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8 commits

Author SHA1 Message Date
Sébastien Guizard
4ec8b025bd
New module: LIMA (#719) 
* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 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

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 👌 IMPROVE: Add channel for each output

* 👌 IMPROVE: Remove comments

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 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

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 🐛 FIX: Fill contains args

* 📦 NEW: Add module lima

* 👌 IMPROVE: Move .pbi output to reports channel

* 🐛 FIX: Fix report channel definition

* 👌IMPROVE; Remove options from command line

update test script with removed options

* 🐛 FIX: Add pbi input

* 👌 IMPROVE: Add parallelization to lima

* 👌 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

* 👌 IMPROVE: The accept one channel (primers move into the first channel)

* 👌 IMPROVE: Assign a value channel for pimers 

Improve code workflow readability

* 👌 IMPROVE: Update module to last template version

* 🐛 FIX: Correct Singularity and Docker URL

* 👌 IMPROVE: Update to the last version of modules template

* 👌 IMPROVE: Update test_data.config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: Fill contains args

* 👌 IMPROVE: Add channel for each output

* 👌 IMPROVE: Remove comments

* 🐛 FIX: Clean test_data.config

* Update modules/lima/main.nf

Add meta to each output

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update modules/lima/main.nf

Remove useless parenthesis

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* 🐛 FIX: Keep version number only

* 🐛 FIX: Reintegrate prefix variable and use it to define output file name

* 👌 IMPROVE: add suffix arg to check output files names

* 👌 IMPROVE: Use prefix for output filename

* 🐛 FIX: Set optional output

Allow usage of different input formats

* 👌 IMPROVE: Update meta file

* 👌 IMPROVE: Update test

One test for each input file type

* 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files

* 👌 IMPROVE: Update with last templates / Follow new version.yaml rule

* 🐛 FIX: Fix typos and include getProcessName function

* 👌 IMPROVE: Update .gitignore

* 👌 IMPROVE: Using suffix to manage output was not a my best idea

Add a bash code to detect extension and update output file name

* 👌 IMPROVE: clean code

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2021-09-27 16:14:35 +01:00
Gregor Sturm
ab67a1d41b
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 10:01:54 +01:00
Sébastien Guizard
bbf268c5d3
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 11:48:18 +01:00
Daniel Lundin
d7a3286a9a
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 11:21:24 +01:00
Chris Cheshire
1aa7ed187a seacr | Updated gitignore to ignore output folder 2020-12-17 14:23:07 +00:00
Gregor Sturm
f7c42ac4fd Add tests for fastqc module 2020-07-15 09:48:14 +02:00
Gregor Sturm
4ee6ddc7ab Update README 2020-07-14 10:55:38 +02:00
drpatelh
ef8c13a7d8 Fill out repo 2019-07-26 10:19:07 +01:00