Commit graph

2730 commits

Author SHA1 Message Date
GCJMackenzie
f479d4fb8d
Learnreadorientationmodel (#794)
* files for learnreadorientationmodel initialised for first commit

* finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted

* updated test data location

* versions file updated, test data added

* updated versions file, edited test file

* small formatting update to main.nf

* Update main.nf

* Update test_data.config

* updated tests main.nf

* Update test_data.config

* Apply suggestions from code review

* Update modules/gatk4/learnreadorientationmodel/main.nf

* Update modules/gatk4/learnreadorientationmodel/meta.yml

* fixed tests failing

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-07 13:55:06 +01:00
Sébastien Guizard
5a49d2c1bf
New module: isoseq3/cluster (#801)
* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 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 module accept one channel (primers moved into the first channel)

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add bamtools module

* 👌 IMPROVE: Ignore test data

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/cluster module

* 🐛FIX: Fix reports channel and add .pbi to it

* 🐛FIX: Fix report channel definition

* 👌IMPROVE: Move .pbi file into reports channel

* 👌IMPROVE: remove --use_qvs option from command line

* 👌 IMPROVE: Add in addParams removed options from command line

* 👌 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 module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: add singletons parameter and improve outputs

* 🐛 FIX: Update test with last module model

* 👌 IMPROVE: Add test tag

* 👌 IMPROVE: Update test data config

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Remove unused index

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 👌 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: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update code to new versions capture + better output channels

* 👌 IMPROVE: Update with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* 👌 IMPROVE: Clean output file names + correct typo

* 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
2021-10-07 10:06:02 +01:00
Sébastien Guizard
79d38a306b
New module: isoseq3/refine (#748)
* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

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

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 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 module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Fill contains args

* 👌 IMPROVE: Add one channel per output file

* 👌 IMPROVE: Minor updates

* 👌 IMPROVE: Minors Update

- Remove TODO from test.yml
- Remove useless piece of code

* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 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 module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Fill contains args

* 📦 NEW: Add isoseq3/refine module

* 👌 IMPROVE: Add parallelization

* 🐛 FIX: Correct Typo

* 👌 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 module accept one channel (primers moved into the first channel)

* 👌 IMPROVE: Assign a value channel to primers input 

Improve workflow code readability

* 👌 IMPROVE: Update to the version of templates

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Remove pbi from input files

* 👌 IMPROVE: Update test file

* 👌 IMPROVE: Add one channel per output file

* 👌 IMPROVE: Minor updates

* 👌 IMPROVE: Minors Update

- Remove TODO from test.yml
- Remove useless piece of code

* 🐛 FIX: Remove unwanted files

* 🐛 FIX: Protect \

* 🐛 FIX: Remove test files

* Apply suggestions from code review

* Apply suggestions from code review

* Update tests/modules/isoseq3/refine/test.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-06 11:13:48 +01:00
Jose Espinosa-Carrasco
84f2302920
Correct parsing versions with trailing zeros (#795)
* Correct parsing versions with trailing zeros

* Fix test

* Update modules/custom/dumpsoftwareversions/main.nf

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

* Fix tests and go back to output versions.yml

* Update tests/test_versions_yml.py to use BaseLoader

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-06 08:16:36 +02:00
Sébastien Guizard
bcf2681b03
New module: pbbam/pbmerge (#752)
* 👌 IMPROVE: Add some pacbio test files

* 📦 NEW: Add pbbam/pbmerge module

* 🐛 FIX: Add optional arguments to command line

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config and test script

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Add some pacbio test files

* 📦 NEW: Add pbbam/pbmerge module

* 🐛 FIX: Add optional arguments to command line

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update module to last template version

* 👌 IMPROVE: Update test data config and test script

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update and clean code

* 🐛 FIX: Update module path in test

* 🐛 FIX: Add missing () + correct module path in test

* 👌 IMPROVE: Update pbmerge from version 1.6.0 to 1.7.0

* 👌 IMPROVE: Change output filename suffix for something more generic

* 🐛 Update test.yml

* Apply suggestions from code review

* Update tests/modules/pbbam/pbmerge/test.yml

* Update tests/modules/pbbam/pbmerge/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 23:16:45 +01:00
GCJMackenzie
aa32a8a72e
new module: gatk4/calculatecontamination (#778)
* initiated files for calculate contamination

* pushing local repo to remote

* created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data

* added option and tests for outputting optional segmentation file

* saving for test push

* versions updated, test data added

* Update main.nf

* fixed versions info, should report correctly now

* small update to main.nf outputs formatting

* Apply suggestions from code review

* Update test_data.config

* Apply suggestions from code review

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:52:00 +01:00
Robert A. Petit III
053797510d
add pirate module (#777)
* new module pirate

* remove md5 check for non reproducible binary files

* get those to-dos out

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:28:25 +01:00
Robert A. Petit III
e77b3d72f3
add spatyper module (#784)
* add spatyper module

* lint fix

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:21:35 +01:00
Robert A. Petit III
ad0f4d2e24
patch output extension in csvtk/concat (#797)
* patch output extension

* Update main.nf

* Update main.nf

* Update main.nf

* whitespace

* Update main.nf

* Update main.nf

* Update modules/csvtk/concat/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:15:08 +01:00
Robert A. Petit III
0ba88fb869
add roary module (#776)
* add module roary

* Update meta.yml

* Update meta.yml

* Update meta.yml

* Update meta.yml

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:08:47 +01:00
Robert A. Petit III
8d04c34934
add ismapper module (#773)
* add ismapper module

* Update main.nf

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:55:41 +01:00
Robert A. Petit III
8179bab819
add csvtk/concat module (#785)
* add csvtk/concat module

* Update modules/csvtk/concat/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* allow alternate delimiters

* Update main.nf

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

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

* Update modules/csvtk/concat/main.nf

* Apply suggestions from code review

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:48:47 +01:00
Robert A. Petit III
bb7beff497
add hicap module (#772)
* add hicap module

* add info on optional inputs

* fix typo

* Update meta.yml

* Update main.nf

* Update meta.yml

* Update modules/hicap/main.nf

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

* Update modules/hicap/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:42:09 +01:00
Robert A. Petit III
7d98bf1d7d
add mashtree module (#767)
* add mashtree module

* remove todo

* whitespace adjustment

* remove un-reproducible md5sum

* Update main.nf

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:27:30 +01:00
Abhinav Sharma
3868c3ab4b
Add gtdbtk/classifywf module (#765)
* initial commit [ci skip]

* reuse the modules code from nf-core/mag [ci skip]

* add contextual information for the module [ci skip]

* add stubs to avoid downloading db [ci skip]

* trigger test

* iterate on tests [ci skip]

* itereate tests [ci skip]

* add bins [ci skip]

* fix stubs [ci skip]

* interation on tests with stubs [ci skip]

* use the existing pattern and fasta for input

* accomodate the new version file format

* use variable for the stub [ci skip]

* update the versions file in meta.yml

* Accomodate code review regarding publishDir function [ci skip]

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

* remove extra newline

* use bioconda channel

* update the description for filtered file

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update modules/gtdbtk/classifywf/meta.yml

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

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:23:01 +01:00
Lee Katz
f20c427339
added classic mlst module (#742)
* added classic mlst module

* removed nf-core TODO comments

* included drpatelh suggestions

* adjust version capture identation

* update main to pass lint

* follow output expected by test.yml

* suggested prefix change from rpetit3

* Apply suggestions from code review

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:49:46 +01:00
Jose Espinosa-Carrasco
714ec6823e
Fix sortmerna docker container pointer (#791) 2021-10-05 12:05:37 +02:00
Harshil Patel
a38508fcbb
Update SortMeRNA to 4.3.4 (#790) 2021-10-05 10:36:14 +01:00
Harshil Patel
515793c73e
Fix bug with SortMeRna not working on a single db file (#788)
* Fix bug with SortMeRna not working on a single db file

* Remove tag for instances when running just to create index
2021-10-04 12:37:21 +01:00
Harshil Patel
49da864287
Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
Harshil Patel
cf15ece503
Address Jose's comments in #780 (#781)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names

* Address Jose's comments in #780
2021-10-01 15:54:50 +02:00
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
Harshil Patel
de14533964
Fix version command for qualimap/rnaseq (#779) 2021-10-01 13:29:02 +01:00
Jose Espinosa-Carrasco
5b1cea7f7f
Add bbmap/bbsplit module (#771)
* Add bbmap/bbsplit module

* Conda complains about md5sum

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-30 13:37:35 +01:00
James A. Fellows Yates
01cc326c23
add Amps (#768)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start work, continue once on non-mobile internet

* finished and working on conda

* Update modules/amps/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-30 12:54:16 +02:00
Ramprasad Neethiraj
216dc8c984
remove cpu restrictions (#760)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-30 10:26:52 +02:00
Harshil Patel
22ec5c6007
Dump version for /custom/dumpsoftwareversions module itself (#764) 2021-09-30 09:00:33 +01:00
Harshil Patel
5a757b2981
Fix tyop in custom/dumpsoftwareversions (#762)
* Add custom/dumpsoftwareversions modules for nf-core pipeline template

* Remove md5sums due to differing NF versions

* Fix tyop in custom/dumpsoftwareversions
2021-09-29 14:35:43 +01:00
Harshil Patel
b2c2d4deb4
Add custom/dumpsoftwareversions modules for nf-core pipeline template (#761)
* Add custom/dumpsoftwareversions modules for nf-core pipeline template

* Remove md5sums due to differing NF versions
2021-09-29 14:27:00 +01:00
Harshil Patel
b932210f27
Fix flash and cat/fastq modules (#759)
* Fix version commands: round 3

* Fix seqkit/split2 modules

* Fix flash and cat/fastq modules

* Remove md5sums on gz files
2021-09-28 21:14:11 +01:00
Robert A. Petit III
5c463ca6b4
few version and test data config fixes (#758)
* update kleborate version info

* fix stderr capture

* few more version fixes

* fix version info on more tools
2021-09-28 20:42:04 +01:00
Gregor Sturm
c3687ef54b
fix more ver yml (#757)
* Fix featurecounts

* whitespace change to trigger CI on yara/mapper

* update test yaml
2021-09-28 20:25:10 +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
512f5dfc27
Better error message for FileNotFoundErrors (#755)
* Better error message for FileNotFoundErrors

* Update tests/test_versions_yml.py

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update test_versions_yml.py

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-28 16:51:35 +02:00
Harshil Patel
9c31cf1566
Fix version commands: round 3 (#754)
* Fix version commands: round 3

* Fix seqkit/split2 modules
2021-09-28 14:37:47 +01:00
James A. Fellows Yates
e971f538a9
Module new version reporting fixes (#753)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Fix IQ tree

* Fix picard markdup and merge sam

* Fix plink/vcf version

* Fix plink version output

* Fix prokka version command

* Fix pydamage

* Try fixing markduplicates

* Fix snpEff

* Fix vcftools version

* Fix pydamage and filtersamreads test run

* Fix MarkDuplicates tests

* Add missing unsorted checks

* Remove MD5 sym due to stochasicity in BAM file
2021-09-28 10:51:19 +01:00
Harshil Patel
3c5492b4a3
Fix more version commands (#750)
* Fix outstanding tests

* Fix more version commands

* Fix remaining modules
2021-09-28 06:56:27 +01:00
Harshil Patel
43c2779258
Fix version commands (#749)
* Fix version commands

* Fix version commands: again
2021-09-27 22:10:37 +01:00
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
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
Gregor Sturm
d73a988ff7
Cover case when processes have been imported under different name (#744)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:40:50 +01:00
Gregor Sturm
3d0b873584
Run CI only on pull-requests and on the master-branch. (#743)
* Run CI only on pull-requests and on the master-branch.

* also for the other workflows
2021-09-27 08:03:30 +02:00
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
Chris Cheshire
4866421777 Merge remote-tracking branch 'nf-core/master' 2021-09-23 09:54:26 +01:00
Stephen Ficklin
ca53f7525b
Diamond (#710)
* Added diamond

* minor tweaks & yml fix

* Fixed spacing issues due to failing lint

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/blastx/main.nf

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

* Update modules/diamond/makedb/main.nf

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

* Update modules/diamond/makedb/main.nf

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

* Update tests/modules/diamond/blastp/main.nf

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

* Update tests/modules/diamond/blastx/main.nf

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

* Update tests/modules/diamond/blastx/main.nf

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

* Update tests/modules/diamond/blastp/main.nf

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

* Update modules/diamond/blastp/meta.yml

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-23 09:13:04 +01:00
Ramprasad Neethiraj
25943a4c23
Add glnexus (#729)
* Add glnexus

* Fix lint error

* Refactor

* Suggested changes

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-22 13:31:01 +01:00
James A. Fellows Yates
5758e9f451
Unzip update (#730)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Change test dataset
2021-09-22 11:02:32 +01:00
Abhinav Sharma
77a2895785
Add module kleborate (#711)
* initial commit [ci skip]

* remove todo from the module files [ci skip]

* add a sample test case [ci skip]

* push the latest work [ci skip]

* bump kleborate build

* test passing with the new build for kleborate [ci skip]

* ready for review

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 20:45:42 +01:00
Robert A. Petit III
8e9d6cd5e4
Update agrvate to latest version (#728)
The new version of agrvate fixes an issue where sample names with a `.` (dot) in there names caused the name to be truncated

https://github.com/VishnuRaghuram94/AgrVATE/releases/tag/v1.0.1

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 20:28:53 +01:00
Abhinav Sharma
0d53a34eed
module fastani (#695)
* initiate agrvate module

* remove todos [ci skip]

* initiate fastani draft [ci skip]

* clean stubs [ci skip]

* interim commit [ci skip]

* accomodate the batch/per-sample processing [ci skip]

* use the meta map [ci skip]

* run first test [ci skip]

* remove extra spaces [ci skip]

* change output file name [ci skip]

* update the expected output [ci skip]

* update the files used for test [ci skip]

* fix typo [ci skip]

* test passing [ci skip]

* update the description

* remove extra files

* accomodate CR suggestions [ci skip]

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

* accomodate CR suggestions [ci skip]

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

* accomodate CR suggestions [ci skip]

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

* use meta map for batch analysis

* fix the tests

* rely upon tuples

* Apply suggestions from code review

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 20:20:26 +01:00