Commit graph

335 commits

Author SHA1 Message Date
GCJMackenzie
5b975cc20d
Add gatk somatic paired calling subworkflow (#1067)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

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

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

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

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

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

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* tests should now work after the yml update

* Update pytest_modules.yml

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-11-17 11:34:07 +01:00
GCJMackenzie
071b1d50a8
Add gatk somatic tumour calling subworkflow (#1064)
* initial commit to set up new branch

* save changes to checkout

* workflow working, still needs test.yml and meta.yml, also fix versions file

* subworkflow finished

* Update pytest_subworkflows.yml

* Update pytest_subworkflows.yml

* Update pytest_subworkflows.yml

* fix config subworkflow name

* Update main.nf

* Update pytest_subworkflows.yml

* fixed md5sum issue likely caused by gatk version update

* tumour changed to tumor

* old dir deleted

* Comments added to explain use of placeholders '[]'

* updated index names, input channel renamed to input

* Apply suggestions from code review

* updated to perform new subworkflow testing

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-17 11:07:17 +01:00
Sateesh
d5f6985607
add new nucmer module (#945)
* add new nucmer module

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* update tests with file produced by input

* Update main.nf

* Update meta.yml

Co-authored-by: Michael Cipriano <mcipriano@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 22:05:34 +00:00
JIANHONG OU
52c541b080
Cooler cload (#634)
* rebuild cooler cload.

* update test file path of cload.

* add pytest for cload

* update to version.yml

* update the test data path

* Update tests/modules/cooler/cload/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update modules/cooler/cload/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update tests/config/test_data.config

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update main.nf

Remove a lonely curly bracket.

* Update test.yml

Updated with new workflows.

* update the test files

* merge the conflicts.

* update the test.yml

* update for change of cooler/dump

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 21:43:55 +00:00
Robert A. Petit III
c2bba7a65d
add clonalframeml module (#974)
* add clonalframeml module

* Update main.nf

* try recommended gzip

* Update main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 19:43:53 +00:00
tamara-hodgetts
13b8a16f4a
Add module get_chrom_sizes (#1063)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* init getchromsizes

* add tests for getchromsizes

* Included meta.yml

* removed whitespace

* Moved getchromsizes to custom folder

* Update modules/custom/getchromsizes/main.nf

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

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 19:22:12 +00:00
Robert A. Petit III
2294ff7826
add ncbi-genome-download module (#980)
* add ncbi-genome-download module

* Update modules/ncbigenomedownload/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:32:53 +00:00
SusiJo
ad46010385
Added new module csvtk/split (#1014)
* added module csvtk/split

* removed todo statement

* adjusted meta map names

* changed tests to use generic input files

* added module in pytest

* updated test-data paths

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:29:55 +00:00
Edmund Miller
2af071ed0d
Fix subworkflows seperate from modules (#933)
* ci: Remove pytest_subworkflows

* ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow

Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* ci: Revert back to one job branch

* ci(align_bowtie2): Run tests that depend on bam_sort_samtools

* ci: Fix anchor not being created yet

* ci: Update sra_fastq tags and pytest_modules

* fix(bam_sort_samtools): Update nextflow.config with params

* test(subworkflows): Update gatk_create_som_pon tags

* ci: Point to subworkflow_hacks branch of nf-core tools

Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-11-15 18:18:46 +00:00
avantonder
527ccdb419
Add Miniasm module (#962)
* add racon

* add miniasm module

* edit miniasm module

* edit miniasm module

* Update tests/modules/racon/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update tests/modules/racon/test.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update modules/miniasm/meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update main.nf

Add some spaces.

* Update meta.yml

Correct DOI

* Update main.nf

* Apply suggestions from code review

* Update tests/modules/miniasm/test.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:50:56 +00:00
mjakobs
466b964b37
add Kronatools KTImportTaxonomy (#928)
* created and initialised krona module

* Added kronatools/ktimporttaxonomy module

* removing previous redundant work

* added contains info for html

* edited contains in test.yml

* Update get versions

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* remove old syntax

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* rewording module description

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* added detailed keywords

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* update syntax and tool version

* fixed meta.yml issues

* remove contains line from test.yml

* re-wrote module after nf-core/tools update - should work now

* removed md5

* Update modules/kronatools/ktimporttaxonomy/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* update meta save

* removed typo

* double quotes to single quotes around html

* re-ran test, which updated md5

* removed md5

* 'classifier' removed to fix linting

* update version

* removed erroneous ktimporttaxonomy2

* Updated input to include meta and database

* fixed tab issues in yaml

* added `contains` to test.yml

* edited `contains` in test.yml

* trying another `contains`

* retrying `contains`

* contains with extra line

* removed classifier from tag

* Apply suggestions from code review

* Update meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:40:46 +00:00
avantonder
8d9e8ae839
Add Medaka module (#992)
* add racon

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* Indentation

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update main.nf

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:26:37 +00:00
JIANHONG OU
4398056204
Macs2 calllpeak (#1038)
* Add tests and yml file for macs2/callpeak

* add format option for macs2

* update macs2/callpeak to accept format argument

* update test.yml

* update the container version.

* try to fix the issue in conda container.

* Update conda and containers

* Going back to previous container versions

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-11-15 18:17:40 +01:00
James A. Fellows Yates
632587a7fc
Add bamutil/trimbam (#1060)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

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

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-11-15 16:44:12 +00:00
louperelo
eff515891d
new module fargene (#1068)
* new module fargene

* Update main.nf

* Update modules/fargene/main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 16:42:48 +00:00
JIANHONG OU
7ad42eae1b
Cooler zoomify (#514)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/zoomify

* Apply suggestions from code review

* update functions.nf to new version.

* update the test file to test-datasets.

* update the test method of zoomify

* update dump test file.

* update version.txt to version.yml

* Update modules/cooler/dump/main.nf

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

* fix the output bug of versions update to pytest_modules.yml

* update the test file path and fix the output versions.

* Update modules/cooler/dump/main.nf

* indent

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:18:02 +01:00
mjakobs
f93c2f2604
add Krona_db module (#995)
* add Krona_db module

* removed md5 sum

* Update tests/modules/kronatools/kronadb/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* added input information

* removed trailing white spaces

* changed krona version to 2.7.1

* Apply suggestions from code review

* Update modules/kronatools/kronadb/meta.yml

* Update modules/kronatools/kronadb/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
2021-11-15 16:01:46 +00:00
Sébastien Guizard
4a9bfec61d
New module: Ultra (#871)
* 👌 IMPROVE: Update .gitignore

* 📦 Add ultra module

* 👌 IMPROVE: Update test input

* 👌 IMPROVE: Update and clean code

- Update to last versions.yml file
- Update meta.yml
- Correct typos

* 👌 IMPROVE: Update output channels + Rename following subtool

* 👌 IMPROVE: Remove old ultre files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 👌 IMPROVE: Remove old ultra files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 🐛 Fix: add unsaved modifications

* 🐛 FIX: Remove one inconstant md5sum

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Remove md5sums for pickle files (not constant).

* Update modules/ultra/pipeline/main.nf

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

* Update modules/ultra/pipeline/main.nf

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

* 👌 IMPROVE: update output directory, update meta.yml

* 👌 IMPROVE: Use modules to gunzip and sort gtf

* 🐛 FIX: Set up channel correctly

* 👌 IMPROVE: Remove pickles files and databases

Those data might be useful in a debugging purpose.

* Apply suggestions from code review

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 15:57:58 +00:00
Michael J Cipriano
0754d49db8
Initial commit mummer module (#940) 2021-11-15 16:53:41 +01:00
santiagorevale
1a4c7cec1b
New modules added: issues #200 and #310 (#884)
* New modules added: issues #200 and #310

* Update main.nf

* Update meta.yml

* Update tests/modules/gatk4/genotypegvcfs/main.nf

* Apply suggestions from code review

* Update main.nf

* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config

* Some minor changes on one of the test files I forgot to include

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
JIANHONG OU
a6ca2b006b
Cooler merge (#515)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/merge

* remove the bin_size from metadata.

* update the test_data to test-datasets

* update pytest_modules.yml

* update the test file from single input file to two input file.
update the output file from hdf5 to bedpe.

* update the version.txt to version.yml and functions.nf

* change version.yml to versions

* update the test file path and fix the output versions.

* Update meta.yml

Correct "version" to "versions"

* Update main.nf

Fix typo

* Update main.nf

Remove some spaces

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-15 15:18:43 +00:00
Robert A. Petit III
b5b3ff16ce
add module for fastq-scan (#935)
* add module for fastq-scan

* change fastq to reads

* remove uncompressed support

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:41:36 +01:00
Robert A. Petit III
7be60774b6
add module for tbprofiler (#947)
* add module for tbprofiler

* Update test.yml

* Update meta.yml

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:35:55 +01:00
James A. Fellows Yates
2c3c87a10f
Add leehom module (#1052)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add leeHom module

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/leehom/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:26:06 +01:00
Ilya Pletenev
c48244b677
Add new module 'ataqv/ataqv' (#998)
* Add new module 'ataqv/ataqv'

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 12:51:40 +00:00
alexandregilardet
94851901d5
add new module pmdtools/filter #847 (#963)
* commit but won't be used because pmdtools should have a submodule

* added submodule pmdtools/filter

* removed pmdtools module created before deciding to design two submodules

* oops forgot to remove a TODO

* removed white space meta.yml, removed v in version and manually added submodule /filter to test

* Update pytest_modules.yml

* Update main.nf

added split_cpus for multi-tools module resources

* Update test.yml

added .pmd extension to match modules/ main.nf

* Update test.yml

update md5sum

* Update singularity and docker build in main.nf

From build 4 to 5 in order to match the conda one

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update main.nf adding samtools version

we need both pmdtools and samtools versions

* Update main.nf remove .pmd extension

* Update test.yml md5sum

Because file extension changed

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
Robert A. Petit III
4bd530135f
add ngmaster module (#1024)
* add ngmaster module

* add docker container

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 11:25:50 -07:00
Maxime Borry
56d5eb9834
Add Bacillus fragilis alignments to test_data.config (#1054)
* 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>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

* add bacillus fragilis alignments

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 17:40:07 +01:00
Mei Wu
7fdeed5b79
Picard/collecthsmetrics (#927)
* added template

* integrated module

* added fasta index info

* test works, have placeholder data for baits until test-data PR is merged

* added new files to config

* updated test files

* fixing fails 

* okay final fix here on the md5sum :face_palm:

* md5sum variable

* update meta.yml to reflect consistency to main.nf

* reverted version so conda works

* Apply suggestions from code review

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* md5sum can't be generated consistently for output

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-10 10:52:54 +01:00
Maxime Borry
b399f22af2
Add new module: cmseq/polymut (#918)
* 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>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* first cmseq commit

* compressing and removing not reproducible md5sums

* save intermediate work

* follow symlinks while decompressing

* add cmseq/polymut

* add polymut

* add extra test with optional input file

* remove metabat2

* Update modules/cmseq/polymut/main.nf

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

* Update modules/cmseq/polymut/meta.yml

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

* Update modules/cmseq/polymut/meta.yml

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

* fix file extension

* Update modules/cmseq/polymut/meta.yml

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

* add test without bam index

* split tests in workflows

* answer PR review

* report version from variable

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 16:12:51 +01:00
Benjamin Wingfield
6bb4a6a7ee
Implement plink/extract module (#901)
* Implement PLINK_EXTRACT module

* fix plink version number

* Update main.nf

* Update test_data.config

* Update modules/plink/extract/main.nf

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

* just use one channel

* fix test with new channel input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 14:03:13 +00:00
anan220606
6d3d8306e1
Add new module Mapdamage2 (#975)
* Fitst attempt at mapdamage2

* Add new module mapdamage2

* Removed __pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc

* Modify main.nf and meta.yml

* Modify main.nf and meta.yml

* Modify main.nf and meta.yml

* Modify meta.yml

* Update pytest_modules.yml

* Apply suggestions from code review

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

* edit the meta.yml and main.nf after reviews

* Update meta.yml

* Update meta.yml

Co-authored-by: AIbrahim <AIbrahim@apate.hki-jena.de>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-09 14:05:23 +01:00
GCJMackenzie
9573cb1bec
Add panel of normals subworkflow (#1044)
* commiting changes to switch branch

* commit to setup remote branch

* first draft of the sompon workflow

* keep branch in line with gendb bugfixing

* Update test.yml

* tidy up main.nf

* fixed md5sum

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-11-09 10:16:43 +00:00
Maxime Borry
e0ada7d219
New module: metabat2 (#875)
* 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>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 21:08:26 +01:00
Robert A. Petit III
c10f9eb817
add lissero module (#1026)
* add lissero module

* Update test.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:52:07 +01:00
Robert A. Petit III
8ca8da46c2
add emmtyper module (#1028)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:43:15 +01:00
Robert A. Petit III
729d9ae450
add meningotype module (#1022)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:44:26 +01:00
Robert A. Petit III
22aa168622
add scoary module (#1034)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 16:34:39 +01:00
Lasse Folkersen
e560fbbc3e
Imputeme (#882)
* first commit with imputeme as a module. Extensive re-write of imputeme-code, resulting in release v1.0.7 that is runnable in the next-flow framework.


Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Pontus Freyhult <pontus_github@soua.net>
2021-11-05 10:25:54 +01:00
Francesco L
02892ef654
New module: Samblaster (#954)
* add base code from samblaster

* added test yml

* fixing versions files, should this be the cause of online lint failures

* removed tmp files that shouldn't be there

* fixing output file name - 1

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

* fixing output file name - 2

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

* fixing output file name - 3

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

* fixing output file name - 4

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

* fixing output file name - 5

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

* fixing output file name - 6

* fixed indent

* fixed input name and updated test.yml file with new name

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-04 18:18:56 +01:00
Robert A. Petit III
fc4f3e8822
add seqsero2 module (#1016)
* add seqsero2 module

* correct lint errors

* Update modules/seqsero2/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* set output directory

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-04 07:49:30 +00:00
James A. Fellows Yates
08b71fa85f
New module: gunc run (+ gunc downloaddb) (#880)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add GUNC download_db and run commands

* Bump with version without zgrep

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* Harshil formatting

* 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>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-03 17:01:23 +01:00
Maxime U. Garcia
9767b081b9
Merge freebayes subtools (#1015)
* feat: merge freebayes subtools

* fix: typo

* assess comments from review

* fix: path to module
2021-11-03 11:22:06 +01:00
Simon Pearce
374d81e0b3
readcounter module for hmmcopy (#1001)
* readcounter module for hmmcopy

* Changed version number

* Fix indentation

* Update main.nf

* Update modules/hmmcopy/readcounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 11:01:13 +00:00
Simon Pearce
cac6dc83bb
gccounter module for hmmcopy (#1003)
* hmmcopy gccounter working

* Update modules/hmmcopy/gccounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

* Update main.nf

Changed version to 0.1.1 as the container says

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 09:59:25 +00:00
Simon Pearce
81d65d4978
Samtools fixmate module (#991)
* Samtools fixmate module

* Update modules/samtools/fixmate/meta.yml

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

* Update modules/samtools/fixmate/main.nf

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

* Update main.nf

* Update modules/samtools/fixmate/meta.yml

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

* Update meta.yml

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-01 12:12:14 +00:00
Harshil Patel
9fb26ae462
Add IDR module (#908)
* Add IDR module

* Add meta and implement main todos

* Modifying idr tests

* Update tests/config/test_data.config

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

* Update tests/config/test_data.config

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

* Update main.nf

* Update tests/config/test_data.config

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

* Update test with new file name

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-30 10:52:13 +02:00
GCJMackenzie
7afb962f0b
New module genomicsdbimport (#857)
* saving changes to checkout

* saving to sort out other branch

* removed yml tracking of files that cant be tracked due to directory name changing between runs

* test data added, ready for pr

* fix eol linting error

* Update modules/gatk4/genomicsdbimport/main.nf

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* merging with master

* update push to show progress

* tests now working untar able to pass data to genomicsdbimport

* commit to checkout

* tests updated, module reworked to simplify and emit updated gendb

* Apply suggestions from code review

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

* update meta.yml 

Priority of input options changed, updated to reflect this

* Update test.yml

name prefix changed in main script, test.yml updated to reflect this

* fix tests due to review changes

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-29 17:21:34 +01:00
FriederikeHanssen
3df4fe6085
add freebayes/somatic and update freebayes/germline (#990)
* add freebayes/somatic and update freebayes/germline to new syntax and cram

* add pytest

* update with new freebayes/germline path
2021-10-29 17:05:06 +02:00
louperelo
a4943a9e57
Mtnucratio (#986)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* add new module mtnucratio

* fix main.nf

* Apply suggestions from code review

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

* Apply suggestions from code review

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

* layout in main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-29 15:02:02 +02:00
avantonder
977d96ed0b
Add Racon module to nf-core/modules (#949)
* add racon

* add racon

* add racon

* add racon module

* add racon module

* edit racon module

* edit racon module

* edit racon module

* edit racon module

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-10-29 13:33:38 +01:00
Francesco L
460a3ed87b
Fgbio group reads by umi (#952)
* adding template for module groupreadsbyumi

* update modules with code

* strategy is required argument so moving it to input rather than options.args

* tests successful committing yml

* added meta to output

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 14:00:54 +02:00
Daniel Lundin
84cb78cc98
Khmer normalizebymedian (#985)
* Templates for new module

* pe only test passing

* only_pe and only_se passing

* only_pe, only_se, mixed passes

* Multiple pe + se tc passes

* Passing args works

* Add 'interleaved' to description

* Fixed linting message

* Update modules/khmer/normalizebymedian/main.nf

Good point.

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2021-10-29 13:23:34 +02:00
Francesco L
4b8c7ac7bd
Bam2fq (#958)
* added template for module

* update main

* added specific code

* wrong variable name in else script

* added tests for both split and nosplit

* docker test successful - updating yaml

* adding echo to version print
2021-10-29 10:46:34 +02:00
Sateesh
5b1fe84bc6
add new assembly scan module (#971)
* add new assembly scan module

* add newline endings

* fix newline ending

* add newline at end

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 10:01:23 +02:00
FriederikeHanssen
1662201102
Add gatk4/estimatelibrarycomplexity (#965)
* Add gatk4/estimatelibrarycomplxity

* forgot to add yml

* Fix placeholder
2021-10-28 17:49:27 +02:00
emnilsson
9402595711
New module seqtk/mergepe (#951)
* First step into creating a seqtk/mergepe module to interleave fastQ input

* First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task

* Modifications to test the new seqtk/mergepe module.

* Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work

* Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well.

* Fix trailing whitespaces

Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
2021-10-28 16:53:33 +02:00
Jose Espinosa-Carrasco
fd1189c2f5
Updating test file for optitype (#782)
* Provide an exisiting bam file for optitype

* Update main.nf

Attempt at fixing this with new testing data

* Trying slightly different approach

* Mini fixes, not sure whats wrong here

* Add bam file with NM tags in all reads for optitype

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
Co-authored-by: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
2021-10-28 14:24:52 +02:00
Gisela Gabernet
d5183a7fec
new module cellranger mkref (#896)
* add cellranger mkref module

* add cellranger mkref tests

* update test yml chksum

* fix module linting

* fix test yml

* fix getprocessname

* fix versions typo

* fix cellranger test.yml

* fix versions.yml

* test versions.yml

* fix grep version

* fix cellranger version

* add dockerfile and readme

* review container statement

* Update modules/cellranger/mkref/meta.yml

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

* add disclaimers

* change location dockerfile

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-28 13:33:57 +02:00
Gisela Gabernet
0b0f87c2f7
add porechop module (#914)
* add module main porechop

* update porechop main

* add porechop functions

* update meta porechop

* add test main porechop

* add porechop pytest yml

* add porechop test.yml

* Update modules/porechop/meta.yml

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* re-add porechop avoid conflict

* Update modules/porechop/meta.yml

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* fix prefix suffix

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-10-28 13:21:36 +02:00
louperelo
263bbe56d2
add new module samtools/depth (#950)
* add new module samtools_depth

* fixed main.nf for samtools/depth

* Apply suggestions from code review

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-28 12:53:21 +02:00
James A. Fellows Yates
e27553b989
Add module: dedup (#907)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add dedup (tests and version not working)

* Fix dedup and tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-28 12:10:21 +02:00
Francesco L
a0bc08732c
Rewritten module fgbio/fastqtobam (#916)
* added template for fastqtobam

* porting old code into new template

* update with missing getprocessname function

* test completed - updating all

* fixed linting issues

* improved reading

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 19:06:06 +02:00
Maxime U. Garcia
80d8e87fa4
adding new manta/germline + manta/tumoronly modules (#906)
* feat: all manta/single to modules

* fix module name

* fix module name

* fix: changes from review comments

* fix: test data
2021-10-27 18:24:48 +02:00
Daniel Straub
12a3f80f33
add filtlong (#919) 2021-10-27 17:00:11 +02:00
FriederikeHanssen
754db250a0
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912)
* remove params statement

* add manta/somatic module

* fix strelka target bed thing

* removing checksums should make this pass

* Update modules/manta/somatic/main.nf

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

* fix indentation

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 16:14:52 +02:00
Matthias Hörtenhuber
b552958341
add paraclu (#909)
* add paraclu

* remove TODOs

* add min_cluster as input parameter, remove option parameters

* add tool_dev_url
2021-10-27 15:48:49 +02:00
James A. Fellows Yates
bd2baa1e7c
New module: maxbin2 (#895)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Added, just need to finish tests once we have bacterial data

* Add prelim test data

* Fix version reporting

* Add tests based on proposed test-dataset

* Finalise new testdata

* Fix md5sum issue by removing it...

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-26 22:07:33 +01:00
James A. Fellows Yates
a740a6ff48
New module: checkm/lineagewf (#899)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Added but test failing due to null on output channel

* fix prefix variable

* Complete checkm_lineagewf

* Remove TODOs

* Add description of fasta_ext parameter

* Improve meta map for this context

* Update meta.yml

* Update modules/checkm/lineagewf/meta.yml

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

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2021-10-26 21:54:10 +01:00
Gregor Sturm
2ad98162f3
Notebook modules (#617)
* Draft rmarkdown module

* stub jupyter notebook module

* Create yaml file with params

* Update meta.yml for rmarkdown module

* Add comment on YAML

* Update notebooks module, clean up parametrize.nf

* Two separate channels for parameters and input files

* Fix Rmd render script

* Add tests for rmarkdown

* Fix tests for rmarkdown module

* Update checksums

* Fix tests for jupyter

* Test without Grab()

* Update software versions

* update rmarkdown dependencies

* Draft for multiple versions

* Fix indent of script

* Fix indent in rmarkdown script

* Emit version.syml

* Update modules/rmarkdown/main.nf

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

* Update modules/rmarkdown/meta.yml

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

* Update modules/rmarkdown/meta.yml

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

* Rename rmarkdown to rmarkdownnotebook

* Add rmarkdown mulled biocontainer

* Write sessionInfo to separate log file

* Update rmarkdownnotebook

* Sessioninfo does not have a stable md5sum

* Update jupyternotebook

* Update meta

* Add jupyternotebook biocontainers

* Handle Groovy Gstrings in parameterize

* Update to versions.yml

* Update functions.nf

* Fix versions yaml

* Fix EC lint

* Update modules/rmarkdownnotebook/main.nf

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

* Update modules/jupyternotebook/main.nf

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

* Use official test data

* Harshilify

* Make parameters channel clearer

* Apply suggestions from code review

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

* Apply suggestions from code review

* Update main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-24 20:51:56 +02:00
GCJMackenzie
3c8ca3fec4
Createsomaticpanelofnormals (#859)
* files created for createsompon, script written, meta written, still needs tests

* updated to 2.0.0 method input, however this requires a genomicsDB input now

* script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests

* versions updated, issue with test data not able to download directory

* updated tests to include repo-side data

* Apply suggestions from code review

* Update modules/gatk4/createsomaticpanelofnormals/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 19:30:14 +01:00
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
GCJMackenzie
7676d9d728
Filtermutectcalls (#796)
* first commit with files for filtermutectcalls initialised

* found missing test file that needs to be resolved

* saving config changes

* fixing pytest_module conflict

* finished module, just needs repository side tests added

* test data added, versions file updated

* modified to emit correct versions file

* Update main.nf

* Update test_data.config

* updated test script

* fixed main.nf

* Update main.nf

* Update main.nf

* removed whitespace from test script

* Update test_data.config

* Update .gitignore

* Update test_data.config

* tests changed to new names, main script edited to match comments on learnreads pr

* Update meta.yml

* Apply suggestions from code review

* Update main.nf

* Apply suggestions from code review

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:45:19 +01:00
Jose Espinosa-Carrasco
32f6191aca
New module: genrich (#877)
* Add genrich module

* Rearrange genrich module from genrich/genrich to genrich

* Remove copy/paste code

* Fix meta.yml

* Implement save_duplicates independently of -r opt
2021-10-22 12:22:02 +02:00
Benjamin Wingfield
4ed5e4eff3
New module: ucsc/liftover (#868)
* add liftOver module

* add liftover module tests

* fix getProcessName

* fix tests

* fix out of date function

* version numbers should be numeric

* drop versions.yml from test.yml

* Update modules/ucsc/liftover/main.nf

Remove software name variable

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

* Update tests/modules/ucsc/liftover/main.nf

Use test chain file

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

* add genome_chain_gz to test data config

* update md5sum for new chain test data

* Fix indentation in file declaration

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-21 18:04:15 +02:00
Chris Cheshire
4d89d6b2f0
I accidently deleted a branch before the PR merged for PR 800 (#881)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* Updated seacr callpeak to include a control threshold

* Whitespace

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
2021-10-21 12:28:59 +01:00
Maxime Borry
eb04a0f1f6
New module: freebayes (#818)
* add pydamage module

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-20 15:19:31 +02:00
James A. Fellows Yates
97fe899f79
fix: reduce number of required input files for damage profiler (#612)
* Reduce number of required input files for damage profiler

* Remove rebugging

* Add optional species list file.

* Working pending updated test-dataset update

* Add genome header to config
2021-10-20 10:02:30 +02:00
Harshil Patel
4e9e732b76
Add strelka/somatic module (#866)
* Add strelka/somatic module

* Fill out meta.yml properly
2021-10-18 22:34:23 +01:00
FriederikeHanssen
b6486ef8b4
Add compressed bed files (#864)
* add cram files to config

* Update tests/config/test_data.config

* Add compressed bed file

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-15 10:10:53 +01:00
FriederikeHanssen
d0e4ee3ccd
Add cram files to config (#862)
* add cram files to config

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-15 09:40:16 +01:00
Moritz E. Beber
c912117972
feat: add sub-workflow for SRA (#836)
* feat: add sub-workflow for SRA
* Combine prefetch and fasterq-dump into one sub-workflow
* tests: add sub-workflow to pytest config
2021-10-14 11:50:31 +02:00
Mei Wu
d1794d1934
Add TIDDIT cov (#822)
* added template for tiddit/cov

* test finished

* quick fix to meta info

* Apply suggestions from code review

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

* applying suggestions

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-13 12:59:35 +02:00
James A. Fellows Yates
7b1e84f7be
Add bcftools/index (#812)
* feat: add bcftools index

* Extend tests to also test gen for TBI

* Update meta.yml

* Update meta.yml
2021-10-13 10:40:04 +02:00
James A. Fellows Yates
359f721cc9
Add MEGAHIT (#810)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-12 16:06:06 +01:00
Moritz E. Beber
de997825de
Add a new module for fasterq-dump (#807)
* chore: use template to create fasterq module

* feat: add fasterq-dump process module

* docs: provide input and output descriptions

* docs: add comment on `--temp`

* fix: use correct variable

* tests: define test output

* refactor: address review comments

* refactor: remove vdb-config input

* chore: add new test data to config

* tests: define single-end and paired-end cases

* refactor: choose specific output

* tests: do not expect single FASTQ for paired-end

* feat: add compression

* Apply suggestions from code review

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

* tests: revert the test data name

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 14:20:58 +01:00
Sébastien Guizard
3a4935d21b
New module: bamtools/split (#798)
* 👌 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: 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 with new versions.yml file

* 🐛 FIX: Update meta.yml + correct typos

* Update modules/bamtools/split/meta.yml

Add bam, split, chunk tags

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

* 🐛 FIX: Correct meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-12 14:43:08 +02:00
Moritz E. Beber
07c0830057
Add a module for sra-tools prefetch (#714)
* chore: apply module template

* refactor: add NCBI settings to options

* docs: complete meta information

* feat: add prefetch process

* fix: correct bash commands

* tests: define the right tests

* style: move option definition to satisfy linting

* fix: extract version correctly

* fix: correct newline issues

* refactor: address review comments

* Apply suggestions from code review

* chore: add retrying via nf-core label

* refactor: validate download thoroughly

* refactor: remove vdb-config input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-11 22:30:41 +01:00
Edmund Miller
c19671dca9
Subworkflow Infrastructure (#662)
* feat(subworkflows): Add align_bowtie2 subworkflow

For testing CI setup

* test(align_bowtie2): Add initial list of changes to test

* test(align_bowtie2): Add initial test

* refactor: Use tags to run subworkflows ci

For every underlying module used by workflow and allow the modules
pytest-modules definition be the source of truth.

* refactor: Use individual directories for subworkflows

* docs(align_bowtie2): Add initial meta.yml

Copied most of it from the bowtie2/align module.

* fix(align_bowtie2): Fix module include paths

* test(bam_sort_samtools): Add initial test

* ci(bam_sort_samtools): Add modules that trigger the tag

* test(bam_stats_samtools): Add initial test

* ci(bam_stats_samtools): Add keys to pick up changes

* docs(bam_samtools): Add initial meta.yml

* test(align_bowtie2): Fix path to subworkflow

* test(align_bowtie2): Update entry point

* fix(bam_sort_samtools): Update include paths

* test(bam_sort_samtools): Fix path

* style: Clean up addParams

* test(samtools_sort): Add suffix for test

* test(align_bowtie2): Add samtools_options for suffix

* test(bam_stats_samtools): Update path

* test(bam_stats_samtools): Use stats input

Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow

* ci(linting): Skip module linting of subworkflows

* ci(linting): Clean up startsWith statement

* test(bam_stats_samtools): Use single end test data for single end test

* test(bam_stats_samtools): Add expected files

* test(align_bowtie2): Add paired-end test

* test(align_bowtie2): Sort order of output

* test(align_bowtie2): Update hashes

* docs(align_bowtie2): Fix typo

* test(align_bowtie2): Update samtools output names

* test(align_bowtie2): Remove md5sums for bam/bai

* feat(subworkflows): Add nextflow.configs

These can be used for default settings in the future. They can then be
included in the conf/modules.config so that the params don't have to be
duplicated in the root nextflow.config.

* docs(subworkflows): Include modules instead of tools

* fix: Update to versions

* chore(align_bowtie2): Remove duplicate tag

* style: Format yamls

* test(subworkflows): Only check versions for modules

* chore: Update subworkflows to match rnaseq dev

* fix(subworkflows): Update paths

* fix(bam_sort_samtools): Fix sort parameters for testing

* Apply suggestions from code review

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

* docs: Update TODOs with a message

* ci: Try using a matrix for strategy

* ci: Try passing an array

* Revert "ci: Try passing an array"

This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-08 16:02:42 +01:00
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
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
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