legacy issues

Error running lobSTR workflow

``` ../../../../tmp/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl:68:3: invalid field `inputs`, expected one of: 'id', 'in', 'out', 'requirements', 'hints', 'label', 'doc', 'run', 'scatter', 'scatterMethod' ../../../../tmp/3ec0d19076841a1140e71cc3a1b330a56099aac2/workflows/lobSTR/lobSTR-workflow.cwl:75:3: invalid field `outputs`, expected one of: 'id', 'in', 'out', 'requirements', 'hints',...

MarkRobbo

Invalid job input record for workflow

2

Hi, I tried to work with cwl workflow and it worked well most of the time. But when I tried to use scatter-gather function, I got an error. I set...

rabi1029

First Dockerfile for subread

Annotation pending.

andersgs

[WIP] CNVkit tool definitions

8

Standing PR to add tool descriptions (created by [argparse2cwl](https://github.com/common-workflow-language/gxargparse/tree/cwl-refactor)) and tests for [CNVkit](https://github.com/etal/cnvkit) tools . Issues I encountered on first steps: - .gitignore prohibits to add bioinformatics stuff, i.e. test...

anton-khodak

Snpeff hocine

2

work in progress

hocinebendou

organization of community maintained tool & workflow descriptions

5

One file per tool. Incomplete descriptions are welcome as long as they are usable. General encouragement to share early & often

mr-c

[WIP] superenhancer-final

bharath-cchmc

Use picard-tools script rather than full path to Picard jar

4

(I commented also [here](https://github.com/common-workflow-language/workflows/commit/84bfbb782d39f1e54c1f6d293d9dd9541468dbd0#commitcomment-17349629) about this.) This is relevant to the Picard sub-tools. I noticed that at least when intalling via apt-get on Ubuntu, you get a `picard-tools` script in...

samuell