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refactor: oligomap output conversion script #115

Merged
merged 18 commits into from
Nov 15, 2023
Merged

refactor: oligomap output conversion script #115

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c197133
refactor: refactor script + static code analysis
deliaBlue Oct 13, 2023
8992b09
refactor: add empty file creation
deliaBlue Oct 13, 2023
c130542
refactr: refactor rules to turn oligomap FASTA to SAM
deliaBlue Oct 13, 2023
f04325c
build: update gffutils version
deliaBlue Oct 18, 2023
6b188e3
refactor: fix input reading
deliaBlue Oct 19, 2023
2fc310e
build: upgrade gffutils
deliaBlue Oct 25, 2023
ae20014
test: add unit testing
deliaBlue Oct 30, 2023
b3847af
test: add files for unit testing
deliaBlue Oct 30, 2023
b0c82b2
refacor: finish script refactoring
deliaBlue Oct 30, 2023
e3a61f2
ci: add oligomap script to the static code analysis
deliaBlue Oct 30, 2023
9093f16
docs: update link to oligomap output to sam script
deliaBlue Oct 30, 2023
1871d47
Merge branch 'dev' into 54-refactor-refactor-and-create-unit-test-for…
deliaBlue Nov 2, 2023
af4eee0
merge with dev
deliaBlue Nov 9, 2023
851b709
test: change unit test to check STDOUT
deliaBlue Nov 12, 2023
33f966a
restore rules calls
deliaBlue Nov 12, 2023
4c1292d
refactor: use STDOUT instead of an output file
deliaBlue Nov 12, 2023
eb8e00b
Merge branch 'dev' into 54-refactor-refactor-and-create-unit-test-for…
deliaBlue Nov 14, 2023
79e8ad3
refactor: modify variable name and main docstring
deliaBlue Nov 15, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/tests.yml
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Expand Up @@ -38,7 +38,7 @@ jobs:

- name: flake8
working-directory: ./scripts
run: flake8 ./*.py --exclude oligomapOutputToSam_nhfiltered.py
run: flake8 ./*.py
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- name: mypy
working-directory: ./scripts
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2 changes: 1 addition & 1 deletion pipeline_documentation.md
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Expand Up @@ -1130,7 +1130,7 @@ alignments in a genomic region of interest.
[custom-script-mir-ext]: scripts/mirna_extension.py
[custom-script-mir-quant]: scripts/mirna_quantification.py
[custom-script-nh-filter]: scripts/nh_filter.py
[custom-script-oligo-sam]: scripts/oligomapOutputToSam_nhfiltered.py
[custom-script-oligo-sam]: scripts/oligomap_output_to_sam_nh_filtered.py
[custom-script-pri-quant]: scripts/primir_quantification.py
[custom-script-remove-dup]: scripts/sam_remove_duplicates_inferior_alignments_multimappers.pl
[custom-script-sam-trx]: scripts/sam_trx_to_sam_gen.pl
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238 changes: 0 additions & 238 deletions scripts/oligomapOutputToSam_nhfiltered.py
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