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Author SHA1 Message Date
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config (#1279) 
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-02-15 11:15:27 +00:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
Harshil Patel
9d0cad583b
Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

* Change syntax from task.ext.suffix to tast.ext.prefix

* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
 2021-12-02 12:39:55 +00:00
Harshil Patel
20d8250d9f
Update all modules to new NF DSL2 syntax (#1099) 
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
 2021-11-26 07:58:40 +00:00
Sébastien Guizard
ec15d0f9fd
Update module: pbccs (#1018) 
* 📦 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

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

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

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

* 🐛 FIX: Update meta.yml

* 🐛 FIX: Update reports filenames with chunk number.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-11-11 14:19:26 +00:00
Sébastien Guizard
8524e6b40f
Update of pbccs (#835) 
* 📦 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

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

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

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-10-23 19:09:41 +01:00
Kevin
3aacd46da2
Backfill software licenses meta (#876) 
* backfilled modules with meta.yml that had no license identifier

* harmonized BSD license names

* whitespace linting at modules/unzip/meta.yml:12

* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'

* Update modules/bcftools/index/meta.yml

`bcftools` is dual-licensed, use associative array to allow for multiple licenses

Co-authored-by: Michael L Heuer <heuermh@acm.org>

Co-authored-by: Michael L Heuer <heuermh@acm.org>
 2021-10-22 15:39:54 -07:00
Harshil Patel
49da864287
Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
Harshil Patel
7b3315591a
Remove def software lines and emit versions channel as plural (#780) 
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
 2021-10-01 14:04:56 +01:00
Jose Espinosa-Carrasco
cde1d827f9
Fix yml ver (#756) 
* Fix kallisto index tests

* Fix nanoplot

* Fix kallistobustools

* Fix pairix

* Fix plasmidid

* Fix pbccs

* Fix raxmlng

* Fix prokka

* Fix shovill

* Fix typo

* Deleted workflow by mistake added again
 2021-09-28 18:33:07 +02:00
Gregor Sturm
906577873b
Bulk update modules to use versions.yml (#739) 
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-09-27 09:41:24 +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