nf-core_modules/.gitignore

.nextflow*
work/
results/
test_output/
output/
.DS_Store
*.code-workspace
.screenrc
.*.sw?
__pycache__
*.pyo
*.pyc
tests/data/
Fill out repo 2019-07-26 09:19:07 +00:00			`.nextflow*`
			`work/`
			`results/`
Add tests for fastqc module 2020-07-14 15:38:20 +00:00			`test_output/`
seacr \| Updated gitignore to ignore output folder 2020-12-17 14:23:07 +00:00			`output/`
Fill out repo 2019-07-26 09:19:07 +00:00			`.DS_Store`
Update README 2020-07-14 08:51:19 +00:00			`*.code-workspace`
New module to use hmmalign from HMMER to align sequences (#470) * Ignore vim tmp files * Added hmmalign module, not yet tests * Test output * Replaced functions.nf for hmmalign with upstream * Update software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/hmmer/hmmalign/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/hmmer/hmmalign/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-04-28 10:21:24 +00:00			`.screenrc`
			`.*.sw?`
Update fastqc to produce multi-version versions.yml (#665) * Update fastqc to produce multi-version versions.yml * Update readme and pull request template * Fix markdownlint * remove variable * Change publish dir to lowercase * Re-add getSoftwareName * Add custom pytest-workflow test to ensure versions.yml is valid * Add docstring * Remove __init__.py as it is not needed * Remove changes to README, since this part went to nf-co.re * Add NF_CORE_TEST env var * Fix editorconfig * Add additional consistency checks for versions.yml * Update multiqc module * Fix output channel 2021-09-24 09:01:54 +00:00			`__pycache__`
			`*.pyo`
			`*.pyc`
new module: pbccs (#688) * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: fill contains args * 👌 IMPROVE: One output => One Channel * 👌 IMPROVE: One input => One channel * 🐛 FIX: Update tests * 🐛 FIX: Remove TODOs from test.yaml * 👌 IMPROVE: Revert and keep bam and pbi together * 🐛 FIX: Remove old rq input from meta.yml * 👌 IMPROVE: Update test to match input channels Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> 2021-09-16 10:48:18 +00:00			`tests/data/`