extra tools

[matthdsm]

No description provided.

[matthdsm]

Hi,

I'm probably missing some things for the new tools to be enables, could you give this PR a quick review?

Nevermind!
Tools check out and generate valid cwl. Ready to merge IMO

Thanks
M

[illusional]

This is looking great!

I'll highlight one feature: secondaries_present_as in the ToolOutput. Essentially, we made the decision for bam indexes to be .bam.bai, but GATK will only recognise ^.bai. So the secondaries_present_as is a way for Janis to automatically tell CWL / WDL to localise a file as the required extension (or pick this back up).

Unfortunately, there's a problem in CWLTool (untested in other engines) that may hinder your ability to run these workflows when collecting these outputs.

I realised that the ToolArgument wasn't in the docs, but it's here now.

A couple of minor things I noticed in the scramble wrapper:

• The tag for quay is 1.14.12--h244ad75_0 to be quay.io/biocontainers/staden_io_lib:1.14.12--h244ad75_0
• A ToolInput has a default= argument. Usually, the only argument a DataType (like String) takes is optional=True/False, for example String(optional=True).
• Within the arguments method, you should return a ToolArgument which has the structure (ToolArgument(value, prefix=none, position=None)).
• The tool arguments should be for values that should never change. For example, if you never wanted to change the version or compressions, you could use:

    [ # ...other args
        ToolArgument("3.0", prefix="-V"),
        ToolArgument("-9")
    ]

[matthdsm]

Great, thanks for commenting.
You can expect a fix shortly.

Cheers
M

[matthdsm]

I think we're good to go now!

Cheers
M

[matthdsm]

I'm trying to fix input errors in the new Gatk4MergeBamAlignment tool.
The ToolInput aligned can be both an array of either Samof Bam inputs. How do I go about declaring that? Atm I have the following

            ToolInput(
                "aligned",
                Array(Sam(), Bam()),
                prefix="--ALIGNED_BAM",
                prefix_applies_to_all_elements=True,
                doc="SAM or BAM file(s) with alignment data.",
                position=10,
            ),

But this still yields
2020-02-27T15:08:25 [CRITICAL]: Mismatch of types when joining 'generateAlignedBam.out' to 'mergeBam.bam': stdout<SAM> -/→ Optional<Array<BAM>>

Thanks for the help
Cheers
M

[illusional]

Hey @matthdsm, at the moment you can't (but proposed in Unions in Janis: PMCC-BioinformaticsCore/janis#10). I'd recommend just letting it be an Array of Bams. Janis will tell you there's a type connection error but it should work anyway.

(Sort of like TypeScript errors, there's an error but it'll finish the transpile)

[matthdsm]

I suppose a squash and merge would be best here 😅

[illusional]

Thanks @matthdsm for the contribution, this is awesome!!

[matthdsm]

No problem! More stuff to come!