Added initial WfExS-backend examples based on toy workflow.

docs/examples/WfExS-backend/README.md

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+# WfExS-backend examples
+
+These RO-Crate Workflow Run examples were generated running WfExS-backend.
+
+There can be two RO-Crates for each execution, as one of them only contains
+details gathered after staging the execution scenario but *before* the
+execution, and the other one contains those details and all the provenance
+gathered through and *after* the execution.
+
+As WfExS-backend can run staged workflows more than once, all the different
+executions are represented inside the generated RO-Crates as several
+`CreateAction`. Also, CWL workflows are packed before they are run, so their
+RO-Crates contain an additional CreateAction explaining the pack process from
+the original workflow to the packed one.
+
+Workflow execution error messages are also included. Also, a graphical representation
+of the executed workflow is included. Due the nature of the different workflow
+engines, this representation could be pre-computed before the execution
+or after it. So, it is provided a copy of the representation for each execution.
+
+
+## WOMBAT-Pipelines
+
+* Nextflow workflow is available at https://github.com/wombat-p/WOMBAT-Pipelines
+
+* Provenance RO-Crate from an execution using Docker containers. It includes a snapshot of the workflow: [wombat-pipelines_provenance](wombat-pipelines_provenance).
+
+
+```bash
+# Example of command line to generate this RO-Crate
+python WfExS-backend.py -L workflow_examples/montblanc_config_gocryptfs.yaml staged-workdir create-prov-crate 047b6dfc-3547-4e09-92f8-df7143038ff4 /tmp/wombat-pipelines_provenance.zip --workflow --orcid 0000-0002-4806-5140 --licence https://spdx.org/licenses/CC-BY-4.0.html
+```
+
+## Wetlab2Variations (CWL flavor).
+
+* CWL workflow is available at https://github.com/inab/Wetlab2Variations/blob/eosc-life/cwl-workflows/workflows/workflow.cwl
+
+* Provenance RO-Crate from an execution using Singularity containers. It includes a snapshot of the consolidated workflow: [Wetlab2Variations_CWL_provenance](Wetlab2Variations_CWL_provenance)
+
+
+```bash
+# Example of command line to generate this RO-Crate
+python WfExS-backend.py -L workflow_examples/local_config_gocryptfs.yaml staged-workdir create-prov-crate a37fee9e-4288-4a9e-b493-993a867207d0 /tmp/Wetlab2Variations_CWL_provenance.zip  --orcid 0000-0002-4806-5140  --licence https://spdx.org/licenses/CC-BY-4.0.html
+```
+
+## nf-core RNASeq
+
+* Nextflow workflow is available at https://github.com/nf-core/rnaseq/
+
+* Provenance RO-Crate from an execution using Singularity containers. It includes a snapshot of the consolidated workflow: [nfcore-rnaseq_provenance](nfcore-rnaseq_provenance).
+
+
+```bash
+# Example of command line to generate this RO-Crate
+python WfExS-backend.py -L workflow_examples/bsclife002_config_docker_gocryptfs_20.yaml staged-workdir create-prov-crate 'sex-linked aortectasis' /tmp/example_nfcore_rnaseq_1.zip --orcid 0000-0002-4806-5140 --licence https://spdx.org/licenses/CC-BY-4.0.html
+```
+
+## COSIFER cwl workflow (using singularity)
+
+* Generated RO-Crates contain a copy of the inputs, outputs and workflow.
+
+* WfExS configuration file: [local_config_gocryptfs.yaml](https://github.com/inab/WfExS-backend/blob/b058b538f3334a4b8c657a541dc9b9fb40434f55/workflow_examples/local_config_gocryptfs.yaml)
+
+* Stage description: [cosifer_test1_cwl_implicit_outputs_github.wfex.stage](https://github.com/inab/WfExS-backend/blob/b058b538f3334a4b8c657a541dc9b9fb40434f55/workflow_examples/ipc/cosifer_test1_cwl_implicit_outputs_github.wfex.stage)
+
+* Staged RO-Crate: [cosifer-cwl_staged](cosifer-cwl_staged)
+
+* Provenance RO-Crate: [cosifer-cwl_provenance](cosifer-cwl_provenance)
+
+
+```bash
+# Example of command line to generate this RO-Crate
+python WfExS-backend.py -L workflow_examples/local_config_gocryptfs.yaml staged-workdir create-prov-crate 2400c32e-f875-4cd4-9d41-be6da8224c67 /tmp/cosifer-cwl_provenance.zip --inputs --outputs --workflow  --orcid 0000-0002-4806-5140 --orcid 0000-0003-4929-1219 --licence https://spdx.org/licenses/CC-BY-4.0.html
+```
+
+## COSIFER Nextflow workflow (using singularity)
+
+* Generated RO-Crates contain a copy of the inputs, outputs and workflow.
+
+* WfExS configuration file: [local_config_gocryptfs.yaml](https://github.com/inab/WfExS-backend/blob/b058b538f3334a4b8c657a541dc9b9fb40434f55/workflow_examples/local_config_gocryptfs.yaml)
+
+* Stage description: [cosifer_test1_nxf.wfex.stage](https://github.com/inab/WfExS-backend/blob/b058b538f3334a4b8c657a541dc9b9fb40434f55/workflow_examples/ipc/cosifer_test1_nxf.wfex.stage)
+
+* Staged RO-Crate: [cosifer-nxf_staged](cosifer-nxf_staged)
+
+* Provenance RO-Crate: [cosifer-nxf_provenance](cosifer-nxf_provenance)
+
+
+```bash
+# Example of command line to generate this RO-Crate
+python WfExS-backend.py -L workflow_examples/local_config_gocryptfs.yaml staged-workdir create-prov-crate 597708f2-952e-47c7-9b86-dbe3a9e5f651 /tmp/cosifer-nxf_provenance.zip --inputs --outputs --workflow --orcid 0000-0002-4806-5140 --orcid 0000-0003-4929-1219 --licence https://spdx.org/licenses/CC-BY-4.0.html
+```

docs/examples/WfExS-backend/Wetlab2Variations_CWL_provenance/README.md

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+# Notes about this generated RO-Crate
+
+RO-Crate from staged WfExS working directory a37fee9e-4288-4a9e-b493-993a867207d0 (meer oxometalate)
+
+This RO-Crate has been generated by WfExS-backend 0.9.3-192-g93901ff (93901ff9f5e88903b917d62cd0302454ae52364c, branch main) ,
+whose sources are available at https://github.com/inab/WfExS-backend.
+
+## Software containers and metadata
+
+Metadata files which are produced and consumed by WfExS-backend in
+order to properly detect when a local cached copy of a software container
+is stale are also included in this RO-Crate. These files are in JSON format.
+
+In case this RO-Crate also contains a copy of the software containers,
+their format will depend on whether they are going to be consumed by
+Singularity / Apptainer, or they are going to be consumed by Docker or Podman.
+
+Singularity / Apptainer images usually have the singularity image format.
+
+Both Docker and Podman images are compressed tar archives obtained through
+either `docker save` or `podman save` commands. These archives have all
+the layers needed to restore the container image in a local registry
+through either `docker load` or `podman load`.
+
+## Posibly used URI schemes
+
+As WfExS-backend is able to manage several exotic CURIEs and schemes,
+you can find here an almost complete list of the possible ones:
+
+* `pride.project`: 'pride' datasets metadata is fetched using the APIs described at https://www.ebi.ac.uk/pride/ws/archive/v2/swagger-ui.html#/projects . Contents are downloaded delegating their associated URIs to other fetchers
+
+* `drs`: GA4GH DRS datasets metadata is fetched using the APIs described at https://ga4gh.github.io/data-repository-service-schemas/. Contents are downloaded delegating their associated URIs to other fetchers
+
+* `wfexs.trs.files`: WfExS internal pseudo-scheme used to materialize files from pure TRS servers
+
+* `trs`: GA4GH TRS metadata is fetched using the APIs described at https://ga4gh.github.io/tool-registry-service-schemas/. Contents are downloaded delegating their associated URIs to other fetchers
+
+* `s3`: Amazon S3 resource path scheme, whose downloads are delegated on libraries implementing its support
+
+* `gs`: Google Cloud Storage resource path scheme, whose downloads are delegated on Google Cloud Storage libraries
+
+* `fasp`: This pseudo-scheme, which mimics ssh scheme, represents datasets behind IBM Aspera servers (quite common in life sciences infrastructures), which follow FASP protocol. Materialization of these datasets are delegated to ascp command line
+
+* `doi`: DOIs resolve to web sites. A subset of the different DOI providers also point to datasets, like the ones from Zenodo, B2SHARE or osf.io. Fetcher implementing DOI support either delegates on other specialized fetchers or delegates the download of the resolved URL.
+
+* `zenodo`: CURIEs following this scheme can be translated to a downloadable dataset, using APIs described at https://developers.zenodo.org/
+
+* `b2share`: CURIEs following this scheme can be translated to a downloadable dataset, using APIs described at https://eudat.eu/services/userdoc/b2share-http-rest-api#get-specific-record
+
+* `osf.io`: CURIEs following this scheme can be translated to a downloadable dataset, using APIs described at https://developer.osf.io/
+
+* `git`: 'git' scheme and pseudo-schemes 'git+file', 'git+https', 'git+ssh' (based on https://pip.pypa.io/en/stable/topics/vcs-support/) and 'github' are managed by using git command line, applying minimal transformations in the URI.
+
+* `git+file`: 'git' scheme and pseudo-schemes 'git+file', 'git+https', 'git+ssh' (based on https://pip.pypa.io/en/stable/topics/vcs-support/) and 'github' are managed by using git command line, applying minimal transformations in the URI.
+
+* `git+https`: 'git' scheme and pseudo-schemes 'git+file', 'git+https', 'git+ssh' (based on https://pip.pypa.io/en/stable/topics/vcs-support/) and 'github' are managed by using git command line, applying minimal transformations in the URI.
+
+* `git+http`: 'git' scheme and pseudo-schemes 'git+file', 'git+https', 'git+ssh' (based on https://pip.pypa.io/en/stable/topics/vcs-support/) and 'github' are managed by using git command line, applying minimal transformations in the URI.
+
+* `git+ssh`: 'git' scheme and pseudo-schemes 'git+file', 'git+https', 'git+ssh' (based on https://pip.pypa.io/en/stable/topics/vcs-support/) and 'github' are managed by using git command line, applying minimal transformations in the URI.
+
+* `github`: 'git' scheme and pseudo-schemes 'git+file', 'git+https', 'git+ssh' (based on https://pip.pypa.io/en/stable/topics/vcs-support/) and 'github' are managed by using git command line, applying minimal transformations in the URI.
+
+* `swh`: Permanent identifiers of files, directories and repos at SoftwareHeritage. These URIs follow what it is described at https://docs.softwareheritage.org/devel/swh-model/persistent-identifiers.html
+
+* `http`: HTTP download URLs
+
+* `https`: HTTPS download URLs
+
+* `ftp`: File Transfer Protocol (see https://www.iana.org/assignments/ftp-commands-extensions/ftp-commands-extensions.xhtml)
+
+* `sftp`: 'sftp' scheme represents contents behind an SSH server
+
+* `ssh`: 'ssh' scheme represents contents behind an SSH server
+
+* `file`: 'file' scheme is used to represent local files and directories. It should be only used either for development or for very isolated environments where paths are stable.
+
+* `data`: 'data' scheme is used to embed very small payloads, as it is described at https://datatracker.ietf.org/doc/html/rfc2397
+