Commit graph

3259 commits

Author SHA1 Message Date
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
James A. Fellows Yates
7830a4a80c
add: MALTEXTRACT (#725)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start maltextract module

* start tests

* Get tests working now we have test data

* Apply suggestions from code review

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

* Changes after review

* Update tests/modules/maltextract/main.nf

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

* Update tests/modules/maltextract/main.nf

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

* Update tests/modules/maltextract/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-21 19:57:27 +01:00
Harshil Patel
1d6f47ce54
Refactor cat/cat module (#723)
* Refactor cat/cat module

* Change gzip terminology
2021-09-21 11:17:00 +01:00
Daniel Lundin
b32c46c6a2
CAT CAT (#722)
* bbmap/align done

* Tests for single end and prebuilt index

* Write bam file directly

* Forgot to use all cpus for bbmap

* Test md5sums

* Added pigz support

* Update modules/bbmap/align/meta.yml

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

* process_medium and fastq

* cat/cat module

* Remove filter from CAT_CAT

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-20 21:02:22 +01:00
Michael L Heuer
60d8bd7c04
Update pangolin to 3.1.11 (#721)
* Update pangolin to 3.1.11.

* Update md5sum for test.pangolin.csv.
2021-09-20 19:59:05 +01:00
James A. Fellows Yates
4f0b02b7b5
Typo fix 2021-09-20 13:00:11 +02:00
James A. Fellows Yates
3a0cd9d75a
Module docs transfer - point people to website! (#720)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Transfer module docs to nf-core website

* Missed a hyperlink

* Update README.md

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

* Update README.md

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

* Update README.md

* Update README.md

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

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-20 11:57:57 +01:00
Daniel Lundin
97b803a8a7
Module to map reads with BBMap (#717) 2021-09-20 11:27:34 +02:00
GCJMackenzie
3c4eaec52b
Update for mutect2: add output channel for stats file (#716)
* added output channel for stats file, updated meta yml with description and test yml with check for stats file

* Update modules/gatk4/mutect2/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-17 09:56:56 +01:00
Maxime Borry
7e45cbf4d1
Add PyDamage filter (#713)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 15:05:49 +02:00
Maxime Borry
d9dfbe9d9d
Add pydamage analyze module (#705)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* simplify PR to analyze subcommand

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 14:03:51 +02:00
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
Abhinav Sharma
1840289068
module for agrvate (#693)
* initiate agrvate module

* remove todos [ci skip]

* remove todos and fix containers [ci skip]

* ready for testing


Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-16 12:42:23 +02:00
Mahesh Binzer-Panchal
e904107c22
Chromap patch (#712)
* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remove samtools version

* Add space

* Remove whitespace
2021-09-16 09:23:07 +01:00
José Fernández Navarro
e9c57083a0
Fix bug in gffread (#686)
* Fix bug in gffread that would cause it to fail if the input has .gtf as extension

* Update test.yml

* Update meta file

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 19:55:08 +01:00
fbdtemme
f4ec33ebc4
Fix kallistobustools version extraction (#691)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 17:56:12 +01:00
Robert A. Petit III
073bbf1b26
add staphopia-sccmec module (#702)
* add staphopia-sccmec module

* add additional test

* change output name

* Update main.nf

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 17:24:11 +01:00
Mahesh Binzer-Panchal
58134cb929
Chromap Module (#659)
* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remake chromap base files with new layout

* Copy chromap

* Copy index

* Add compression

* Update padding

* Update container

* Update chromap input test data

* Add chromap chromap tests

* Add padding

* Update comment

* update yaml file

* Remove TODOs

* Add fasta input to yaml

* Update YAML

* Remove comment, update container

* Remove comments

* Import Chromap index

* Update test.yml

* Fix read input

* Update test.yml

* Add bcftools/concat module. (#641)

* draft for bcftools modules [ci skip]

* initial test for bcftools concat

* Update the params for testing

* fix tests

* Accomodate code review [ci skip]

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

* Update the meta file and open PR for review

* Update the keyword

* Update the tags for module [ci skip[

* add threads

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

* add module for dragonflye (#633)

* add module for dragonflye

* fix tests for dragonflye

* Update test.yml

* Update meta.yml

* Update main.nf

* Update main.nf

* Update modules/dragonflye/meta.yml

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

* update typos. change quote from ' to ". (#652)

* Add bcftools/norm module (#655)

* Initial draft [ci skip]

* trigger first test

* update output file path

* Tests passing

* finishing touches for meta.yml and update checksum

* tweak checksum

* add threads to the module

* skip version info for matching test md5sum [ci skip]

* Add ref fasta and finalize the module

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

* Expansionhunter (#666)


Please enter the commit message for your changes. Lines starting

* adds expansionhunter module

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update test.yml (#668)

* Specify in guidelines one should split CPUs when module has n > 1 tool (#660)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Describe CPU splitting

* Update README.md

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

* More CPU examples

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

* Add dsh-bio export-segments module (#631)

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

* update: `BWA/ALN` (#653)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate.

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

* Update seqwish reported version to match bioconda version. (#678)

* Bbmap index (#683)

BBMap index module

* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remove unnecessary files

* Remove unnecessary files

* Update modules/chromap/index/main.nf

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

* Update modules/chromap/index/main.nf

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

* Update modules/chromap/chromap/main.nf

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

* Update tests/modules/chromap/chromap/main.nf

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

* Update tests/modules/chromap/chromap/main.nf

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

* Update tests/modules/chromap/chromap/main.nf

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

* Update modules/chromap/index/main.nf

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

* Remove pytest_software.yml

* Apply suggestions from code review

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com>
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 17:20:55 +01:00
James A. Fellows Yates
561f16fe74
update: MALT build version bump (#699)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Bump versions

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:46:29 +01:00
James A. Fellows Yates
26fc617983
Update: MALT_RUN (#706)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Bump MALT versions for MALT-run

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:37:46 +01:00
Abhinav Sharma
1bc3f6cf39
module: snp-dists (#697)
* initial commit for draft [ci skip]

* baseline code [ci skip]

* update the test [ci skip]

* finalize the description and all tests passing

* accomodate optional args [ci skip]

* fix the leftover todo statement

* Update modules/snpdists/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:36:49 +01:00
Daniel Lundin
3a8bfc1d33
Get rid of meta map from bbmap/index (#700)
Got rid of meta map from bbmap/index
2021-09-15 12:38:56 +02:00