Some small fixes after testing

Snakefile.main

@@ -270,12 +270,12 @@ def count_up_passing(counts, cutoff=None, include_unclassified=True):
 
 # Global wildcard patterns
 wildcard_constraints:
-    pod5file   = "\w+",
-    fullid     = "[^/]+",
-    barcode    = "[^/_]+",
-    pf         = "pass|fail",
-    pfs        = "pass|fail|skip",
-    _pfs       = "_pass|_fail|_skip|",
+    pod5file   = r"\w+",
+    fullid     = r"[^/]+",
+    barcode    = r"[^/_]+",
+    pf         = r"pass|fail",
+    pfs        = r"pass|fail|skip",
+    _pfs       = r"_pass|_fail|_skip|",
 
 # Main target is one yaml file (of metadata) per cell. A little bit like statfrombam.yml in the
 # project QC pipelines.

Snakefile.rundata

@@ -68,7 +68,7 @@ def i_copy_md5sum_pod5(wc):
 rule copy_md5sum_pod5:
     output:
         pod5 = "{cell}/pod5_{barcode}{_pfs}/{pod5file}.pod5",
-        md5  = "md5sums/{cell}/pod5_{barcode}{_pfs}/{pod5file}.pod5.md5"
+        md5  = temp("md5sums/{cell}/pod5_{barcode}{_pfs}/{pod5file}.pod5.md5")
     input:
         i_copy_md5sum_pod5
     params:

doc/pod5_remake.txt

@@ -43,3 +43,29 @@ May 2024. So ONT have finally fixed the batching of the POD5 files themselves. N
 to copy the files and md5sum them. So I can rip out all the batching logic and just replicate
 what I previously had for fast5. Well I guess that was a waste of my time after all. I'll get
 that sorted when I can.
+
+(Friday 2nd)
+It's working and has made a test report. Let us check:
+
+1) Does the report look OK (Did I ever report the total number of POD5 files)?
+
+Yes it does.
+Snakefile.main get_cell_info() sets ci['Files in pod5'] and this gets saved into
+cell_info.yaml. Here "Files in pod5: 73" which disregards the skipped files and is not
+the same as "pod5_files_in_final_dest: 75" in the final summary. I think this is OK.
+I'll add this to the report.
+
+2) Are all the POD5 files there?
+   With the md5sums? - yes, need to make individual files temp
+   What about the _pass and _fail? - not there
+   What about the _skip? - not there
+
+3) Do the POD5 files segragate by channel? Would be cool if they did.
+
+$ pod5 view pod5_file.pod5 -i "read_id,channel"
+
+No such luck.
+
+4) Data delivery needs testing, and inevitably fixing.
+
+I'll release and run the code first.

make_report.py

@@ -25,6 +25,7 @@ def get_cell_metadata(ci):
                (None,                'Run Time'),
                ('Files in pass',),
                ('Files in fail',),
+               ('Files in pod5',     'POD5 files (excluding skipped)'),
                ('SequencingKit',     'Sequencing Kit'),
                ('Software',          'Software'),
                ('BasecallConfig',    'Basecaller Config'),