Jeremiah H. Savage

``` git clone https://github.com/jeremiahsavage/cwl_schemadef.git cd cwl_schemadef/ ``` with cwltool ``` (cwl) ubuntu@jeremiah-node001:~/cwl_schemadef$ cwltool --debug transform.cwl transform.json /home/ubuntu/.virtualenvs/cwl/bin/cwltool 1.0.20180403145700 Resolved 'transform.cwl' to 'file:///home/ubuntu/cwl_schemadef/transform.cwl' [workflow transform.cwl] initialized from file:///home/ubuntu/cwl_schemadef/transform.cwl [workflow transform.cwl] start...

javascript: error accessing parsed json in ExpressionTool

1

I am getting an error with bunny 1.0.1 and the latest develop with the following cwl: ``` git clone https://github.com/jeremiahsavage/cwl_expressiontool_parse_json.git ``` I can run the example with cwltool successfully: ```...

I would like to begin building models of resource requirements for workflow steps. To do that, I'll need to know input file size for each step, and the runtime metrics...

fail to execute with awscli

9

`git clone https://github.com/jeremiahsavage/cwl_aws_cp.git` with cwltool: ``` (cwl) [jeremiah@localhost ~]$ cwltool cwl_aws_cp/aws_s3_get.cwl cwl_aws_cp/aws_s3_get.yml /home/jeremiah/.virtualenvs/cwl/bin/cwltool 1.0.20170413194156 Resolved 'cwl_aws_cp/aws_s3_get.cwl' to 'file:///home/jeremiah/cwl_aws_cp/aws_s3_get.cwl' [job aws_s3_get.cwl] /tmp/tmpXzacA9$ docker \ run \ -i \ --volume=/home/jeremiah/cwl_aws_cp/aws/config:/var/lib/cwl/stg7baa7395-1376-41a8-bfdc-ac1e41765685/config:ro \ --volume=/home/jeremiah/cwl_aws_cp/aws/credentials:/var/lib/cwl/stgb922b629-4142-439a-93ec-daa3f6bdc669/credentials:ro...

With cwltool, I am able to use urls as workflow and job input, as in: ``` mkdir tmp cache cwltool --tmpdir-prefix tmp/ --cachedir cache/ https://raw.githubusercontent.com/NCI-GDC/gdc-dnaseq-cwl/master/workflows/dnaseq/etl_http.cwl https://raw.githubusercontent.com/NCI-GDC/gdc-dnaseq-cwl/master/workflows/dnaseq/etl_http_NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.json ``` The cwltool fetcher...

fail validation: make-to-cwl/dna.cwl

2

I was looking for an example where the CommandLineTool and Workflow are in one file, and in trying to run https://github.com/common-workflow-language/workflows/blob/master/workflows/make-to-cwl/dna.cwl I get: ``` $ cwltool ~/workflows/workflows/make-to-cwl/dna.cwl /home/ubuntu/.virtualenvs/p2_cwl/bin/cwltool 1.0.20160523144113 No...