Last fix was incomplete. This is tested on run 20240828_MIN2_33150TDL…

…01, which

is now a good test case for future changes.

README.md

@@ -11,7 +11,7 @@ This Hesiod writes reports about your Promethion (or other NanoPore) data.
 * Concatenates .fastq files to a single .fastq.gz
 * Checksums everything
 * Runs NanoPlot
-* Extracts useful metadata from FAST5 files
+* Extracts useful metadata from POD5 files
 * Makes a report, including contamination screen
 * Logs progress (by sending messages to Request Tracker, if available)
 * Tags processed runs for removal from work drive
@@ -20,8 +20,8 @@ This Hesiod writes reports about your Promethion (or other NanoPore) data.
 
 as of version 3 it does not:
 
-* ~~Strip out spike-in controls (eg. lambda)~~
-* ~~Zips down .fast5 files~~ *(they are no longer worth compressing)*
+* ~~Strip out spike-in controls (eg. lambda)~~ *(this feature may come back)*
+* ~~Zips down .fast5/.pod5 files~~ *(they are no longer worth compressing)*
 
 ## Cluster compatibility
 

Snakefile.blob

@@ -151,7 +151,7 @@ rule parse_blob_table:
 # with the U bases.
 rule fastq_to_subsampled_fasta:
     output: "blob/{foo}_{pf}+sub{n}.fasta"
-    input:  "{foo}.fastq.gz"
+    input:  "{foo}_{pf}.fastq.gz"
     threads: 2
     shell:
        r"""set +o pipefail