Thomas Hickman

To fit the format of all the other samtools commands, the usage is now: ``` samtools fastaref [options] Options: -o FILE Output file name [stdout] -k LIST Output the specified...

I've created the function `parseSQLine`, which generates a khash containing the fields of the SQ line and changed the code according to proposed changes

@jmarshall > It's really unclear what this new command actually does. Presumably it uses the CRAM reference-finding machinery to output the reference bases in FASTA form, looking them up based...

@tseemann That sounds like an interesting idea, but this doesn't support extracting an embedded reference from a cram at the moment - this just uses the M5 field in the...

If you want to avoid using an `InlineJavascriptRequirement`, another workaround is: ```cwl cwlVersion: v1.0 class: CommandLineTool arguments: - cat - inputs.json requirements: InitialWorkDirRequirement: listing: - entryname: inputs.json entry: json=$(inputs) inputs:...

Yes, it's in the CWL v1.0 specification (from https://www.commonwl.org/v1.0/CommandLineTool.html#Parameter_references): >If the value of a field has non-whitespace leading or trailing characters around a parameter reference, it is subject to string...

👍 - however I don't really see how a default value could be useful at all. The only plausible default value for this would be `[]` - I can't see...

@lkonstantinov, thanks :), I've applied the patch and published a patch version to apm. I'll have a look at this sometime when I've got free time (I'm quite busy at...

One way to workaround this is to just add `>= sys.stderr` after any `... = local[...]` assignments e.g.: ``` $ python3 Python 3.11.8 (main, Feb 25 2024, 16:39:33) [GCC 11.4.0]...

@lightningtgc, could you have a look at merging this PR? I can't use this package without this PR