classify_trycycler does not output barcode08_for_reconciliation/*

[fredjaya]

The error

In /scratch/tj48/fj9712/ONT-bacpac-nf/work/88/c1dc55defedb0c4679fb8961ad6ae0

Caused by:
  Missing output file(s) `barcode08_for_reconciliation/*` expected by process `classify_trycycler (CLASSIFYING CONTIGS: barcode08)`

Description:

barcode08 has three clusters each with a single contig.

classify_trycycler_clusters.py correctly discards all these because a "good cluster" should have a contig from each assembler.

When all clusters are discarded, the cluster dir is moved to ${barcode}_discarded/ and the required ${barcode}_for_reconciliation/ folder is never created due to improper handling of cases in the elifs.

Solution

Ideally replace classify_trycycler_clusters.py entirely. A suitable replacement will have the following features:

• Does not move any files
• Does not create any intermediate folders
• Outputs an assignment of pass/fail per cluster as a Nextflow/groovy tuple e.g.

[barcode01, cluster01, pass]
[barcode01, cluster02, fail]
[barcode02, cluster01, pass]
...

Some pseudocode for a single barcode:

1. Input: path to directory containing trycycler clusters
2. For each cluster, count the number of contigs per assembly. Maybe tabulate e.g.

| cluster | assemblies |
| ------- | ---------- | 
| 01      | A, B       | 
| 02      | A          | 
| 03      | B          | 
| 04      | B, B       |
| 05      | A, A, B    | 

3. Decide whether each cluster should be reconciled or not

| cluster | assemblies | decision  |
| ------- | ---------- | --------- |
| 01      | A, B       | reconcile |
| 02      | A          | discard   |
| 03      | B          | discard   |
| 04      | B, B       | discard   |
| 05      | A, A, B    | ?         |

4. Output as Nextflow tuple

[barcode01, cluster01, reconcile]
[barcode01, cluster02, discard]
...

or simply a channel with clusters to reconcile

[barcode01, cluster01]