The function was failing since contig names could include integer, whereas " ".join() method expects all elements in the list to be strings. This has now been fixed. Additionally, pd.read_csv() function was updated to ignore commented lines, as some .gtf files include metadata in such manner.
Checklist
[ ] Update CHANGELOG.rst for each commit separately:
Pay attention to write entries under the "Unreleased" section.
Mark all breaking changes as "BACKWARD INCOMPATIBLE:" and put them
before non-breaking changes.
If a commit modifies a feature listed under "Unreleased" section,
it might be sufficient to modify the existing CHANGELOG entry from previous
commit(s).
[ ] Bump the process version:
MAJOR version (first number): Backward incompatible changes (changes
that break the api/interface). Examples: renaming the input/output, adding
mandatory input, removing input/output...
MINOR version (middle number): add functionality or changes in a
backwards-compatible manner. Examples: add output field, add non-mandatory
input parameter, use a different tool that produces same results...
PATCH version (last number): changes/bug fixes that do not affect
the api/interface. Examples: typo fix, change/add warning messages...
[ ] All inputs are used in process.
[ ] All output fields have a value assigned to them.
Additional guidelines
Processes
Code that was once accepted should be kept like it is. It should be changed
only when its functionality has changed. Small parts may be changed
to fix bugs (by changing code only to make it nicer you might introduce a bug).
Set the optimal number of cores that the tool can use (check if parallelization
can be performed).
Description of the tool should be self explanatory with links to the tool's
homepage and publication.
Write explanatory input labels and add short command line parameter names
in square brackets (for example: Maximum length [--maxlength]).
Where possible provide default values for the process input fields.
If they are provided, then required = False is not needed.
Add descriptive error and warning messages.
Use Cmd() for each call in the process (call of a tool, a
Bash command, a Python script or an R script) and handle return codes.
Add self.progress() calls where appropriate.
Commit and PR messages
Each commit should be minimal (i.e. 1 change) and self-contained (including
tests).
Mark incomplete PRs with the [WIP] (Work In Progress) tag.
Do not paste links to private repositories from the public one.
Tests
Add meaningful names of test files:
Genomes: genome_species.fa.gz
Annotations: annotation_species.gtf.gz
Adapters: adapters-name/type-source.
Specific files should be saved in a folder with the name of the tested tool.
This folder should include separate subfolders for inputs and outputs.
Keep test files' size small. If there is no other option, add the large
test file to the files/large directory so it will be tracked with Git LFS.
Pay attention to edge cases: what will happen if any data is
missing, if the length of some list is 0, if a string is given where one
expects an integer, if a file is empty, ...
When testing workflows, try to verify workflow success by checking one
of the last steps. Pick the one that is most likely to fail. Also test
that all steps have 'OK' status.
The function was failing since contig names could include integer, whereas
" ".join()method expects all elements in the list to be strings. This has now been fixed. Additionally,pd.read_csv()function was updated to ignore commented lines, as some .gtf files include metadata in such manner.Checklist
Additional guidelines
Processes
--maxlength]).required = Falseis not needed.Cmd()for each call in the process (call of a tool, a Bash command, a Python script or an R script) and handle return codes.self.progress()calls where appropriate.Commit and PR messages
Tests
genome_species.fa.gzannotation_species.gtf.gzadapters-name/type-source.files/largedirectory so it will be tracked with Git LFS.