sklages

Add flag --total-size, to display the total size of directories

2

Would be a "nice-to-have": This is what it looks like now: ``` drwxrwxr-x@ - user1 user1 2020-08-09 18:22  cr-count_hg38_Sample415 drwxrwxr-x@ - user1 user1 2020-08-09 17:19  cr-count_hg38_Sample416 drwxrwxr-x@ -...

Q: Descriptive documentation of how "things" work together and depend on each other in MISO?

1

Although the documentation of each part of MISO is quite complete and good, there is no (descriptive) "connection" between "things". It is hard, if not impossible, to follow the path...

Would be nice to be able to add attachments to index families (per family, in `Edit Index Family`). There are quite a lot of manufacturers and kits, all with their...

Python: `index_summary` : Cluster Count == # of seq * 2 of a PE run?

3

I haven't noticed before, `index_summary(run_metrics, level='Barcode')` returns as `Cluster Count` the total number of reads of a *PE* run, not the acutal number of clusters (= single reads, R1 seq...

Tiny difference between number of reads in `Stats.json/Fastq` and `InterOp/index_summary`

2

Comparing "number of reads" ### `InterOp` ```python ar = iop.index_summary(run_metrics, level='Barcode') ``` results in: ``` sample1/TTAGGC = 38423040.0 (ClusterCount) sample2/GCCAAT = 71338704.0 (ClusterCount) ``` ### `Stats.json` (bcl2fastq) ``` sample1/TTAGGC =...

Q: Q>=30 fraction per barcode (== library) per lane

6

Currently I am compiling quite a lot of stats for some "demultiplexing / run report" (mainly) using the Python bindings .. However, I didn't find a way to get the...

Custom config being ignored

4

### Description of the bug - Custom config file: ``` process { withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR' { // single job memory = 80.GB cpus = 32 time = 4d }, withName: 'FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX'...

Q: How to add Oxford Nanopore support?

4

We are running a "Promethion P2 solo" and I was wondering how "add support" to MISO/Runscanner. I surely missed in the docs .. Can you help?

`dorado duplex` performance breakdown

1

I have a large *Promethion P2* dataset (1.4 TBytes, PoreC library) to be basecalled in **sup** mode. I have two identical servers with ~360G RAM, fast local storage, "Nvidia A100...

Q: `pod5 subset <..> --threads` takes a lot of resources

2

I just started using `pod5 subset` to regroup my POD5 data per-channel to optimize `dorado duplex` basecalling speed. The default setting for `--threads` is 4, I was brave and set...