$ cwltool --make-template https://dockstore.org:443/api/api/ga4gh/v2/tools/quay.io%Fwtsicgp%Fdockstore-cgpmap/versions/3.0.0/plain-CWL/descriptor/%FDockstore.cwl
/home/mcrusoe/cwltool/env3/bin/cwltool 1.0.20181217162649
sample: a_string # type "string"
reference: # type "File"
class: File
path: a/file/path
mmqcfrac: 0.05 # default value of type "float". (optional)
mmqc: false # type "boolean"
groupinfo: # type "File" (optional)
class: File
path: a/file/path
bwa_idx: # type "File"
class: File
path: a/file/path
bwa: ' -Y -K 100000000' # default value of type "string". (optional)
bams_in: # array of type "File" (optional)
- class: File
path: a/file/path
An interesting issue here:
I have a workflow registerd on Dockstore, it runs fine with this command:
dockstore workflow launch --entry github.com/cancerit/workflow-seq-import/chksum_seqval_wf_interleaved_fq:0.4.0 --json chksum_seqval_wf_interleaved_fq_with_headers.json
it'll fail if I run it like below:
cwl-runner https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/%2Fcwls%2Fchksum_seqval_wf_interleaved_fq.cwl chksum_seqval_wf_interleaved_fq_with_headers.json
Tool definition failed initialization:
Tool definition https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl failed validation:
https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl:27:1: checking field `steps`
https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl:28:3: checking object `https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl#if_file_name_is_bz2_then_return_null_else_return_in_json_to_output`
https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/toolkit/if_input_is_bz2_generate_md5sum_else_return_input_chksum_json.cwl:35:5: Field `run` contains undefined reference to `https://dockstore.org:443/api/api/ga4gh/v2/tools/%23workflow%2Fgithub.com%2Fcancerit%2Fworkflow-seq-import%2Fchksum_seqval_wf_interleaved_fq/versions/0.4.0/plain-CWL/descriptor/toolkit/if_file_name_is_bz2_then_return_null_else_return_in_json_to_output.cwl`
Not Found : version found, but file not found (bad filename, invalid file, etc.)
l$ cwltool --validate https://github.com/cancerit/workflow-seq-import/raw/0.4.0/cwls/chksum_seqval_wf_interleaved_fq.cwl
/home/michael/cwltool/env3/bin/cwltool 1.0.20181217162649
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:name' not recognized, are you missing a $namespaces section?
URI prefix 'foaf' of 'foaf:mbox' not recognized, are you missing a $namespaces section?
https://github.com/cancerit/workflow-seq-import/raw/0.4.0/cwls/chksum_seqval_wf_interleaved_fq.cwl is valid CWL.