* 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
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added seqtk/subseq and checking for seed in seqtk/sample
* Separate authors in software/seqtk/sample/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Align commans in output channesl software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define prefix in software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Use prefix in output file name software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define suffix in options in tests/software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change output file name in tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove a to-do point from tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added --no-name into gzip commands
* Update samtools from 1.10 to 1.12 (#530)
* feat: remove social preview image to use GitHub OpenGraph
* feat: update samtools from 1.10 to 1.12
* fix: CI tests
* fix: add meta.yml file for samtools/merge
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Added seqtk/subseq and checking for seed in seqtk/sample
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Separate authors in software/seqtk/sample/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Align commans in output channesl software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define prefix in software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Use prefix in output file name software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define suffix in options in tests/software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change output file name in tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove a to-do point from tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added --no-name into gzip commands
* Replaced functions.nf in seqtk/subseq
* Refreshed tests for sample and subseq
* Corrected paired-end test and YAML description for sample
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
