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nf-core_modules/tests/modules/seqtk/sample/test.yml

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Feat seqtk update (#503) * 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>
2021-06-14 11:23:15 +00:00
- name: seqtk sample test_seqtk_sample_single_end
Rename software/ directory to modules/ to re-organise module structure (#567) * 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
2021-07-07 09:10:18 +00:00
command: nextflow run tests/modules/seqtk/sample -entry test_seqtk_sample_single_end -c tests/config/nextflow.config
Request to review code for seqtk/sample module (#488) * added files * removed file * added file * changed files * changed files * edited file * edited file * edited files * edited files * edited files * edited tags * edited tags * edited tags * edited tags Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 22:55:35 +00:00
tags:
- seqtk
- seqtk/sample
files:
- path: output/seqtk/test.sampled.fastq.gz
Feat seqtk update (#503) * 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>
2021-06-14 11:23:15 +00:00
md5sum: 73c3e8f113860244f3ed3866a8b9d555
Request to review code for seqtk/sample module (#488) * added files * removed file * added file * changed files * changed files * edited file * edited file * edited files * edited files * edited files * edited tags * edited tags * edited tags * edited tags Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 22:55:35 +00:00
Feat seqtk update (#503) * 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>
2021-06-14 11:23:15 +00:00
- name: seqtk sample test_seqtk_sample_paired_end
Rename software/ directory to modules/ to re-organise module structure (#567) * 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
2021-07-07 09:10:18 +00:00
command: nextflow run tests/modules/seqtk/sample -entry test_seqtk_sample_paired_end -c tests/config/nextflow.config
Request to review code for seqtk/sample module (#488) * added files * removed file * added file * changed files * changed files * edited file * edited file * edited files * edited files * edited files * edited tags * edited tags * edited tags * edited tags Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 22:55:35 +00:00
tags:
- seqtk
- seqtk/sample
files:
- path: output/seqtk/test.sampled_1.fastq.gz
Feat seqtk update (#503) * 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>
2021-06-14 11:23:15 +00:00
md5sum: 73c3e8f113860244f3ed3866a8b9d555
Request to review code for seqtk/sample module (#488) * added files * removed file * added file * changed files * changed files * edited file * edited file * edited files * edited files * edited files * edited tags * edited tags * edited tags * edited tags Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 22:55:35 +00:00
- path: output/seqtk/test.sampled_2.fastq.gz
Feat seqtk update (#503) * 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>
2021-06-14 11:23:15 +00:00
md5sum: 75457ddceea3a5688d05438cdbffba24
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