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nf-core_modules/tests/modules/cellranger/mkfastq/test.yml

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Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
- name: cellranger mkfastq test_cellranger_mkfastq_simple
Add bcl2fastq2 to cellranger dockerfile (#1115) * refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 18:58:22 +00:00
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_simple -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
tags:
- cellranger
- cellranger/mkfastq
Add bcl2fastq2 to cellranger dockerfile (#1115) * refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 18:58:22 +00:00
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
- name: cellranger mkfastq test_cellranger_mkfastq_illumina
Add bcl2fastq2 to cellranger dockerfile (#1115) * refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 18:58:22 +00:00
command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
tags:
- cellranger
- cellranger/mkfastq
Add bcl2fastq2 to cellranger dockerfile (#1115) * refactor: add bcl2fastq to cellranger dockerfile bcl2fastq required for the cellranger mkfastq module and was therefore added to the cellranger dockerfile. Further, cellranger was updated to the latest version, 6.1.2., with naming and containers across cellranger modules updated accordingly. * chore: add bcl2fastq zip to .gitignore * style: fix code linting error * test(cellranger): Add tiles to mkfastq * additional dockerfile for mkfastq * update readme and dockerfiles * update readme * fix: update container for mkfastq * docs: correct typos in readme * test: update md5sum following cellranger update * test: update md5sum following cellranger update * fix: new line for external args in mkfastq * test: update mkfastq tiles argument * test: comment out mkfastq tests until smaller test data found * test: stub-run mkfastq test until smaller test data found * test: fix incorrect file path for mkfastq Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 18:58:22 +00:00
files:
- path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
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