Switch to using a dictionary instead of a namedtuple.

This was somehow losing its namedtupleness, so we're just
avoiding the issue by not using them.

bcbio/pipeline/datadict.py

@@ -9,11 +9,6 @@
 from collections import namedtuple
 import sys
 
-# be explicit about what fields can show up in the nested dictionaries and what they are
-
-TxImport = namedtuple("TxImport", ['gene_tpm', 'gene_counts'])
-TxImport.__new__.__defaults__ = (None,) * len(TxImport._fields)
-
 LOOKUPS = {
     "config": {"keys": ['config']},
     "tmp_dir": {"keys": ['config', 'resources', 'tmp', 'dir']},

bcbio/pipeline/rnaseq.py

@@ -533,7 +533,8 @@ def load_tximport(data):
     tpm_file = os.path.join(out_dir, "tximport-tpm.csv")
     counts_file = os.path.join(out_dir, "tximport-counts.csv")
     if file_exists(tpm_file) and file_exists(counts_file):
-        return dd.TxImport(gene_tpm = tpm_file, gene_counts=counts_file)
+        return {"gene_tpm": tpm_file,
+                "gene_counts": counts_file}
     with file_transaction(tpm_file) as tx_tpm_file, file_transaction(counts_file) as tx_counts_file:
         render_string = (
             f'library(tidyverse);'
@@ -546,4 +547,5 @@ def load_tximport(data):
             f'readr::write_csv(txi$abundance %>% as.data.frame() %>% tibble::rownames_to_column("gene"), "{tx_tpm_file}");'
         )
         do.run([rcmd, "--vanilla", "-e", render_string], f"Loading tximport.")
-    return dd.TxImport(gene_tpm = tpm_file, gene_counts=counts_file)
+    return {"gene_tpm": tpm_file,
+            "gene_counts": counts_file}

bcbio/upload/__init__.py

@@ -845,8 +845,8 @@ def _get_files_project(sample, upload_config):
         else:
             out.append({"path": dd.get_combined_counts(sample)})
     if dd.get_tximport(sample):
-        out.append({"path": dd.get_tximport(sample).gene_tpm, "dir": "tpm"})
-        out.append({"path": dd.get_tximport(sample).gene_counts, "dir": "counts"})
+        out.append({"path": dd.get_tximport(sample)["gene_tpm"], "dir": "tpm"})
+        out.append({"path": dd.get_tximport(sample)["gene_counts"], "dir": "counts"})
     if dd.get_annotated_combined_counts(sample):
         out.append({"path": dd.get_annotated_combined_counts(sample)})
     if dd.get_combined_fpkm(sample):