Error in rule bam2bg when running "no_dedup" option

[epehrsson]

The pipeline fails on bam2bg (and others downstream) when running with "no_dedup" option due to mismatch with column names.

Solution: Replace "nodedup" with "no_dedup"

workflow/scripts/_get_nreads_stats.py, line 29

-stats["nodedup_nreads_genome"] = sum(list(nodedup_idxstats[nodedup_idxstats[0].isin(list(genomelen[0]))][2]))
+stats["no_dedup_nreads_genome"] = sum(list(nodedup_idxstats[nodedup_idxstats[0].isin(list(genomelen[0]))][2]))
-stats["nodedup_nreads_spikein"] = sum(list(nodedup_idxstats[nodedup_idxstats[0].isin(list(spikeinlen[0]))][2]))
+stats["no_dedup_nreads_spikein"] = sum(list(nodedup_idxstats[nodedup_idxstats[0].isin(list(spikeinlen[0]))][2]))

workflow/scripts/_make_alignment_stats_table.R, line 54

-                 "nodedup_nreads_genome",
+                 "no_dedup_nreads_genome",
-                 "nodedup_nreads_spikein",
+                 "no_dedup_nreads_spikein",

workflow/scripts/_make_library_norm_table.R, line 49

-for (dedup_type in c("dedup_nreads_genome","nodedup_nreads_genome")){
+for (dedup_type in c("dedup_nreads_genome","no_dedup_nreads_genome")){

workflow/scripts/_make_library_norm_table.R, line 73
+ df$dedup_type=gsub("no","no_dedup",df$dedup_type)

[epehrsson]

Recapitulated with test data, but only when using "library" normalization instead of "spikein"