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555 commits

Author SHA1 Message Date
SusiJo
3eff67f54d
Added new module snpsift/split (#1031)
* added new module snpsift/split

* added options.args

* added .vcf.gz to input

* removed test and updated to new NF DSL2 syntax

* Updated to new NF DSL2 syntax

* added option to join vcf files

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-17 09:08:14 +01:00
GCJMackenzie
54e0ac4ed9
add module: Variantrecalibrator (#1088)
* committing to pull updated nf-core files

* saving changes to checout other branch

* committing progress so far, difficulty with test data

* uploading to be used as draft PR

* fix linting error in meta.yml

* attempt to group reference inputs together

* updated input format for resources

* meta.yml updated with new resource names

* added output channel for recal index

* module only takes single vcf file input now

* committing to checkout

* update to new syntax, remove indel test for now

* updated to use memory options and new test data

* Update modules/gatk4/variantrecalibrator/main.nf

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

* Update main.nf

* Update modules/gatk4/variantrecalibrator/main.nf

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

* remove duplicate test keys from test_data.config

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-16 10:54:49 +00:00
GCJMackenzie
9f8d9fb615
Add applyvqsr (#1101)
* 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

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* add applyvqsr

* added memory options, new test data used

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-16 08:44:50 +00:00
Harshil Patel
67571c4e79
Add RSeqC tin.py module (#1174)
* Add RSeqC tin.py module

* Fix EC lint for unrelated hmmcopy module

* Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
Simon Pearce
ae92159762
New subtool: hmmcopy/generatemap (#1168)
* Initial structure

* Working with local singularity image

* Working generateMap.pl script

* Remote not working bioconda

* Working generateMap with biocontainer

* Lint changes

* Updated hmmcopy container version to be consistent

* Fix failing test

* Remove path to perl

* No hardpath to script

* Update main.nf

Moved version outside of process, add support for zipped fasta file

* Revert to not allowing gzip via pipe, as perl script can't cope

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2021-12-15 16:57:42 +01:00
GCJMackenzie
61376425fb
BugFix: add missing tbi output channel to genotypeGVCFs (#1153)
* 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

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-14 16:10:08 +00:00
Anan Ibrahim
1f3f2b18bb
Add new module macrel/contigs (#1109)
* Add new module macrel/contigs

* removed trailing whitespace

* removed whitespace

* linting cleanup

* Apply suggestions from code review

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

* Updated the test.yml

It didnt upload the updated version earlier for some reason :(

* Update test.yml

* Update test.yml

* Update test.yml as generated by pytest

* Update test.yml

* updated the version issue

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Update modules/macrel/contigs/main.nf

* Update pytest_modules.yml

* Update pytest_modules.yml

* Update modules/macrel/contigs/main.nf

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

* Zipped all fasta outputs

* Update main.nf

* Update test.yml

* Update test.yml

* Update main.nf

* Update main.nf (gzip -n)

* Update test.yml

* Update main.nf

* Update main.nf

* Update test.yml

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Apply suggestions from code review

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

Co-authored-by: darcy220606 <ananhamido@hotmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-09 13:17:50 +01:00
FriederikeHanssen
a9dd46f010
add gatk4/gatherbqsr (#1130)
* nf-core modules create

* add module files

* indent

* remove templte code

* manually revert pytest changes from tools

* manually revert pytest changes from tools

* add include statement back in

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 23:43:36 +01:00
Maxime U. Garcia
31d4099f38
Add subworkflows for ensemblvep and snpeff (#1124)
* greatly simplify syntax

* feat: add subworkflows to annotate (+ bgzip/tabix index) with ensemblvep and snpeff

* feat: get versions from all tools

* add commented infor for new annotation modules
2021-12-07 17:12:35 +01:00
Edmund Miller
f3ffa69b8d
Dragmap (#1108)
* feat(dragmap): Add initial hastable module

* feat(dragmap): Add initial align module

* test(dragmap): Remove md5sum

Forgot sam files have a header. Might pipe this through samtools.

* build(dragmap): Add mulled container

* chore(dragmap): Update prefix

* feat(dragmap): Output a bam file

* feat(dragmap): Add log files

* Update modules/dragmap/align/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-12-06 09:56:41 +01:00
Edmund Miller
e2ba70ed9a
Add Cell Ranger mkfastq, mkgtf, and count (#979)
* feat(cellranger): Add initial count module

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* feat(cellranger): Add mkgtf module

* test(cellranger): Fix count test with mkgtf

* fix(cellranger): Generalize gtf attribute filters

* chore: Add .gitignore for cellranger tar

* build(cellranger): Update dockerfile

https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/

* Apply suggestions from code review

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* Apply suggestions from code review

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

* Update modules/cellranger/mkgtf/main.nf

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

* style: Capitalize README

* test(cellranger): Update pytest_modules

* feat(cellranger): Add initial mkfastq module

* ci: Update pytest modules

* refactor(cellranger): Update modules to new syntax

* docs(cellranger): Update meta files

There is some terrible copy-pasting going on.

* fix(cellranger): Add args

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
Harshil Patel
20d8250d9f
Update all modules to new NF DSL2 syntax (#1099)
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

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

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

* Replace {task.cpus} with task.cpus

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

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

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

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

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
Annick Renevey
45985ff6f0
Peddy nf core2 2dev0 (#1048)
* Updated module to fit nf-core2.2dev0 templates

* Updated module to fit nf-core2.2dev0 templates

* Linked test files to nf-core/test-dataset branch:raredisease raw files

* Change order of input: vcf and tbi with meta, ped without

* Change order of input: vcf and tbi with meta, ped without/adapt test

* Change order of input: vcf and tbi with meta, ped without/adapt test, bugfix

* Indent and rename files

* Update modules/peddy/main.nf

Removed newline

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update pytest_modules.yml

* 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>
2021-11-21 20:14:09 +00:00
Florian De Temmerman
1455498152
CNVkit: Make targets file optional when running in WGS mode (#1030)
* Make targets.bed optional when running in wgs mode

* added test for cram

* Update test_data_config with new reference.cnn

* Update main.nf to allow tumor-only running

Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn

* re-writing previous changes, but now it wont crash the entire CI-setup

* fixing overlooked merge conflict

* last overlooked merge-conflict

* move all files to batch subfolder

* adding an optional input for a reference file (needed when running germline and tumoronly)

* minor typo

* update meta.yml

* aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal

* Update pytest_modules.yml

Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 19:56:57 +00:00
Abhinav Sharma
15fd90ffe8
Add phyloflash module (#786)
* initial stubs [ci skip]

* remove comments and add main command [ci skip]

* design iteration [ci skip]

* add new standard functions.nf [ci skip]

* update the version string [ci skip]

* accomodate the db stubs and single/double ends [ci skip]

* add FIXME for missing info [ci skip]

* Accomodate the results folder [ci skip]

* Update main.nf

* Apply suggestions from code review

* Update main.nf

* Apply suggestions from code review

* Add version file to stubs [ci skip]

* Tweak the output dir pattern [ci skip]

* Update modules/phyloflash/main.nf

* Update modules/phyloflash/main.nf

* Update modules/phyloflash/main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-21 19:43:58 +00:00
Robert A. Petit III
29c669766d
add bakta module (#1085)
* add bakta module

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:17:25 +00:00
Robert A. Petit III
5ebe62612c
add ectyper module (#948)
* add ectyper module

* fix-lint

* try zcat

* Update main.nf

* fix lint

* Update main.nf

* Apply suggestions from code review

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

* Update main.nf

* pass lint

* Update main.nf

* fix lint

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:14:02 +00:00
veitveit
7e56e38f2a first maxquant 2021-11-21 10:47:16 +01:00
Maxime Borry
72c94dbed9
Add new module: Das Tool (#1004)
* 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

* add dastool/scaffolds2bin

* add dastool

* remove non reproducible md5sum check for compressed files

* 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

* remove metabat2 from PR

* fix linting errors

* remove traling whitespace

* 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

* PR review updates

* update from PR review

* update test files

* add bacillus fragilis alignments

* switch tests to bacillus fragilis

* add string check

* update test string

* add pr comment answer

* last fixes for PR review

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>
2021-11-19 08:33:29 +01:00
Robert A. Petit III
f052dc445c
use underscores in anchors and references (#1080)
* use underscores in anchors and references

* Dummy change to trigger CI

* use dev branch

* underscore anchor
2021-11-18 18:09:09 +00:00
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
Robert A. Petit III
bb7beff497
add hicap module (#772)
* add hicap module

* add info on optional inputs

* fix typo

* Update meta.yml

* Update main.nf

* Update meta.yml

* Update modules/hicap/main.nf

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

* Update modules/hicap/main.nf

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

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

* remove todo

* whitespace adjustment

* remove un-reproducible md5sum

* Update main.nf

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

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

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

* add contextual information for the module [ci skip]

* add stubs to avoid downloading db [ci skip]

* trigger test

* iterate on tests [ci skip]

* itereate tests [ci skip]

* add bins [ci skip]

* fix stubs [ci skip]

* interation on tests with stubs [ci skip]

* use the existing pattern and fasta for input

* accomodate the new version file format

* use variable for the stub [ci skip]

* update the versions file in meta.yml

* Accomodate code review regarding publishDir function [ci skip]

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

* remove extra newline

* use bioconda channel

* update the description for filtered file

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update modules/gtdbtk/classifywf/meta.yml

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

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

* removed nf-core TODO comments

* included drpatelh suggestions

* adjust version capture identation

* update main to pass lint

* follow output expected by test.yml

* suggested prefix change from rpetit3

* Apply suggestions from code review

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:49:46 +01:00
Jose Espinosa-Carrasco
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
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
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
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
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
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
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
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
Daniel Lundin
97b803a8a7
Module to map reads with BBMap (#717) 2021-09-20 11:27:34 +02:00
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
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
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
James A. Fellows Yates
c485109d9b
Add module: bamaligncleaner (#676)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bamAlignCleaner module

* Add container tags

* Update modules/bamaligncleaner/main.nf
2021-09-15 10:31:49 +02:00
Abhinav Sharma
6ff995e93d
Add bcftools/query module (#670)
* initial commit [ci skip]

* add basic structure [ci skip]

* finalized the bcftools/query module

* add optional files [ci skip]

* Add the vcf index file as param [ci skip]

* update the md5sum for output file [ci skip]

* all tests passing
2021-09-14 09:19:01 +02:00
Davi Marcon
59ca7444cf
Adding plink/vcf module (#656)
* adding plink module using nf-core tool [ci skip]

* Restructures the project for plink/vcf (#1)

* Add version string for plink
* Create a plink/vcf module

* small tweaks on main.nf and started to test [ci skip]

* small changes on test args, local test with docker passed!

* Update plink/vcf module listing

* Update tag

* fix tags as per linting guidelines

* revert to the original state of tags

* adding --threads to `main.nf` and `meta.yml` information

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
2021-09-14 08:51:40 +02:00
GCJMackenzie
bd68797ffb
Mutect2 (#682)
* mutect2 files added, first draft of module code entered

* removing comment from main.nf

* removing comment from main.nf

* test added, commit made before editing yaml

* tests added, still needs final check and info/comments added

* gatk4 version changed to gatk4=4.2.0.0

* multiple sample support added, information added to module yaml file

* Update meta.yml

fixed linting error

* add keywords to meta.yml

* Corrections made to meta.yml

* removed whitespace from meta.yml

Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 16:16:23 +01:00
GCJMackenzie
1023a98b51
Getpileupsummaries (#689)
* first commit, added template files for new module

* created getpileupsummaries script, tests and both yml files

* fixed typo in meta.yml

* Update modules/gatk4/getpileupsummaries/meta.yml

changed gz_tbi to gz.tbi as suggested

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

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 16:04:14 +01:00
Abhinav Sharma
c5634ba99b
Add bcftools/view module (#669)
* initial commit [ci skip]

* add stubs [ci skip]

* Finalize the bcftools/view module

* accomodate optional files

* add optional region file

* refer the targets file in the tests

* all tests passing

* documen the optional parameters
2021-09-12 19:51:40 +02:00
Edmund Miller
669fb5caed
Homer Modules (#75)
* feat(homer): Add initial makeTagDirectory

* feat(homer): Add initial findPeaks module

* feat(homer): Update with new options

See 1d30e2c21a

* fix(homer): Correct findpeaks process name

* fix(homer): Takes a bam file instead of bed

* feat(homer): Add initial makeTagDirectory test

* fix(homer): Hardcode genome and configureHomer

I'd like to modularize configureHomer, but I need to figure out how
exactly the genomes work.

* fix(homer): bam => bed

Bam requires samtools to be present, which it's not in this docker image

* feat(homer): Add initial configureHomer script

* ci(homer): Add initial test

* test(homer): Reproducible configuration workaround

- I can't run both tests(one file and two files) at the same time because it breaks
- I can't copy the genome stuff from the configurehomer module because it's read only
- So I can't make the makeTagDirectory module depend on configureHomer

* test(homer): Add placeholder annotatepeaks

The required inputs are necessarily required for all workflows from what
I've used, but I'll need to look at the actual docs

* test(homer): Add missing B.bed

* test(homer): Rename two => groseq

Then all of the various workflows that homer provides can be e2e tested

* feat(homer): Add initial makeUCSCfile module

* test(homer): Add start to makeUCSCfile testing

* chore(homer): Add various cleanups

* test(homer): Rewrite annotatepeaks

Not passing yet

* test(homer): Rewrite configurehomer

* test(homer): Rewrite findpeaks

Still failing

* test(homer): Rewrite makeucscfile

Not passing yet

* test(homer): Rewrite maketagdirectory

All homer modules now follow the new structure. Time to make them pass.

* test(homer): Fix typo for workflow name

* fix(homer): Use correct container

* fix(homer): Accept fasta in maketagdirectory

Apparently all of the homer stuff can just take any old fasta and you
don't need to configure the genome ahead of time with configureHomer

* test(homer): makeTagDirectory passes now

* fix(homer): Update containers in makeucscfile

* test(homer): Rewrite makeucscfile

Takes input from maketagdirectory which is how the module should be used

* fix(homer): Update makeUCSCFile bedgraph path

* test(homer): Update makeucscfile expected output

* fix(homer): Update containers in findpeaks

* fix(homer): Change findpeaks args

The user is just going to have to know what they're doing for now

* test(homer): findPeaks rewrite with tagDir input

* test(homer): Update expected files for findPeaks

And bump filters

* style: Appease editorconfig

* ci: Remove old workflow

* tests(homer): Add md5sums

* test(homer): Add meta test

* style(homer): Capitalize HOMER

* docs(homer): Add maketagdirectory meta.yml

* docs(homer): Add makeucscfile meta.yml

* docs(homer): Add findpeaks meta.yml

* test(homer): Update to new test data standards

* chore: Remove stuff that got revived in the rebase

* chore: software => modules

* test(homer): Update tags

* test(homer): Update annotatepeaks

* ci: Fix uploading of artifacts

GitHub actions doesn't like the / in the tags

* test(homer): Remove annotate md5sum

This is failing and breaking new tests

* test(homer): Use bams instead of beds

* test(homer): Fix meta maketagdirectory

* test(homer): Fix input in all tests

* test(homer): Move back to bed files

Forgot samtools isn't present

* chore(homer): Add TODOs for tests

* test(homer): Add bed format arg

* test(homer): Update md5sums

* test(homer): Fix tags tsvs

* style(homer): Appease nf-core linting

* docs(homer): Be in line with what is in the main.nf file

Co-authored-by: Kevin Menden <kevin.menden@live.com>

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
Kevin Brick
0732028e15
Add bedtools/makewindows module (#658)
* Add bedtools/makewindows module
2021-09-07 14:36:06 -04:00
Daniel Lundin
0f59b07945
Bbmap index (#683)
BBMap index module
2021-09-03 09:28:28 +02:00
Michael L Heuer
bc7b5b3a12
Add dsh-bio export-segments module (#631)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-17 15:53:41 +02:00
Anders Jemt
b261c1f549
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>
2021-08-16 17:47:42 +02:00
Abhinav Sharma
0954204f9e
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>
2021-08-16 17:40:03 +02:00
Robert A. Petit III
653e9e05b1
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>
2021-08-16 11:51:30 +02:00
Abhinav Sharma
67cc3bd116
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>
2021-08-10 15:10:27 +02:00
James A. Fellows Yates
292e8eceb9
module: MALT/RUN (#646)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add MALT with incomplete tests

* Parameter typo fix

* Clean up test yaml

* Finish MALT module prior UNZIP and MALT_BUILD modiules

* Add required modules for tests

* Sync test out with malt-build

* Fix input parameters in tests based on final build module

* Update modules/malt/run/meta.yml

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

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-04 11:06:08 +02:00
James A. Fellows Yates
6913da9d2d
module: MALT/BUILD (#645)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Start MALT-build

* Start MALT build (missing meta files and outputs specS)

* Local tests

* Correct test map_type

* Finished module, just waiting for UNZIP module to finalise tests

* Correct tests in preparation for Unzip

* Ouptut log file too

* Update meta.yml

* Rename log file

* Rename log file

* Remove debugging stuff

* Add Unzip module

* Linting update

* Linting update

* Fix input db

* Fix db file in cmd

* Update modules/malt/build/main.nf

* Update modules/malt/build/main.nf

* Update main.nf
2021-08-03 16:24:19 +02:00
James A. Fellows Yates
4f1c1601cf
module: bwa/sampe (#625)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* Add sampe

* Fix container paths

* Update based on code review from @grst

* Update input docs
2021-08-02 15:37:48 +02:00
James A. Fellows Yates
8a2f01c416
module: bwa/samse (#626)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* Add bwa samse

* Fix container paths

* remove TODO comment

* Updated based on code from from @grst on bwa/sampe

* Clarify output docs
2021-08-02 15:21:23 +02:00
James A. Fellows Yates
e01a98a704
module: unzip (#642)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add unzip module

* Remove missing TODOs update mtea

* Apply changes after code-review from @grst

* Account for user trying to supply two input archives

* Remove debugging test

* Update modules/unzip/main.nf

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

* Correct output path

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-08-02 09:40:57 +02:00
James A. Fellows Yates
45dee96bdf
module: bwa/aln (#624)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Add bwa/aln module

* Also output reads as required with SAI

* fix container paths

* Sync bwa version samese/sampe

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-27 08:13:48 +01:00
Johnathan D
a21cc95c69
Add variantbam (#618)
* template created for variantbam (#616)

* Add bcftools reheader (#585) (#608)

* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

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

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

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

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* 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>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>

* fixed autogenerated biocontainter links

* variantbam module passing all tests/lints (#616)

* Added an optional output junction channel in STAR (#621)

* Added an optional output channel for chimeric junctions

* Fix in test.yml

* Apply suggestions from code review

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

* removed qcreport output

fixes #616

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-26 19:07:29 +01:00
Johnathan D
a813e2e3a6
Add bcftools reheader (#585) (#608)
* local tests and linting passing (#585)

* fix: picard filtersamreads input (#610)

* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

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

* fix test

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

* Added module arriba (#611)

* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

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

* added test for new header

* enhance module fastp: add `save_merged` (#598) (#614)

* enhance module fastp: add `save_merged` (#598)

* removed md5sum checks from log and json

* 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>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-23 22:24:19 +01:00
praveenraj2018
3cabc95d0e
Added module arriba (#611)
* Updated the version of STAR in align and genomegenerate modules

* Changes in test.yml

* Changes in test.yml

* Added module arriba

* Changes in test configs

* Added module Arriba for fusion detection

* Fixed review comments

* Added an output option for discarded fusions

* Resolved some conflits

* conflicts

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-22 15:19:42 +01:00
James A. Fellows Yates
3cc43838e1
module: picard filtersamreads (#602)
* Start work filtersamreads

* Refactored to allow optional input

* Use proper readlist test data

* Remove typo

* Fix if else condition

* Remove debugging code

* Fix container URLs

* Add required input specification meta

* Cleanup

* Apply suggestions from code review

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

* Fix suffixing

* Additional formatting tweaks

* Update modules/picard/filtersamreads/main.nf

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

* Update modules/picard/filtersamreads/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 15:22:19 +01:00
James A. Fellows Yates
1a26d48104
module: picard sortsam (#603)
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place
2021-07-21 13:48:07 +02:00
Harshil Patel
e4df336294
Add hifiasm module (#596)
* Add hifiasm module

* Tidy up module

* Add pacbio files to test_data.config
2021-07-20 21:50:22 +01:00
Johnathan D
2e619add87
Add samtools ampliconclip (#590)
* created template for `samtools/ampliconclip` (#584)

* All tests passing (#584)

* Linting fixed (#584)

* Final linting fixed (#584)

* Optional output flags moved to `input` (#584)

* typo fix (#584)

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-20 21:31:31 +01:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00
Svyatoslav Sidorov
95dfa7bc8d
Enhance bedtools (#557)
* 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

* 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

* Generalized intersect and genomecov

* Finished subtract and tests for intersect and genomecov

* Finished up meta YAMLs

* Replaced functions.nf in subtract

* do not add "." in prefix when suffix is set (#550)

when using the suffix option in the fastqc module it gets added with a "." to the ${meta.id}, this leads to sample name clashing when passing the fastqc output of raw and processed files suffixed with "trim" or "clean" to multiqc.
I suggest to remove the "." this would also be more consistent with the prefix def in most of the other nf-core modules.

##' Ref:
https://nfcore.slack.com/archives/CJRH30T6V/p1625129138043900

* Modules TLC (#551)

* Modules TLC

* Fix all the tests

* Fix linting failures (#552)

* Modules TLC

* Fix all the tests

* Fix linting failures

* Soft-link build files to bypass lint error

* Update software/rseqc/junctionannotation/main.nf

* Fix rsem (#555)

* bump bcftools filter

* fix bcftools

* rsem/preparereference

* added calculateexpression

* meta.yml and pytest_software

* paired end

* add test.yml

* fix rseqc/junctionsaturation (#553)

* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools

* Adapt linting action (#556)

* bump bcftools filter

* fix bcftools

* adapt module linting

* Update software/bedtools/genomecov/main.nf

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

* Update software/bedtools/genomecov/main.nf

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

* Update software/bedtools/genomecov/main.nf

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

* Update software/bedtools/genomecov/main.nf

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

* Update software/bedtools/genomecov/meta.yml

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

* Update software/bedtools/genomecov/meta.yml

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

* Update software/bedtools/genomecov/meta.yml

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

* Update software/bedtools/genomecov/meta.yml

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

* Update software/bedtools/genomecov/meta.yml

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

* Update software/bedtools/intersect/main.nf

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

* Update software/bedtools/genomecov/main.nf

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

* Update software/bedtools/genomecov/main.nf

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

* Update software/bedtools/intersect/main.nf

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

* Update software/bedtools/intersect/main.nf

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

* Update software/bedtools/intersect/main.nf

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

* Update software/bedtools/intersect/meta.yml

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

* Update software/bedtools/intersect/meta.yml

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

* Update software/bedtools/intersect/meta.yml

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

* Update software/bedtools/intersect/meta.yml

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

* Update software/bedtools/intersect/meta.yml

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

* Update software/bedtools/subtract/main.nf

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

* Update software/bedtools/subtract/main.nf

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

* Update software/bedtools/subtract/meta.yml

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

* Update software/bedtools/subtract/meta.yml

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

* Update tests/software/bedtools/genomecov/main.nf

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

* Update tests/software/bedtools/genomecov/main.nf

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

* Update tests/software/bedtools/intersect/main.nf

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

* Update tests/software/bedtools/intersect/main.nf

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

* Fixed variable names in intersect and genomecov

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: riederd <dietmar.rieder@i-med.ac.at>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-07-07 09:44:09 +01:00
Maxime U. Garcia
e0d820f9f4
Add snpeff (#546)
* feat: add snpeff

* fix: linting

* fix: tests

* fix: add csv output

* fix: add params information

* fix: improve script

* Update software/snpeff/environment.yml

* Update software/snpeff/environment.yml

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>

* 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>

* Apply suggestions from code review

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 13:40:55 +01:00
Maxime U. Garcia
7b4a28b6e8
feat: add VEP module (#547)
* feat: add VEP module

* fix: name

* fix: EC lint]

* feat: add info about params

* fix: params as params, not input

* fix: improve script

* Update software/ensemblvep/environment.yml

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>

* Apply suggestions from code review

* Apply suggestions from code review

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 14:11:11 +02:00
Mei Wu
3f4eccbf0f
Delly/call (#565)
* testing works but need to fix paths and add exclude list

* edited meta file and removed TODOs

* left over TODOs

* test passed, final push

* resolving initial comments

* Update software/delly/call/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 12:54:14 +01:00
Johnathan D
79f3a55f6e
Lofreq call (#564)
* created templates

* updated functions.nf to the one on dev

* Created test main

* Fasta added and docker, conda, singularity passing

* Fixed output version lint
2021-07-06 10:41:00 +01:00
Ravneet Bhuller
42adce7af1
Pull request for module: lofreq/callparallel (#562)
* first commit

* updated file

* edited files

* Update test.yml

* Update software/lofreq/callparallel/main.nf

* Update test.yml

* Update tests/software/lofreq/callparallel/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-06 09:51:38 +01:00
Johnathan D
fbab00238f
Lofreq filter (#559)
* Created module template (#558)

* Created meta and implemented main (#558)

* Conda test and lint passing (#558)

* Updated functions.nf to the one on dev (#558)

* Update software/lofreq/filter/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-05 10:24:45 +01:00
Ravneet Bhuller
cd8bacc90a
PR for lofreq/indelqual module (#539)
* first commit

* edited functions.nf

* edited functions.nf

* version line updated

* Update software/lofreq/indelqual/main.nf

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

* Update software/lofreq/indelqual/main.nf

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

* Update software/lofreq/indelqual/main.nf

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

* Update software/lofreq/indelqual/meta.yml

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

* Update tests/software/lofreq/indelqual/test.yml

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

* Update tests/software/lofreq/indelqual/main.nf

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

* updated files

* updated file

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-05 10:17:57 +01:00
Kevin Menden
b59e8054e4
fix rseqc/junctionsaturation (#553)
* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools
2021-07-02 13:31:09 +02:00
Kevin Menden
fce4e60864
Fix rsem (#555)
* bump bcftools filter

* fix bcftools

* rsem/preparereference

* added calculateexpression

* meta.yml and pytest_software

* paired end

* add test.yml
2021-07-02 13:09:48 +02:00
Harshil Patel
b5f6a1da79
Fix linting failures (#552)
* Modules TLC

* Fix all the tests

* Fix linting failures

* Soft-link build files to bypass lint error

* Update software/rseqc/junctionannotation/main.nf
2021-07-01 19:50:14 +01:00
Harshil Patel
b3278a1e63
Modules TLC (#551)
* Modules TLC

* Fix all the tests
2021-07-01 16:13:01 +01:00
James A. Fellows Yates
394273f173
damageprofiler (#545)
* Add damageprofiler module

* Fix tests

* Bump container hopefully with font fix

* Following code review
2021-06-30 09:46:24 +02:00
MGordon09
af4b8814b8
update muscle (#542) 2021-06-28 08:20:02 +02:00
Maxime U. Garcia
81aba5734c
Add modules bgziptabix (#544)
* feat: add modules bgziptabix

* fix: add module to config

* fix: lint

* fix: tests
2021-06-25 10:52:02 +02:00
MGordon09
4d711a1428
Add metaphlan3 module (#543)
* Add metaphlan3 module

* remove whitespace
2021-06-25 08:15:15 +02:00
JIANHONG OU
e0b7952b56
Pairtools select (#523)
* add software/pairtools

* create a branch for pairtools/select

* fix the different output of conda and docker.

* rmove the md5sum for gzip files.

* Update software/pairtools/select/main.nf

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

* update test file and documentation.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-23 15:58:31 +02:00
Svyatoslav Sidorov
01dc6a289d
Feat seqtk update (#503)
* 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

* 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

* Added seqtk/subseq and checking for seed in seqtk/sample

* Separate authors in software/seqtk/sample/meta.yml

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

* Align commans in output channesl software/seqtk/subseq/main.nf

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

* Define prefix in software/seqtk/subseq/main.nf

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

* Use prefix in output file name software/seqtk/subseq/main.nf

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

* Define suffix in options in tests/software/seqtk/subseq/main.nf

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

* Change output file name in tests/software/seqtk/subseq/test.yml

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

* Remove a to-do point from tests/software/seqtk/subseq/test.yml

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

* Added --no-name into gzip commands

* Update samtools from 1.10 to 1.12 (#530)

* feat: remove social preview image to use GitHub OpenGraph

* feat: update samtools from 1.10 to 1.12

* fix: CI tests

* fix: add meta.yml file for samtools/merge

* Update software/samtools/merge/meta.yml

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

* Update software/samtools/merge/meta.yml

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

* 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

* Added seqtk/subseq and checking for seed in seqtk/sample

* 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

* Separate authors in software/seqtk/sample/meta.yml

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

* Align commans in output channesl software/seqtk/subseq/main.nf

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

* Define prefix in software/seqtk/subseq/main.nf

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

* Use prefix in output file name software/seqtk/subseq/main.nf

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

* Define suffix in options in tests/software/seqtk/subseq/main.nf

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

* Change output file name in tests/software/seqtk/subseq/test.yml

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

* Remove a to-do point from tests/software/seqtk/subseq/test.yml

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

* Added --no-name into gzip commands

* Replaced functions.nf in seqtk/subseq

* Refreshed tests for sample and subseq

* Corrected paired-end test and YAML description for sample

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-14 12:23:15 +01:00
JIANHONG OU
d9e48b70ca
Pairtools restrict (#522)
* add software/pairtools

* create a branch for pairtools/restrict

* fix the different output of conda and docker

* remove customized code.

* add newline to Frag.bed file.

* change the folder of frag.bed.

* change \n to \r\n

* Remove work.frag.bed

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-06-10 19:39:35 +02:00
JIANHONG OU
580d1e194a
Cooler digest (#517)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/digest

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-09 11:39:22 +02:00
JIANHONG OU
8d4c6de50d
Cooler dump (#516)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/dump

* remove the bin size from metadata.
2021-06-09 11:14:17 +02:00
aleksandrabliznina
0745213729
New last/mafconvert module to convert MAF alignments. (#527)
* New last/mafconvert module to convert MAF alignments.

The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5)
format and converts them in another format (axt, blast, blasttab, chain,
gff, html, psl, sam, tab).

This new module is part of the work described in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency.
We will upgrade it later.

* Delete white space.

* Update the function.nf file to the dev version.
2021-06-09 08:38:57 +02:00
Charles Plessy
ca321ce69d
New module last/postmask to filter alignment files (#526)
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
filters alignments in a MAF file to remove those with too many masked
(lower-case) positions compared with their score.

As other filter modules like `last/split`, its output file risks to
overwrite its input file as their names are constructed from the sample
ID when multiple filters are chained in the pipeline.  I added a check
that gives a clearer error message in this case.  Please let me know
what you think about; I can add this test to the existing LAST modules
as well.

This new module is part of the work discribed in Issue #464. During this
development, we fix the version of LAST to 1219 to ensure consistency.
We will upgrade it later.
2021-06-08 11:14:08 +02:00
Charles Plessy
f7ebc2fc48
New last/dotplot module for pairwise similarity plots (#529)
* New last/dotplot module for pairwise similarity plots

The `last-dotplot` tool takes a pairwise alignment in
[MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format,
possibly compressed with gzip, or in a tabular format produced by the
`maf-convert` tool, and produces a similarity dot-plot of the two
sequences in one of the graphical formats supported by the Python
Imaging Library.

A the tool guesses the output format by the file extension of the file,
which is constructed by the module at run time, I have used the `args2`
option to convey this information to the module.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence please ignore lint's version warning).

* Update the functions.nf file to the dev branch.

https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
2021-06-08 11:13:51 +02:00
Michael L Heuer
68c678de93
Remove docker.runOptions in favor of docker.userEmulation. (#525) 2021-05-27 18:29:17 +01:00
JIANHONG OU
a303c6ed5b
Pairtools sort (#524)
* add software/pairtools

* create a branch for pairtools/sort

* fix the different output of conda and docker.

* remove customized code.

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 18:25:23 +01:00
JIANHONG OU
9842a10833
Pairtools parse (#521)
* add software/pairtools

* create a branch for pairtools/parse

* fix the issue of bioconda output is different from docker.

* remove customized code from test.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 18:15:54 +01:00
JIANHONG OU
cc8439a167
Pairtools flip (#520)
* add software/pairtools

* create a branch for pairtools/flip

* fix the issue of PG line in output

* remove custom code from test.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 18:09:28 +01:00
JIANHONG OU
912f30e95a
Pairtools dedup (#519)
* add software/pairtools

* create a branch for pairtools/dedup

* remove dedup from the filename.
2021-05-27 17:51:27 +01:00
JIANHONG OU
18440df87a
add genmap/mappability (#509)
* add genmap/mappability

* Add index module.
Remove -w parameter from mappability module.

* change the output of genmap/index

* fix the lint error which can not handle stageAs.

* Apply suggestions from code review

* Update main.nf

* Update test.yml

* Update main.nf

* Update test.yml

* Update tests/software/genmap/mappability/main.nf

* Update software/genmap/mappability/main.nf

* Update software/genmap/mappability/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 22:12:10 +01:00
Charles Plessy
207930139a
New last/lastal module to align query sequences on a target index (#510)
* New last/lastal to align query sequences on a target index

`lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last)
suite.  It align query DNA sequences in FASTA or FASTQ format to a
target index of DNA or protein sequences.  The index is produced by
the `lastdb` program (module `last/lastdb`).  The score matrix for
evaluating the alignment can be chosen among preset ones or computed
iteratively by the `last-train` program (module `last/train`).  For
this reason, the `last/lastal` module proposed here has one input
channel containing an optional file, that has to be dummy when not used.

The LAST aligner outputs MAF files that can be very large (up to
hundreds of gigabytes), therefore this module unconditionally compresses
its output with gzip.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).

* Apply suggestions from code review

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

* Un-hardcode the path to the LAST index.

Among multiple alternatives I have chosen the following command to
detect the sample name of the index, because it fails in situations
where there is no index files in the index folder, and in situations
were there are two indexes files in the folder.  Not failing would
result in feeding garbage information in the INDEX_NAME variable.

    basename \$(ls $index/*.bck) .bck

In case of missing file, a clear error message is given by `ls`.  In
case of more than one file, the error message of `basename` is more
cryptic, unfortunately.  (`basename: extra operand ‘.bck’`)

Alternatives that do not fail if there is no .bck file:

    basename $index/*bck .bck
    find $index -name '*bck' | sed 's/.bck//'

Alternatives that do not fail if there are more than one .bck file:

    basename -s .bck $index/*bck
    ls $index/*.bck | xargs basename -s .bck
    find $index -name '*bck' | sed 's/.bck//'

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 22:10:48 +01:00
JIANHONG OU
34f555a26a
add software/pairix (#508)
* add software/pairix

* Update the functions.nf to new version.
Remove -p parameter and fix version output command.
fix the duplicated documentation.
2021-05-25 21:22:57 +01:00
aleksandrabliznina
4575e5455c
New last/split module to find split alignments. (#511)
* New last/split module to find split alignments.

The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
finds split or spliced alignments in a MAF file that is produced with, for
example, LAST `lastal` command.

This new module is part of the work discribed in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency. We will
upgrade it later.

* Update software/last/split/main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-24 20:15:57 +01:00
JIANHONG OU
ce68395240
add additional ucsc tools (#506)
* add additional ucsc tools

* Update software/ucsc/wigtobigwig/meta.yml

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Update the functions.nf and software name for ucsc/wigtobigwig and bigwigaverageoverbed.

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-05-20 15:39:33 -04:00
Charles Plessy
e75f88c68a
New module last/mafswap to reorder sequences in alignments (#500)
* New module last/mafswap to reorder sequences in alignments

The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reorders sequences in alignment files in Multiple Alignment Format.
When run without command-line arguments, it will swap the target and the
query sequences.  This is useful when turning a many-to-many alignment
into a many-to-one and then a one-to-one alignment in conjunction with
the `last-split` command (split, swap, split and swap again).

The LAST aligner outputs MAF files, but other tools also use this
format.  As MAF files can be very large (up to hundreds of gigabytes),
the module expects its input to be compressed with gzip and will
compress its output.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).

* Update MD5 sum.

Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of
an empty file compressed with `gzip --no-name`…  This happened
because I forgot to update the config file after correcting the
module… sorry !

* Apply suggestions from code review

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

* Change name as suggested in pull request.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 08:59:23 +01:00
aleksandrabliznina
b592cea30b
New last/train module to train alignment parameters. (#492)
* New last/train module to train alignment parameters.

The last-train command creates a parameter file that
will be used by last/lastal module for sequence alignment.
It takes indexed sequences and query sequences as input
and we use the metadata of both to create an id of the
parameter output file.

Submission of the LAST modules is discussed in more
details in the issue #464. For consistancy, we use LAST
version 1219 for this whole development and will upgrade later.

* Corrected files according to the nf-core v1.14 standards.

* Fixed function.nf file for the last-train module.

* Apply suggestions from code review

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

* Find index name.

* Correct after the input channels were changed.

* Use double underscore as a name separator.

Single underscores can happen in ids, therefore, we would like to keep two underscores.

* Remove extra spaces.

* Fixed the passing of the "score matrix" line.

* Apply suggestions from code review

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

* Update software/last/train/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 08:37:08 +01:00
praveenraj2018
598ca152ec
Intervallisttools (#491)
* added intervallisttools module

* add intervallisttools module

* arguments are now supplied using options.args

* removed java heapsize settings

* changes in main.nf and it is tested

* comment added

* Update software/gatk4/intervallisttools/meta.yml

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

* Update tests/software/gatk4/intervallisttools/test.yml

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

* review comment on tags in bedtointerval

* modified the test to get input from bedtointerval module

* Update software/gatk4/intervallisttools/meta.yml

* Apply suggestions from code review

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Apply suggestions from code review

* Update tests/config/pytest_software.yml

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Apply suggestions from code review

* Apply suggestions from code review

Co-authored-by: @praveenraj2018 <praveen.raj.somarajan@ki.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-05-12 11:44:36 +02:00
Jose Espinosa-Carrasco
cdff9a056d
Increase conda build time (#489)
* Add module description to yml

* Increase conda build time
2021-05-10 12:23:52 +01:00
MGordon09
1f465a63d0
Bbmap/bbduk (#487)
* bbmap/bbduk module created

* created bbmap/bbduk module

* updated main.nf

* changed test.yml tags

* removed whitespaces

* Adjusted main.nf spacing

* whitespace, tags

* fix optional files, tags, tidy code

* fix suffix

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-10 11:45:52 +01:00
Ravneet Bhuller
12ebce50f7
Request to review code for seqtk/sample module (#488)
* added files

* removed file

* added file

* changed files

* changed files

* edited file

* edited file

* edited files

* edited files

* edited files

* edited tags

* edited tags

* edited tags

* edited tags

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 23:55:35 +01:00
Jose Espinosa-Carrasco
f8ea9828cd
Add artic minion (#486)
* Add artic minion module

* Add fast5 to test data configuration

* Add test for artic minion
2021-05-07 16:37:35 +01:00
Harshil Patel
b6e4ecabba
Add Nextclade module (#484)
* Bump pangolin version

* Add nextclade to software list

* Add nextclade module

* Update md5sum for Pangolin due to version bump

* Adding some URL to meta.yml

* Adding new line at end of file

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-05-06 15:48:15 +01:00
Yuk Kei Wan
faf77d6fee
add nanolyse module (from nanoseq modules) (#471)
* add nanolyse modules

* add clean.fastq.gz path and md5sum

* fix errors

* remove unreproducible md5sum

* solve linting problem

* address PR suggestions

* GET_NANOLYSE_FASTA as a local module

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/meta.yml

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

* Update software/nanolyse/meta.yml

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

* Update tests/software/nanolyse/test.yml

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

* Update tests/software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* update to the version from nf-core/tools-dev

* input and output files cannot have the same names

* Update test.yml

* Update software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* Update test.yml

* revert

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-05 11:20:09 +01:00
Michael L Heuer
e3cf4c822c
Update dsh-bio modules to version 2.0.4 (#482)
* Update dsh-bio modules to version 2.0.4

* update docker tag

* update md5 checksums

* Update software/dshbio/filtergff3/main.nf

* Update software/dshbio/splitgff3/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 14:28:44 +01:00
Edmund Miller
bdee7804ca
build: Bump version to 21.04.0 (#481)
* build: Bump version to 21.04.0

Recent stable release https://github.com/nextflow-io/nextflow/releases/tag/v21.04.0

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 00:38:29 +01:00
Kevin Menden
5e86245388
updated paths to test data (#478)
* updated paths to test data

* Update test_data.config

changed file names
2021-05-03 07:13:07 +01:00
Yuk Kei Wan
6ad50f8ec4
Add stringtie merge module (from nanoseq modules) (#475)
* add stringtie merge module

* add md5sum and path for stringtie.merged.gtf

* fix errors

* try fixing stringtie check error

* add tag

* remove unreproducible md5sum

* address PR suggestions

* hopefully fix linting error
2021-05-03 07:18:51 +02:00
Charles Plessy
16d20a7cc4
New last/lastdb module to index sequences before alignment. (#476)
* New last/lastdb module to index sequences before alignment.

The `lastdb` command creates a sequence index for the LAST aligner
(https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ
format, and compression is handled automagically.  DNA or protein
sequences can be indexed.

The sequence index is a collection of files sharing the same basename.
This module sets the basename to the sample identifier (`$meta.id`) and
creates the index in a directory always called `lastdb`.  The module's
output channel then conveys a copy of the metadata and the path to the
`lastdb` directory.

Other modules will follow (see Issue #464).  The LAST aligner can align
proteins to proteins, DNA to DNA and can translate DNA align to
proteins.

* Remove trailing whitespace.

* Apply suggestions from code review

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

* Update as suggested in PR.

* Attempt to pass linting.

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 11:36:31 +01:00
Harshil Patel
466ab67808
Fixes for nanoseq modules (#479)
* Fix minimap2 index module

* Fix minimap2 index tests

* Fix graphmap2 index module

* Fix graphmap2 module

* Fix ECLint

* Fix bedtools bamtobed module

* Fix tests for bedtools bamtobed module

* Add tag for graphmap2 align module

* Fix EClint

* Fix qcat module

* Add md5sum for graphmap2/align module

* Remove non-started test data file

* Remove md5sum for graphmap2 align
2021-04-30 15:57:43 +01:00
Yuk Kei Wan
05f479f03a
add qcat module (from nanoseq modules) (#469)
* add qcat module

* remove md5sum(nom-reproducible)
2021-04-30 13:20:56 +01:00
Yuk Kei Wan
3f804ee667
add bedtools bamtobed module (from nanoseq modules) (#466)
* add bedtools bamtobed module

* fix erros

* fix linting problem
2021-04-30 13:20:31 +01:00
Yuk Kei Wan
a8720463ac
add graphmap index and align modules (from nanoseq modules) (#468)
* add graphmap index module

* add graphmap2/index

* add graohmap2 align module

* remove graphmap2 align md5sum
2021-04-30 13:18:58 +01:00
Yuk Kei Wan
05b067e907
add minimap2 index module (#467) 2021-04-30 13:18:11 +01:00
Florian Wuennemann
88dda738ac
Added kallistobustools/count (#409)
* Basic kb-python count functionality for scRNA-seq quantification working.

* Added tests and test data for workflow kite.

* Removed trailing whitespace

* Changed output channels to tuples with meta

Based on suggestions by @KevinMenden.

* Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message.

* Update software/kallistobustools/count/main.nf

@KevinMenden fixed wrong path definition

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Increased version of kb-python

* Updated tests with raw links.

* Fixed subtool referencing: kallistobustools/count

* Added newline

* Update software/kallistobustools/count/main.nf

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-04-30 07:27:17 +02:00
FriederikeHanssen
9ce4427275
Add gvcf index files (#472) 2021-04-28 20:23:10 +01:00
Daniel Lundin
d7a3286a9a
New module to use hmmalign from HMMER to align sequences (#470)
* Ignore vim tmp files

* Added hmmalign module, not yet tests

* Test output

* Replaced functions.nf for hmmalign with upstream

* Update software/hmmer/hmmalign/main.nf

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

* Update software/hmmer/hmmalign/main.nf

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

* Update software/hmmer/hmmalign/meta.yml

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

* Update tests/software/hmmer/hmmalign/main.nf

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

* Update tests/software/hmmer/hmmalign/main.nf

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

* Update tests/software/hmmer/hmmalign/test.yml

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

* Update tests/config/pytest_software.yml

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

* Update software/hmmer/hmmalign/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-28 11:21:24 +01:00
Jose Espinosa-Carrasco
d63ff4ba1b
Add artic guppyplex (#455)
* Adding artic guppyplex module

* Adding guppyplex tests

* Fix tests

* Correcting typo

* Fix lint

* Fix test

* Missing description

* Missing descriptions

* Update functions to last version as suggested

* Bump newest version of nanoplot
2021-04-27 15:57:34 +01:00
FriederikeHanssen
ae154b8c3f
Add human data paths (#458)
* Add new human data and fix sarscov paths

* Fix filename typo

* Apply code review

* replace index with to match sarscov data

* lower case

* indent everythin

* Adapt sarscov keys to new naming convention

* Update test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 15:30:43 +01:00
Kevin Menden
f7e3b8260c
change process.time for tests to 2h (#452) 2021-04-16 13:08:03 +01:00
Harshil Patel
defaca4f1b
Add ucsc/bedclip module (#450)
* Add ucsc/bedclip module

* Fix tests

* Fix nf-core lint
2021-04-15 22:04:59 +02:00
Anthony Underwood
2ed9b6ae28
Raxmlng (#443)
* new raxml module

* new raxml module

* pass in args for bootstrap and add test for support file

* remove unnecessary tag

* ensure tags meet guidleines

* Apply suggestions from code review

* Update to latest functions file

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-14 08:38:59 +01:00
Jose Espinosa-Carrasco
750bd8c3e3
Finish deeptools modules (#442)
* Adding bigWig and deeptools computeMatrix files to config

* Adding meta.yml for deeptools modules

* Add test for deeptools modules

* Fixing and reordering tags

* Fixing conda test that worked in local...

* Apply suggestions from code review

* Changing bigwig file pattern to include bigwig extension

* Saving after last change is a good practice

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 21:48:43 +01:00
Jose Espinosa-Carrasco
a9fcbd93cc
Move assembly test files from genome to illumina (#441)
* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes

* Update test path in config for illumina assembly files

* Update modules using assembly files

* Correctly setting path of assembly files

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 12:52:11 +02:00
Kevin Menden
1d874bb0d0
Finish rseqc modules (#439)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

* added rseqc/bamstat tests

* added tests/meta.yml for rseqc/inferexperiment

* added test/meta.yml for rseqc/inner_distances

* added meta.yml and tests/main.nf for junctionannotation (test not running)

* added test/meta.yml for rseqc/readdistribution

* finished test/meta.yml for rseqc/readduplication

* added entries to pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 08:49:32 +01:00
Harshil Patel
c99ab09f8d
Add kraken2 pigz multi-tool container for compressing output fastq files (#434)
* Add kraken2 pigz multi-tool container for compressing output fastq files

* Add untar to pytest config

* Add untar process to kraken2 tests

* Remove unneeded tags
2021-04-12 18:47:34 +02:00
Anthony Underwood
df8910de4e
Iqtree (#435)
* Resolve suggests after PR review

* add newline to functions

* need variable interpolation using double quotes; remove unnecessary tag

* add a more resilient link to raw github files

* remove trailing slash

* Update software/iqtree/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 17:01:26 +01:00
Jose Espinosa-Carrasco
3ac21ff0dc
Add abacas module (#431)
* Add abacas module

* Add test for abacas module

* Add Harshil to authorship

* Updating test with the data uploaded to nf-core/datasets

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 15:37:08 +01:00
Kevin Menden
0b402ffda8
Move test data to nf-core/test-datasets (#432)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

* move test data directory to nf-core/test-datasets

* bump multiqc version

* remove the test data

* updated test data link

* update README

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 12:32:39 +01:00
Jose Espinosa-Carrasco
2c43c39ccc
Add pycoqc module (#424)
* Add pycoqc module

* Adding pycoqc module tests

* Update pycoqc wilth new functions.nf

* Update tests to check for json report content
2021-04-12 10:52:14 +01:00
Anthony Underwood
575df10781
add new iqtree module (#427)
* add new iqtree module

* Resolve suggests after PR review

* add newline to functions
2021-04-12 09:45:56 +01:00
Thanh Lee
ec15bae344
🏋️‍♀️ new submodule mash/sketch🕺 (#426)
* new submodule mash/sketch

* fixed submodule naming

* OK, tag is diff to keyword

* OK  another round 🤣

* removed TODO comments

* updated as per review comments 🙆‍♂️

* updated functions.nf 😁

* Update software/mash/sketch/main.nf

* Update main.nf

Removed blank line at the 12th

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-10 16:24:23 +01:00
Harshil Patel
5e18e36895
Update and check tests are running for all modules (#420)
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
Thanh Lee
5a59e61052
new module: rasusa (#413)
* new module: rasusa

* Removed blank line in software/rasusa/main

* updated code as per reviewcomments

* removed blank line as failed for lint

* updated as per review comments

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 13:10:32 +01:00
Anthony Underwood
ca776e76a2
add rapidnj module (#421)
* add rapidnj module

* remove trailing whitespace

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 13:04:54 +01:00
Florian Wuennemann
0f53c3b96b
Added kallistobustools/ref (#408)
* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me

* Removed trailing whitespace line 29

* Moved workflow from meta to options.

* Update main.nf

* Forgot to remove previous testing input channel for workflow.

* Apply suggestions from code review

Applied changes suggested by @drpatelh

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

* Added gtf to meta.yml.

* Apply suggestions from code review

Adding @drpatelh suggested changes.

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

* Moved workflow to input value. Fixed tests.

* Update tests/software/kallistobustools/ref/test.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 09:41:41 +01:00
Yuk Kei Wan
16e8d21477
Nanoplot and sequencing_summary.txt for Nanopore test data (#364)
* add nanoplot

* add Nanopore 100 read subset bam and fastq

* add nanoplot module and sequencing_summary.txt

* Update pytest_software.yml

* Update main.nf

* test directory path

* testing one output file

* Update main.nf

* fix typo

* remove path to test outputs (it worked locally)

* use test_data.config in test

* add meta.yml

* allowing either summary.txt or fastq.gz inputs

* fix linting and test.yml

* test whether github check can catch the output

* add summary.txt test output paths

* check Nanoplot-report.html output
2021-04-09 08:31:38 +01:00
Anthony Underwood
6927f1d086
New Snpsites module (#416)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* revert to gubbins test on upstream

* add new lines

* renove whitespace

* Apply suggestions from code review

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 08:00:33 +01:00
Anthony Underwood
63b3975292
Update gubbins module to use new files (#417)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* remove snpsites from gubbins branch

* remove redundant test_fas alignment

* update md5 sums

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 07:54:11 +01:00
Jose Espinosa-Carrasco
f90dde0d88
Add plasmidid module (#410)
* Adding plasmidid module

* Adding test for plasmidid module

* Update plasmidid version to 1.6.4

* Adding contigs.fasta file

* Update tests

* Adding output files on test.yml
2021-04-08 22:44:30 +01:00
Anthony Underwood
be390a25e5
adding fasttree module (#412)
* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* remove TODO

* update test data naming

* further test data naming updates

* remove options in favour of $options.args

* ensure non standard exit codes don't cause an issue

* update md5sum
2021-04-08 18:15:23 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389)
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
avantonder
710ab76b90
new module: gubbins (#377)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-07 16:31:24 +01:00
Robert A. Petit III
c9256616b9
update tests for new config (#384)
* update tests for new config

* fix quast, update more

* more updates!

* more tests updated

* fix tests, added tabix gff3.gz

* Delete main.nf

Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 20:22:06 +01:00
Nicholas Toda
f126d980d7
Add tests for subread #106 (#393)
* inital commit

* added meta.yaml info

* add initial logic for featurecounts test

* add args and change SE/PE to strandedness for featurecounts test

* added tests to pytest

* added test.yml

* removed GTF flag in options

* corrected test meta params

* meta yaml corrected tool info

* update test.yml

* fix lint errors meta.yml

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
2021-04-01 20:02:36 +01:00
Ravneet Bhuller
c5c59d44a1
PR for sequenzautils/bam2seqz (#395)
* added files

* edited files

* removed file

* README.md edited

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 07:08:27 +02:00
sruthipsuresh
983ba000c1
New modules: Fgbio callmolecularconsensusreads and sortbam (#352)
* Added fgbio callmolecularconsensusreads and sortbam modules

* Fixed naming issue in meta.yml

* fix: test.yml and config lint

* Revert "fix: test.yml and config lint"

This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail.

* style: Fix test names

* style: Remove trailing whitespace

* fixed test.yml

* fix: test data in sortbam

* fix: data format

* fix: test data for callmolecularconsensusreads

* Corrected with updated test data

* Apply suggestions from code review

Applied changes from code review, mainly syntactical changes

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

Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 20:38:50 +01:00
JJ
e50a525715
gatk4 markduplicates (#356)
* new module gatk4/markduplicates

* add tests

* add gatk4_markduplicates entry in pytest_software.yml

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update tests/software/gatk4/markduplicates/main.nf

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

* Update tests/software/gatk4/markduplicates/main.nf

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

* Apply suggestions from code review

* Fix EC lint

* Update md5sum

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
suzannejin
989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update tests/software/gatk4/haplotypecaller/main.nf

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

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 12:46:46 +01:00
Nicholas Toda
e526eae472
Add tests for hisat2 (#366)
* initial commit hisat2/build

* initial commit hisat2/build

* changed names for hisat2

* fixed directory structure and args

* added splice site test data

* added splice site inputs

* replaced list with individual args

* fixed removed commas

* added test yml file

* updated hisat2 conda version

* added meta.yml

* added meta.yml description

* added meta.yml inputs

* added meta.yml outputs

* update conda version for hisat2

* removed trailing whitespace meta.yml

* fixed version number for containers

* added test data to test config

* updated for new test logic

* fix pytest issue?

* fix pytest issue

* fixed wrong tool in meta.yaml

* updated tets.yaml name

* handle build bug for testing

* handle build bug for testing in yaml

* moved test folder to fix build bug

* use old hisat2 version to avoid conda giving inconsistent md5sum

* initial commit

* removed temp file

* added meta yaml

* add to pytest

* added tests

* added test yml

* add align meta yaml

* add hisat2 align to pytest

* remove need for splice data by calling process

* add hisat2 align se test

* add hisat2 align pe test

* update names hisat2 align

* update software pytest for using mutiple modules

* remove splice site test data since using module instead

* remove splice site from config since using module instead

* fixed extra brace

* added hisat2 align test.yml

* removed md5sum for bam files

* updated build md5sums

* Apply suggestions from code review

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 21:08:46 +00:00
kevbrick
fead37d57a
Add module: nf-core hackathon #207 : new module: msisensor/msi (#343)
* Add module: nf-core hackathon #207 : new module: msisensor/msi

* Add module: nf-core hackathon #207 : new module: msisensor/msi

* Fix 4-spacing issues (caught in PR linting)

* Code review fixes & update configs

* Code review: remove stray echo

* Code review: Add msisensor modules

* Slashes to underscores to get tests to run on github

* Update software/msisensor/scan/main.nf

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

* Update software/msisensor/scan/main.nf

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

* Update software/msisensor/msi/main.nf

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

* Update software/msisensor/msi/main.nf

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

* Add all outputs to meta.ymls

* Fixes from code review

* Fixes from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 16:46:00 -04:00
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data (#386)
* Adding tar.gz kraken2 db to test data

* Update test path files for untar module

* Update test path files for kraken2/run module

* Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
Alexander Peltzer
0337916f8a
Add YARA module (#353)
* Initial work on yara module

* Adding in index basics

* Updated the index stuff

* Adding in proper tests

* Fix editorconfig

* Odd paths

* that should do it

* Fix tests

* Fix tests

* FFS

* Once more

* Mapping is not deterministic
2021-03-24 17:14:52 +01:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests (#365)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint

* Initial commit for test data config

* Rename test data

* Include test config

* Update indents

* Update test for FastQC via config

* Remove quotes of bottom-level variables

* Use underscores in key names

* Get tests working for fastp

* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Gisela Gabernet
22eaefe583
Add module kallisto/index (#357)
* add kallisto index module

* update kallisto module

* add kallisto module tests

* update kallisto index test.yml

* update test data paths

* fix version

* fix kallisto index test yml

* remove TODOs

* Update software/kallisto/index/main.nf

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

* Update software/kallisto/index/main.nf

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

* output folder instead

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 12:25:39 +00:00
arontommi
86bb832fae
Strelka germline (#340)
* nf-core template created

* boilerplate and sarek_dsl2 code merged

* adding an option to give it args

* bai got away

* seperating vcf files and vcf index files into seperate streams

* some minor spacefixes

* adding standard information about the module

* removing typos

* some basic tests based on tiddit tests

* removed the bed parameter, should be provided via options.args instead

* removing typos

* adding indexed bam file instead

* Adding changing out fasta with reference to deal with empty fasta input

* adding the correct fasta

* removing the empty test

* adding the correct data to the testoutput and removing the md5sum since
it constantly changes

* adding  target_bed to input

* adding info on target bed

* adding target bed to test

* adding more files to the test

* adding meta for target bed test

* adding a test for target_bed

* typo

* fixing pytest with master
2021-03-24 05:07:29 +00:00
Erkison Ewomazino Odih
67b3e00f58
add flash module (#341)
* add flash module

* remove todo

* run tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 05:05:45 +00:00
Ravneet Bhuller
a70abc236b
PR for sequenzautils/gcwiggle (#345)
* added files

* edited files

* edited files

* edited file

* test(sequenzautils): Remove md5sum

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-24 05:03:03 +00:00
Robert A. Petit III
3f14b1fabe
Update shovill module (#337)
* add shovill module

* removed deprecated shovill module

* fix line ending in functions.nf

* fix yaml indentation

* reduce spades memory usage

* update md5sums

* remove non reproducible md5sum

* Update test.yml

Remove last non-reproducible md5sum.

* purely cosmetic order change

* proper process label, improve output readability

Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00
Yuk Kei Wan
af3bc225c0
ucsc_bed12tobigbed (previous pull request had conflicts) (#302)
* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Update pytest_software.yml

* Update main.nf

* fix linting error

* Delete test.yml

* Create functions.nf

* Update main.nf

* change test data

* revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
Mark-S-Hill
399b58043d
add vcftools module (#334)
* add vcftools module

* fix padding issue

* fix linting errors
2021-03-24 04:54:23 +00:00
Kevin Menden
fe8a783cef
Homer (#330)
* started with homer

* added tests for homer annotatepeaks

* fix md5

* remove md5 sum
2021-03-23 11:24:54 -07:00
Gregor Sturm
e33860a2e8
Prodigal (#333)
* WIP add prodigal

* Implement module and add tests

* Fix EC lint
2021-03-23 11:03:58 -07:00
yocra3
5e3c9dfbf0
Add gatk4/baserecalibrator (#327)
* Add gatk4 BaseRecalibrator

* Solve format in main.nf

* Correct functions

* Add pytest
2021-03-23 18:32:37 +01:00
Alexander Peltzer
d13e22dcbe
Add in OptiType (configbuilder, type) module(s) (#301)
* Adding in optitype prototype (To be worked on these days)

* I've tried my best 😆

* No idea

* Add in YML stuff

* Fix paths

* Ok, lets try this

* Adding proper options

* Replacec configbuilder thing

* Fix seq_type

* Adding human bam - sarscov doesnt work

* Fix a bunch of things

* -def

* Make this test run

* Fancy as fuck

* Update tests/software/optitype/test.yml

* Add proper tag

* Remove md5sums

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 16:48:05 +01:00
Anthony Fullam
3d720a24fd
Add alleleCounter module (#313)
* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Remove newline

* Fix pytest_software.yml

* Update pytest_software.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-23 14:37:53 +01:00
yocra3
614d61dc13
Add gatk4/applybqsr (#331)
* Add applybqsr module

* Solve problem in functions.nf

* Add to pytest
2021-03-23 14:15:26 +01:00
suzannejin
9115c12f88
new module: samtools/fastq (#316)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem
2021-03-23 12:13:07 +01:00
Robert A. Petit III
c2aa95cb6c
add prokka module (#298)
* add prokka module

* adjust test outputs

* fix prokka command

* adjust test outputs

* handle optional input

* update pytest

* update pytest

* adjust test outputs

* adjust test outputs

* switch to lists for optional inputs, add md5sums for non-timestamped outputs

* add optional prodigal training file

* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module (#173)
* Normal bam file added

* Normal bam.bai file added

* Tumour bam bai files added

* human dir added

* annotation dir added

* cnvkit dir added

* cnvkit dir added

* Update software/cnvkit/main.nf

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

* Update software/cnvkit/main.nf

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

* Update software/cnvkit/main.nf

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

* changed input filenames

* edited main.nf

* edited main.nf

* edited meta.nf

* edited test.yml

* filters.yml

* edited main

* edited main

* edited meta

* edited meta

* edited main

* removed unwanted lines

* edited the path to the main.nf

* removed function.nf

* added functions.nf

* deleted 2 workflows and craeted a common workflow

* deleted paths for 2 workflows and created paths for a common workflow

* Deleted annotation dir

* deleted params.modules

* Edited meta.with_normal

* deleted normal_280_sub_chr21.bam

* deleted normal_280_sub_chr21.bam.bai

* deleted tumour_278_sub_chr21.bam

* deleted tumour_278_sub_chr21.bam.bai

* Edited input and script parts

* Edited input part

* Added

* Edited args

* Edited script

* Edited input

* Changed annotation to annotationfile

* Changed description of the tool

* edited singularuty container

* edited input

* line 44 removed trailing whitespace

* Edited addParams

* Deleted pdf output

* Deleted pdf output

* edited the path to main.nf

* edited path to the main.nf

* Added docker image version

* Removed extra ../

* added md5sums

* added md5sums

* Update software/cnvkit/main.nf

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

* Update software/cnvkit/main.nf

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

* Edited the script

* Edited the input

* Edited main.nf

* Edited main.nf

* edited md5sum for reference.cnn

* removed human fasta

* removed human fasta.fai

* added GRCh38 fasta

* added GRCh38 fasta.fai

* added hg19 fasta.fai

* added hg19 fasta

* Edited fasta file name

* Edited bed file names and md5sums

* Edited md5sums

* edited the input and script section

* edited input section

* added targetfile

* changed the files

* changed the output files

* added bam files

* added bam files

* remove files

* added md5sums

* replace file

* added files

* edited tests/software/cnvkit files

* edited tests/software/cnvkit files

* edited authors list

* removed files

* added files

* added files

* added files

* added files

* added file

* added file

* added file

* added file

* edited files

* edited files

* edited files

* edited files

* edited files

* edited files

* added new module

* added new module

* edited files

* edited file

* edited file

* edited file

* removed files

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Nicholas Toda
53109d53c0
add gatk4/fastqtosam #198 (#311)
* Inital nf-core create

* remove TODO comments, input and output files defined

* add get version in script

* added flow control for single/paired end data

* added script main commands

* removed completed TODO messages

* removed completed TODO messages

* added software info

* added input reads description

* added output description

* added description and keywords

* added single end test

* added paired end test

* fixed sample name flag

* fixed reverse read variable

* added test yaml

* update for pytest_software

* order in pytest_software was different

* replaced functions.nf with copy from another module

* simplify read command line

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

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
Maxime Borry
aa76c6d870
new module: AdapterRemoval (#309)
* add adapterremoval module

* fix indentations

* switch to process_medium

* update docker tests

* remove duplicated entry

* fix line ending

* Update software/adapterremoval/main.nf

* Update software/adapterremoval/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
Jose Espinosa-Carrasco
cfa8f64c4f
Adding unicycler module (#307)
* Adding unicycler module

* Do not forget to change default keywords on meta.yml
2021-03-22 18:14:24 +01:00
Patrick Hüther
7fe6f9fab2
bismark: remove underscores from process names (#303)
* sanitize process names

no underscores allowed

* remove underscores from process names
2021-03-22 17:46:11 +01:00
Florian Wuennemann
592002aa23
add picard_collectwgsmetrics (#304)
* Added new module picard/collectwgsmetrics.

* Removed unused outputs from meta.yml

* Added version.txt file back to meta.yml

* Updated test.yml

* Removed md5sum from test.yaml and added contain tests.

* Update functions.nf

Fixed missing newline formatting.

* Update main.nf

Fixed missing newline formatting.

* style(picard): Remove trailing whitespace

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 17:05:59 +01:00
Patrick Hüther
eb9178970f
add bismark/summary (#295)
* add bismark/align module

* bismark/align: add tests

* bismark/align: update meta.yml

* bismark/align: skip checksum for alignment logs

they contain timestamps

* bismark/align: restore correct checksum

caused some mixup in the last commit

* bismark/align: add genome_preparation to filters

* Fix conda version pin

* change options to be a global var

* remove params from meta.yml

* add bismark/summary

* remove md5sum check for bismark_summary_report.html

it contains a timestamp

* fix tests

* update meta.yml

* remove mysterious index files
2021-03-22 14:58:54 +01:00
Yuk Kei Wan
134c8ef6ce
add samtools merge (#296)
* add samtools merge

* Update pytest_software.yml

* get it back to 20.11.0-edge

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml
2021-03-22 13:48:23 +01:00
Patrick Hüther
f9ce8664ba
add bismark/report (#297)
* add bismark/align module

* bismark/align: add tests

* bismark/align: update meta.yml

* bismark/align: skip checksum for alignment logs

they contain timestamps

* bismark/align: restore correct checksum

caused some mixup in the last commit

* bismark/align: add genome_preparation to filters

* Fix conda version pin

* change options to be a global var

* remove params from meta.yml

* add bismark/report

* fix test filepaths

* remove mysterious index files
2021-03-22 13:38:08 +01:00
Patrick Hüther
04704c2034
add bismark/methylation_extractor (#274)
* add bismark/methylation_extractor

* add tests for bismark/methylation_extractor

* bismark/methylation_extractor: add genome_preparation to filters

* Apply suggestions from code review

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

* remove params from meta.yml

* pytest: remove md5sum checks for gzipped output

gzip stores timestamps in the file header, so the checksum will be different each time

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
Jose Espinosa-Carrasco
72e81d6e90
Add spades module (#277)
* Add spades module

* Reorder gatk4 modules alphabetically

* Update software/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
Jose Espinosa-Carrasco
313241749c
Add kraken2 run module (#266)
* Add kraken2 run module

* Add kraken2 run module

* Add coronavirus kraken2 db

* Adding kraken2 run tests

* Update software/kraken2/run/meta.yml

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

* Fixing files commited by mistake

* Remove params for meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
Harshil Patel
d1cb9a845f
Check for minimum NF version (#278) 2021-03-18 12:00:32 +01:00
Kevin Menden
a90332906b
add mergebamalignment (#259)
* add mergebamalignment

* fix test.yml

* update to latest gatk4 version

* Update software/gatk4/mergebamalignment/main.nf

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

* Update tests/data/README.md

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

* Update software/gatk4/mergebamalignment/main.nf

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

* Update software/gatk4/mergebamalignment/meta.yml

* fixed unmapped/unaligned

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 15:56:56 +01:00
Kevin Menden
3c4d9466f4
Adding minia for viralrecon (#267)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 12:54:15 +01:00
Kevin Menden
17dbff52f4
added gatk4 variantfiltration (#265)
* added gatk4 variantfiltration

* replace merge with filter

* Update software/gatk4/variantfiltration/main.nf

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

* updated input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 09:42:35 +01:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds (#273)
* Fix bowtie  build test

* Forgot to delete old bowtie_build

* Fix bowtie2 build tests

* Add initOptions include on hisat2 extractsplicesites
2021-03-15 15:39:42 +01:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml (#271)
* Rename pytest filters.yml

* Change filters.yml name

* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
MaxUlysse
4968458b6c chores: add cpus, memory and time requirements to limit resource consumption 2021-02-16 14:18:29 +01:00
drpatelh
fe3cb87f6d
Direct download Singularity containers 2021-02-03 20:03:45 -06:00
Edmund Miller
467d1595c4
test: Use docker image with singularity 2021-02-02 18:14:39 -06:00