Sébastien Guizard
|
001d5071c2
|
Update: gstama/collapse (#1057)
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add gd-tama module
* 🐛 FIX (TEMP): Update singularity container address
* 📦 NEW: Add bamtools module
* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE: Remove junk files
* 👌 IMPROVE: Update output
* 👌 IMPROVE: Add channel for publishing tama's metadata outputs
* 👌 IMPROVE: Update process label
* 🐛 FIX: Use depot.galxyproject.org url for singularity
* 👌 IMPROVE: autoselect running mode
* 🐛 FIX: correct gstama collapse bash test
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update tama package and label
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update test
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add gd-tama module
* 🐛 FIX (TEMP): Update singularity container address
* 📦 NEW: Add bamtools module
* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE: Update output
* 👌 IMPROVE: Add channel for publishing tama's metadata outputs
* 👌 IMPROVE: Update process label
* 🐛 FIX: Use depot.galxyproject.org url for singularity
* 👌 IMPROVE: autoselect running mode
* 🐛 FIX: correct gstama collapse bash test
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update tama package and label
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update test
* 👌 IMPROVE: delete unnecessary files
* 👌 IMPROVE: Update + clean
- Remove unnecessary files
- Update to new versions.yml file
- Better output channels
* 👌 IMPROVE: Update meta.yml and output channels
* 👌 IMPROVE: Remove useless files
* 👌 IMPROVE: Remove automatic MODE setup
* 👌 IMPROVE: Applied @jfy133 code modification suggestions
* Update modules/gstama/collapse/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 🐛 FIX: Add missing fasta option in meta.yml
* 🐛 FIX: Fix typo
* 🐛 FIX: Update package version
* Update main.nf
* Update meta.yml
* Update modules/gstama/collapse/meta.yml
* Apply suggestions from code review
* Update tests/modules/gstama/collapse/main.nf
* Update main.nf
* 👌 IMPROVE: Update to gs-tama 1.0.3
* Update modules/gstama/collapse/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-11-11 14:57:55 +00:00 |
|
Sébastien Guizard
|
d3369789da
|
New module: gstama/merge (#813)
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add bamtools module
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE : add test bed files
* 📦 NEW: Add gstama/merge module
* 🐛 FIX: Change process label
* 👌 IMPROVE: do not merge empty bed
* 🐛 FIX: Change 0 lines files detection
* 🐛 FIX: replace spaces by tab
* 🐛 FIX: Remove tuple for report channel and add version output channel
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update module to last template version
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Update test
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Fix Typos
* 👌 IMPROVE: Updates + clean code
- Update to last versions.yml file
- Better output channels
- Update meta.yml
* 👌 IMPROVE: Correct typo
* 👌 IMPROVE: Remove included filelist creation and add an input channel
* 🐛 FIX: Correct typo
* 👌 IMPROVE: Add filelist file
* 🐛 FIX: tama_merge.py emit a version number
* Update modules/gstama/merge/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 👌 IMPROVE: Update meta.yml
* Update main.nf
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-10-23 19:00:39 +01:00 |
|
Sébastien Guizard
|
481d3c811d
|
New module: gstama/collapse (#809)
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add gd-tama module
* 🐛 FIX (TEMP): Update singularity container address
* 📦 NEW: Add bamtools module
* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE: Remove junk files
* 👌 IMPROVE: Update output
* 👌 IMPROVE: Add channel for publishing tama's metadata outputs
* 👌 IMPROVE: Update process label
* 🐛 FIX: Use depot.galxyproject.org url for singularity
* 👌 IMPROVE: autoselect running mode
* 🐛 FIX: correct gstama collapse bash test
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update tama package and label
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update test
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add gd-tama module
* 🐛 FIX (TEMP): Update singularity container address
* 📦 NEW: Add bamtools module
* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE: Update output
* 👌 IMPROVE: Add channel for publishing tama's metadata outputs
* 👌 IMPROVE: Update process label
* 🐛 FIX: Use depot.galxyproject.org url for singularity
* 👌 IMPROVE: autoselect running mode
* 🐛 FIX: correct gstama collapse bash test
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update tama package and label
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update test
* 👌 IMPROVE: delete unnecessary files
* 👌 IMPROVE: Update + clean
- Remove unnecessary files
- Update to new versions.yml file
- Better output channels
* 👌 IMPROVE: Update meta.yml and output channels
* 👌 IMPROVE: Remove useless files
* 👌 IMPROVE: Remove automatic MODE setup
* 👌 IMPROVE: Applied @jfy133 code modification suggestions
* Update modules/gstama/collapse/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 🐛 FIX: Add missing fasta option in meta.yml
* 🐛 FIX: Fix typo
* 🐛 FIX: Update package version
* Update main.nf
* Update meta.yml
* Update modules/gstama/collapse/meta.yml
* Apply suggestions from code review
* Update tests/modules/gstama/collapse/main.nf
* Update main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
|
2021-10-23 18:55:28 +01:00 |
|