John Wiedenhoeft

Set upload privileges administratively

2

I am tasked by a rather large institution to explore options for a data sharing platform. After defining the specs (fine-grained access control, DOI, version control etc.), it turns out...

+ sign not found where expected

15

I'm using iSAAC-03.17.03.01. I have created simulated fastq.gz files using VarSim v0.7.8. My reference genome is hg38, and I built the index according to the instructions provided. Using the call...

Wrong numbers at risk with time-varying covariates

2

I have a table of 299 rows with (highly sensitive) patient survival information in the format required for time-varying covariates. i.e. with start and end time columns for each interval....

fixmate creates invalid SAM flags

1

#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify. Yes, 1.20. #### Please describe your environment. - OS: Linux 5.16.2-051602-generic - machine architecture: x86_64...

Options for batch runs

1

**Is your feature request related to a problem? Please describe.** The `--batch` option is great, e.g. when testing the pipeline on a small subset of data. However, it suffers from...

Add key to rule definitions to postpone scheduling of a job based on runtime-dependent user criteria

1

**Is your feature request related to a problem? Please describe.** There are many instances when I would like to postpone the execution of a specific job based on runtime conditions,...