pvanheus

I'm on 1.0.4 on Ubuntu 16.04, but hitting a similar issue. Gets stuck on "Syncing initial data" although it has already been used (i.e. it has synced initial data before)....

Hi @mvdbeek the only steps that are *not* involved in generating the consensus are the final "SnpSift Extract Fields" and "Collapse Collection" steps. Everything else goes into computing the consensus....

Commenting separately on the `ivar` / amplicon story. The majority of genomes out there are being generated using ARTIC amplicon protocol detailed [here](https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-be3wjgpe) for Illumina and [here](https://artic.network/ncov-2019) for ONT. My...

As discussed on a previous call, each addition to the standard imposes a burden on those implementing CWL executors. There is a tension between this cost and the benefit of...

@AleksandrSl I ran into exactly the same thing in https://github.com/common-workflow-library/bio-cwl-tools/pull/95. As @mr-c notes, you can get that expression to work with: `glob: '$(inputs.output_file_name ? inputs.output_file_name : inputs.input_bam.nameroot + ".bed")'` or...

I get exactly the same error and had a dive into the code. Turns out (from https://github.com/ogotoh/spaln/blob/master/src/spaln.c#L396) that the `-d` flag is only used if you set `-Q` to a...

I looked at the documentation a bit more clearly and using `-Q7` works, for example: `spaln -ospaln_q7.out -Q7 -O0 -dhard_masked_seabass_genome fish_proteins_0.fasta`

> It would be nice to handle numpy arrays as well. Something like: > > ```python > elif np_available and _isinstance_safe(o, np.ndarray): > result = o.tolist() > ``` Thanks, I...

@kingcohn1 The ALN_TAB environment variable must refer to the directory where the contents of the `table` directory from the spaln source is located. Similarly the ALN_DBS environment variable must refer...

@jwasmuth which search mode (i.e. `-Q`) parameter are you using?