Make output bam name unique (by using sample uuid)

This ensures bams aren't overwritten if the same output is used for multiple samples

README.md

@@ -18,7 +18,7 @@ RNA-seq fastqs are combined, aligned, and quantified with 2 different methods (R
 
 This pipeline produces a tarball (tar.gz) file for a given sample with 3 main subdirectories: Kallisto, RSEM, and QC.
 If the pipeline is run with all possible options (`fastqc`, `bamqc`, etc), the output tar
-will have the following structure (once uncompressed):
+will have the following structure (once uncompressed), where **SAMPLE** is the unique name of the sample:
 
 ```
 SAMPLE
@@ -49,10 +49,10 @@ SAMPLE
 
 If the user selects options such as `save-bam` or `wiggle`, additional files will appear in the output directory:
 
-- SAMPLE.sorted.bam OR rnaAligned.sortedByCoord.md.bam if `bamQC` step is enabled.
+- SAMPLE.sorted.bam OR SAMPLE.sortedByCoord.md.bam if `bamQC` step is enabled.
 - SAMPLE.wiggle.bg
 
-The output tarball is prepended with the UUID for the sample (e.g. UUID.tar.gz). 
+The output tarball is prepended with the unique name for the sample (e.g. SAMPLE.tar.gz). 
 
 # Dependencies
 

src/toil_rnaseq/qc.py

@@ -40,9 +40,11 @@ def run_bam_qc(job, aligned_bam_id, config):
     # Save output BAM
     if config.save_bam:
         bam_path = os.path.join(work_dir, 'rnaAligned.sortedByCoord.md.bam')
+        new_bam_path = os.path.join(work_dir, config.uuid + '.sortedByCoord.md.bam')
+        os.rename(bam_path, new_bam_path)
         if urlparse(config.output_dir).scheme == 's3' and config.ssec:
-            s3am_upload(fpath=bam_path, s3_dir=config.output_dir, s3_key_path=config.ssec)
+            s3am_upload(fpath=new_bam_path, s3_dir=config.output_dir, s3_key_path=config.ssec)
         elif urlparse(config.output_dir).scheme != 's3':
-            copy_files(file_paths=[bam_path], output_dir=config.output_dir)
+            copy_files(file_paths=[new_bam_path], output_dir=config.output_dir)
 
     return fail_flag, job.fileStore.writeGlobalFile(os.path.join(work_dir, 'bam_qc.tar.gz'))