Remove calc_prob step and NUPACK dependency

docs/pipeline_output.md

@@ -41,9 +41,8 @@ The columns in DNA probe files are:
 | 5 | on-target score (0-100) | hybridization prediction at the target site of the probe |
 | 6 | off-target score (0-10,000) | sum of the hybridization predictions for all off-target sites (up to 100) for the probe |
 | 7 | repeat (0 or 1) | 0 if the sequence contains no repeat-masked bases, and 1 if it does  |
-| 8 | prob | the probability that the probe has no secondary structure |
-| 9 | max k-mer | max count out of all k-mers in the probe sequence |
-| 10 | strand | probe strand, `+` or `-` |
+| 10 | max k-mer | max count out of all k-mers in the probe sequence |
+| 11 | strand | probe strand, `+` or `-` |
 
 #### Isoform-resolved RNA probe sets
 
@@ -59,12 +58,11 @@ The columns in isoform-resolved RNA probe sets are:
 | 5 | on-target score (0-100) | hybridization prediction at the target site of the probe |
 | 6 | off-target score (0-10,000) | sum of the hybridization predictions for all off-target sites (up to 100) for the probe |
 | 7 | repeat (0 or 1) | 0 if the sequence contains no repeat-masked bases, and 1 if it does  |
-| 8 | prob | the probability that the probe has no secondary structure |
-| 9 | max k-mer | max count out of all k-mers in the probe sequence |
-| 10 | strand | probe strand, `+` or `-` |
-| 11 | refseq | The transcript ID that the probe targets, stripped of any version suffixes e.g. NM_001180043 |
-| 12 | transcript_id | The unmodified transcript ID of the transcript that the probe targets e.g. NM_001180043.1 |
-| 13 | gene_id | The gene ID of the gene whose transcript the probe targets e.g. PAU8 |
+| 8 | max k-mer | max count out of all k-mers in the probe sequence |
+| 9 | strand | probe strand, `+` or `-` |
+| 10 | refseq | The transcript ID that the probe targets, stripped of any version suffixes e.g. NM_001180043 |
+| 11 | transcript_id | The unmodified transcript ID of the transcript that the probe targets e.g. NM_001180043.1 |
+| 12 | gene_id | The gene ID of the gene whose transcript the probe targets e.g. PAU8 |
 
 #### Isoform-flattened RNA probe sets
 
@@ -80,11 +78,10 @@ The columns in isoform-flattened RNA probe sets are:
 | 5 | on-target score (0-100) | hybridization prediction at the target site of the probe |
 | 6 | off-target score (0-10,000) | sum of the hybridization predictions for all off-target sites (up to 100) for the probe |
 | 7 | repeat (0 or 1) | 0 if the sequence contains no repeat-masked bases, and 1 if it does  |
-| 8 | prob | the probability that the probe has no secondary structure |
-| 9 | max k-mer | max count out of all k-mers in the probe sequence |
-| 10 | strand | probe strand, `+` or `-` |
-| 11 | gene_id | The gene ID of the gene whose transcript the probe targets e.g. PAU8 |
-| 12 | transcripts |  The number of isoforms that this probe targets |
+| 8 | max k-mer | max count out of all k-mers in the probe sequence |
+| 9 | strand | probe strand, `+` or `-` |
+| 10 | gene_id | The gene ID of the gene whose transcript the probe targets e.g. PAU8 |
+| 11 | transcripts |  The number of isoforms that this probe targets |
 
 ### Reporting
 

example_run/config.yml

@@ -1,5 +1,5 @@
 #
-# PaintSHOP Pipeline Run Configuration -- pipeline version v1.2
+# PaintSHOP Pipeline Run Configuration -- pipeline version v1.3
 #
 
 ########################################################################
@@ -32,13 +32,6 @@ annotation_file: 'data/example.gtf'
 # current options are: 37, 42, 47, 52, 60
 # model_temp: 42
 
-# NUPACK 4 model specification https://piercelab-caltech.github.io/nupack-docs/model/#model-specification
-# nupack_material: 'dna'
-# nupack_ensemble: 'stacking'
-# nupack_celsius: 74.5
-# nupack_sodium: 0.39
-# nupack_magnesium: 0.0
-
 # OPTIONAL: it is possible to provide already designed DNA-FISH probes to the pipeline
 # and then run downstream steps, including thermodynamic, specifity, and secondary
 # structure analysis, as well as intersection with the genome annotations file to yield