* 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>
* 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>
