids=os.path.join(outdir, "demux", "read_ids", "{sample}.txt"),
+        read_ids=os.path.join(outdir, "demux", "read_ids", "{sample}", "{sample}.txt"),
     log:
         os.path.join(outdir, "logs", "extract_sample_reads", "{sample}"),
     params:
@@ -217,7 +217,9 @@ rule extract_sample_reads:
 
 def get_sample_read_ids(wildcards):
     """Get the read ID file for a sample."""
-    return os.path.join(outdir, "demux", "read_ids", f"{wildcards.sample}.txt")
+    return os.path.join(
+        outdir, "demux", "read_ids", wildcards.sample, f"{wildcards.sample}.txt"
+    )
 
 
 def get_sample_merged_pod5(wildcards):
@@ -234,7 +236,7 @@ rule split_pod5:
         pod5=get_sample_merged_pod5,
         read_ids=get_sample_read_ids,
     output:
-        os.path.join(outdir, "demux", "pod5", "{sample}.pod5"),
+        os.path.join(outdir, "demux", "pod5", "{sample}", "{sample}.pod5"),
     log:
         os.path.join(outdir, "logs", "split_pod5", "{sample}"),
     shell: