Dummy commit to test docs deploy

See merge request eosc/prefactor3-cwl!68

Deplay docs when files in subdir change

See merge request eosc/prefactor3-cwl!67

CI fixes

See merge request eosc/prefactor3-cwl!65

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Restructure output

See merge request eosc/prefactor3-cwl!63

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Switch to Dp3 master

See merge request eosc/prefactor3-cwl!62

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Add more info regarding output data

See merge request eosc/prefactor3-cwl!64

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Tidy up

See merge request eosc/prefactor3-cwl!60

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Base dockerfile on Ubuntu 20.04

See merge request eosc/prefactor3-cwl!58

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Add requirements.txt file for creating virtual env for running Prefactor

See merge request eosc/prefactor3-cwl!61

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Marcel Loose authored 3 years ago and Mattia Mancini committed 3 years ago

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Remove all references to sevenbridges tags

See merge request eosc/prefactor3-cwl!59

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RabixComposer, which uses the `sevenbridges` namespace and `sbg` tags, cannot
handle CWL version 1.2 files. Removed all references to the namespace and tags.


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Bump CWL Version to v1.2

See merge request eosc/prefactor3-cwl!57

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CWL v1.2 is more explicit about the way that strings in embedded code that contain a dollar sign ($) must be escaped. See https://www.commonwl.org/v1.2/Workflow.html#String_interpolation. It turned out that a few workflow steps contained inline Bash code with improperly escaped variables references. This has been fixed.


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Let inline bash scripts exit on error

See merge request eosc/prefactor3-cwl!56

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Most of the inline bash scripts in the CWL files *ignore* errors, which is undesirable. This fix adds a `set -e` to all the inline scripts that did not have one yet. Note that adding a `-e` to the `#!/bin/bash` does *not* work, because the script is not invoked as an executable but as `bash <script-file>`.


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Give inline scripts sensible names

See merge request eosc/prefactor3-cwl!55

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Some of the inline scripts (bash or python) have names like "script.py",
which is not very helpful for debugging. Renamed the scripts for those
workflows that contained either script.py or script.sh.


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Update soltab name to new one

See merge request eosc/prefactor3-cwl!54

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Only deploy docs if they were built

See merge request eosc/prefactor3-cwl!53

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Tammo Jan Dijkema authored 3 years ago and Marcel Loose committed 3 years ago

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Move residual step before smooth one

See merge request eosc/prefactor3-cwl!52

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Improve CI checks

See merge request eosc/prefactor3-cwl!51

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David Rafferty authored 3 years ago and Marcel Loose committed 3 years ago

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Fix typo in true/false check

See merge request eosc/prefactor3-cwl!50

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Fix incorrect installation of CWL files

Closes RAP-249

See merge request eosc/prefactor3-cwl!49

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Many CWL files were being installed in the wrong directory. This
has been fixed. This commit fixes RAP-249.


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Fix true/false check

See merge request eosc/prefactor3-cwl!48

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