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nf-core_modules/tests/modules/sratools/fasterqdump/test.yml

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Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
- name: sratools fasterqdump test_sratools_fasterqdump_single_end
command: nextflow run tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_single_end -c tests/config/nextflow.config
tags:
Fix subworkflows seperate from modules (#933) * ci: Remove pytest_subworkflows * ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow Co-authored-by: Harshil Patel <drpatelhh@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * ci: Revert back to one job branch * ci(align_bowtie2): Run tests that depend on bam_sort_samtools * ci: Fix anchor not being created yet * ci: Update sra_fastq tags and pytest_modules * fix(bam_sort_samtools): Update nextflow.config with params * test(subworkflows): Update gatk_create_som_pon tags * ci: Point to subworkflow_hacks branch of nf-core tools Co-authored-by: Harshil Patel <drpatelhh@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-11-15 18:18:46 +00:00
- subworkflows/sra_fastq
Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
files:
- path: output/sratools/SRR13255544.fastq.gz
md5sum: 1054c7b71884acdb5eed8a378f18be82
- path: output/untar/SRR13255544/SRR13255544.sra
md5sum: 466d05dafb2eec672150754168010b4d
- name: sratools fasterqdump test_sratools_fasterqdump_paired_end
command: nextflow run tests/modules/sratools/fasterqdump -entry test_sratools_fasterqdump_paired_end -c tests/config/nextflow.config
tags:
Fix subworkflows seperate from modules (#933) * ci: Remove pytest_subworkflows * ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow Co-authored-by: Harshil Patel <drpatelhh@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * ci: Revert back to one job branch * ci(align_bowtie2): Run tests that depend on bam_sort_samtools * ci: Fix anchor not being created yet * ci: Update sra_fastq tags and pytest_modules * fix(bam_sort_samtools): Update nextflow.config with params * test(subworkflows): Update gatk_create_som_pon tags * ci: Point to subworkflow_hacks branch of nf-core tools Co-authored-by: Harshil Patel <drpatelhh@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-11-15 18:18:46 +00:00
- subworkflows/sra_fastq
Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
files:
- path: output/sratools/SRR11140744_1.fastq.gz
md5sum: 193809c784a4ea132ab2a253fa4f55b6
- path: output/sratools/SRR11140744_2.fastq.gz
md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e
- path: output/untar/SRR11140744/SRR11140744.sra
md5sum: 065666caf5b2d5dfb0cb25d5f3abe659
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