I am not able to publish my workflows as the publish button looks to be toggled off.
I am wondering why this could be? Is this because of relative paths in the .dockstore.yml if so is there a way for getting the relative paths working on dockstore?
In version 'master' of workflow 'Single_cell_WDLworkflows/scsorter_run':
- File '/task/scsorter_run.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/scsorter_run.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/multisample_seurat':
- File '/task/multisample_seurat.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/multisample_seurat.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/linear_chain_adddoublets_seurat':
- File '/task/linear_chain_adddoublets_seurat.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/linear_chain_adddoublets_seurat.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/singleR_immune_nonimmune_pipeline':
- File '/task/singleR_immune_nonimmune_pipeline.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/singleR_immune_nonimmune_pipeline.wdl'.
I more meant, in which organization do you have the github app installed?
Error messages are organized by organization and will only show up if you have the app installed and after a change is made/pushed.
I’m attaching a screenshot of what it looks like for the databiosphere organization for example
This is how my app logs look like. I have done code commits on github (make changes to work it with dockstore) but as you can see it has not updated in the past day for some reason on dockstore.
One thing I noticed about your .dockstore.yml is that it references files in the directory /task, which doesn’t exist in the repo and is why the files are not being found. However, the directory /tasks does exist, and it appears to contain the files, so you could try adjusting the file paths in your .dockstore.yml accordingly and pushing again.
This is how my .dockstore.yml file looks like. It never had an entry with ./task folder it was always ./tasks but not sure why dockstore is not reading it correctly.
This is how they look at this moment. They have not updated even after multiple commits to my github repo in trying to fix this Issue.
In version 'master' of workflow 'Single_cell_WDLworkflows/scsorter_run':
- File '/task/scsorter_run.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/scsorter_run.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/multisample_seurat':
- File '/task/multisample_seurat.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/multisample_seurat.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/linear_chain_adddoublets_seurat':
- File '/task/linear_chain_adddoublets_seurat.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/linear_chain_adddoublets_seurat.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/singleR_immune_nonimmune_pipeline':
- File '/task/singleR_immune_nonimmune_pipeline.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/singleR_immune_nonimmune_pipeline.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/plot_qc':
- File '/task/plot_qc.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/plot_qc.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/SingleR_singleref':
- File '/task/SingleR_singleref.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/SingleR_singleref.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/add_doubletinfo':
- File '/task/add_doubletinfo.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/add_doubletinfo.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/clustering_n_pca_simple':
- File '/task/clustering_n_pca_simple.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/clustering_n_pca_simple.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/rpca_integration':
- File '/task/rpca_integration.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/rpca_integration.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/htmap_degs':
- File '/task/htmap_degs.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/htmap_degs.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/add_cellid_results_to_seurat':
- File '/task/add_cellid_results_to_seurat.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/add_cellid_results_to_seurat.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/Doublet_calling':
- File '/task/Doublet_calling.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/Doublet_calling.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/make_gene_featplots':
- File '/task/make_gene_featplots.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/make_gene_featplots.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/LinearChain_htmapdegs':
- File '/task/LinearChain_htmapdegs.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/LinearChain_htmapdegs.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/single_sample_seurat':
- File '/task/single_sample_seurat.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/single_sample_seurat.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/subset_renormalize_recluster':
- File '/task/subset_renormalize_recluster.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/task/subset_renormalize_recluster.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/recluster_renorm_rerun_singleR':
- File '/subworkflow/recluster_renorm_rerun_singleR.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/recluster_renorm_rerun_singleR.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_gather_singleR':
- File '/subworkflow/scatter_gather_singleR.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_gather_singleR.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/single_sample_filtering_nd_doublets':
- File '/subworkflow/single_sample_filtering_nd_doublets.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/single_sample_filtering_nd_doublets.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_deg':
- File '/subworkflow/scatter_deg.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_deg.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_gather_Doubletcall_multisample':
- File '/subworkflow/scatter_gather_Doubletcall_multisample.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_gather_Doubletcall_multisample.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/seurat_counts_to_anndata':
- File '/subworkflow/seurat_counts_to_anndata.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/seurat_counts_to_anndata.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_gather_scsorter':
- File '/subworkflow/scatter_gather_scsorter.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_gather_scsorter.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/single_sample_filtering_n_clustering':
- File '/subworkflow/single_sample_filtering_n_clustering.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/single_sample_filtering_n_clustering.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_gather_doublet_singlesample':
- File '/subworkflow/scatter_gather_doublet_singlesample.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_gather_doublet_singlesample.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_gather_singleR_bysample':
- File '/subworkflow/scatter_gather_singleR_bysample.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_gather_singleR_bysample.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/scatter_rpca':
- File '/subworkflow/scatter_rpca.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/subworkflow/scatter_rpca.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/multisample_seurat_doublet_singler':
- File '/pipeline/multisample_seurat_doublet_singler.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/pipeline/multisample_seurat_doublet_singler.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/end_to_end_seurat_singlesample':
- File '/pipeline/end_to_end_seurat_singlesample.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/pipeline/end_to_end_seurat_singlesample.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/end_to_end_multisample':
- File '/pipeline/end_to_end_multisample.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/pipeline/end_to_end_multisample.wdl'.
In version 'master' of workflow 'Single_cell_WDLworkflows/seurat_single_sample_nomerging':
- File '/pipeline/seurat_single_sample_nomerging.wdl': Primary descriptor file not found.
- File '/.dockstore.yml': Could not find the primary descriptor file '/pipeline/seurat_single_sample_nomerging.wdl'.
If you have the Dockstore CLI installed, you can validate your .dockstore.yml locally. It not only does YAML validation, but also checks that your paths are correct. Just navigate to the directory on your local machine:
dockstore yaml validate --path .
Your .dockstore.yml is invalid:
./.dockstore.yml is not a valid yaml file:
while parsing a block mapping
in 'string', line 1, column 1:
version: 1.2
^
expected <block end>, but found '-'
in 'string', line 111, column 1:
- name: Seurat_single_sample
^
I just updated my .dockstore.yml file. Now it appears to be working fine. Although my github has multiple wdl files and they all show up as separate workflows. Is there a way that everything appears as part of one github repository instead?
Dockstore represents each workflow as a separate entry. Each item in the workflows field of .dockstore.yml will be registered as a separate workflow that can be viewed/searched/run independently of the others…
Conceptually, GitHub organizations/repos and Dockstore organizations are somewhat similar, but not tied together. If identical files reside in two GitHub repos, and each is registered, two corresponding sets of workflows will appear on Dockstore.
