* Make samtools/merge cram compliant
* samtools/stats cram compliance
* update yml file
* samtools/view to deal with crams
* Update tests to make sure cram works
* also fix tmp dir and min mem in one go
* basequalityrecal test for cram + min mem + tmpdir
* update haplotypecaller for sarek
* update haplotype yml
* update markdup to allow multiple bams, take out params to be passed with options.args
* remove TODO statement
* Remove variable md5sum
* add emtpy input to stats module in subworkflows
* subworkflows seem to work now on my side
* Apply code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* replace bam with input to be more inclusive
* rename everywhere
* rename input
* remove variable checksum
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* added template for module
* update main
* added specific code
* wrong variable name in else script
* added tests for both split and nosplit
* docker test successful - updating yaml
* adding echo to version print
* add new module samtools_depth
* fixed main.nf for samtools/depth
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* feat(subworkflows): Add align_bowtie2 subworkflow
For testing CI setup
* test(align_bowtie2): Add initial list of changes to test
* test(align_bowtie2): Add initial test
* refactor: Use tags to run subworkflows ci
For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.
* refactor: Use individual directories for subworkflows
* docs(align_bowtie2): Add initial meta.yml
Copied most of it from the bowtie2/align module.
* fix(align_bowtie2): Fix module include paths
* test(bam_sort_samtools): Add initial test
* ci(bam_sort_samtools): Add modules that trigger the tag
* test(bam_stats_samtools): Add initial test
* ci(bam_stats_samtools): Add keys to pick up changes
* docs(bam_samtools): Add initial meta.yml
* test(align_bowtie2): Fix path to subworkflow
* test(align_bowtie2): Update entry point
* fix(bam_sort_samtools): Update include paths
* test(bam_sort_samtools): Fix path
* style: Clean up addParams
* test(samtools_sort): Add suffix for test
* test(align_bowtie2): Add samtools_options for suffix
* test(bam_stats_samtools): Update path
* test(bam_stats_samtools): Use stats input
Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow
* ci(linting): Skip module linting of subworkflows
* ci(linting): Clean up startsWith statement
* test(bam_stats_samtools): Use single end test data for single end test
* test(bam_stats_samtools): Add expected files
* test(align_bowtie2): Add paired-end test
* test(align_bowtie2): Sort order of output
* test(align_bowtie2): Update hashes
* docs(align_bowtie2): Fix typo
* test(align_bowtie2): Update samtools output names
* test(align_bowtie2): Remove md5sums for bam/bai
* feat(subworkflows): Add nextflow.configs
These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.
* docs(subworkflows): Include modules instead of tools
* fix: Update to versions
* chore(align_bowtie2): Remove duplicate tag
* style: Format yamls
* test(subworkflows): Only check versions for modules
* chore: Update subworkflows to match rnaseq dev
* fix(subworkflows): Update paths
* fix(bam_sort_samtools): Fix sort parameters for testing
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* docs: Update TODOs with a message
* ci: Try using a matrix for strategy
* ci: Try passing an array
* Revert "ci: Try passing an array"
This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add blacklist of modules that shouldn't be updated to .nf-core.yml
* nf-core modules bump-versions for all modules
* Remove TODO statements identified by linting
* Fix md5sums for failing tests
* Fix more tests
* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
