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

- name: cellranger count test_cellranger_count
  command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
  tags:
    - cellranger
    - cellranger/count
  files:
    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
    - path: output/cellranger/sample-123/outs/metrics_summary.csv
      md5sum: 707df0f101d479d93f412ca74f9c4131
    - path: output/cellranger/sample-123/outs/molecule_info.h5
      md5sum: cf03b2b3ca776a1c37aa3518e91268ba
    - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
      md5sum: 15441da9cfceea0bb48c8b66b1b860df
    - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
      md5sum: 7c3d49c77016a09535aff61a027f750c
    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
      md5sum: 40c8df814eb8723b7317b234dc8222e9
    - path: output/cellranger/sample-123/outs/web_summary.html
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 count test_cellranger_count`
			`command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config`
			`tags:`
			`- cellranger`
			`- cellranger/count`
			`files:`
			`- path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5`
			`- path: output/cellranger/sample-123/outs/metrics_summary.csv`
			`md5sum: 707df0f101d479d93f412ca74f9c4131`
			`- path: output/cellranger/sample-123/outs/molecule_info.h5`
			`md5sum: cf03b2b3ca776a1c37aa3518e91268ba`
			`- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam`
			`md5sum: 15441da9cfceea0bb48c8b66b1b860df`
			`- path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai`
			`md5sum: 7c3d49c77016a09535aff61a027f750c`
			`- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix`
			`- path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5`
			`md5sum: 40c8df814eb8723b7317b234dc8222e9`
			`- path: output/cellranger/sample-123/outs/web_summary.html`