Commit graph

80 commits

Author SHA1 Message Date
Moritz E. Beber
9c386c5dd8
Add bracken (#1423)
* feat: add template for Bracken

* chore: update version

* refactor: change command build

* refactor: rename report variable, change quotes

* docs: remove refactored input parameter

* fix: correctly assign arguments to options

* tests: set up single and paired end tests

* style: apply prettier

* chore: change data sources to official ones

* refactor: rename test workflows

* tests: use correct input to the new UNTAR module

* chore: update md5sums
2022-03-22 16:40:21 +01:00
Ramprasad Neethiraj
5297d27fbf
update svdb to version 2.5.2 (#1390)
* update svdb version and tests

* update link
2022-03-21 10:39:34 +01:00
Michael L Heuer
73aaecbc3a
Add BAM indexes as input for optitype module. (#1388) 2022-03-15 17:02:40 +01:00
Sima Rahimi
86ac223916
Cnvpytor (#1297)
* Added cnvpytor/importreaddepth module

* Corrected process name in meta.yml file

* added -chrom argument

* space correction

* Added complementary info

* fixed typo

* md5sum added

* modified the module to work on cram files as well

* Added cnvpytor/histogram module and test files

* Added cnvpytor/partition module and test files

* added cnvpytor/callcnvs module and tests

* modified by new modules

* Added test file and fixed input path in modules

* added when block

* little fixes

* skip tracking test.yml

* removed changes to test if conflicts get resolved

* updated outfile name

* corrected the version.yml content
2022-03-15 10:20:46 +01:00
Benjamin Wingfield
de0d57a562
implement plink2/score module (#1259)
* implement plink2/score module

* fix test yml

* fix typo :(

* set cpu

* set mem

* fix input process input block

* fix tests

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-03-07 13:02:40 -05:00
James A. Fellows Yates
4983f77796
Add hamronization/deeparg (#1364)
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add when condition

* Apply suggestions from code review

* Update modules/hamronization/deeparg/meta.yml
2022-03-02 13:04:22 +01:00
FriederikeHanssen
c189835b1b
add controlfreec (#1333)
* add drafty controlfreec

* get sofatware version

* use maps in map

* update paths to new and soon-to-be merged test files, add more input docu

* Stab at documenting args map

* Update syntax

* Bit more description

* Make the linter happy

* tests pass locally

* Add outputs & docu

* tests are failing locally now :/ but cpn file can also be added

* All tests passing, need to update test data again to add folder

* Clean up files

* Clean up files

* Clean up files

* Don't know how to get the test to run with the direcotry for now. they pass locally though

* Make linter happy

* Name process back

* Update to use tar folder

* fix the checksum
2022-02-28 19:08:58 +01:00
Mei Wu
38ffbfdb63
bcftools/annotate follow up corrections (#1359)
* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

* using match instead of find

* bcftools/annotate refactored with complete test

* rm trailing white space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-28 10:16:29 -05:00
Mei Wu
2597c31d6b
refactored vcfanno (#1266)
* final refactor: using tarball instead
2022-02-21 11:49:21 +01:00
FriederikeHanssen
f5d5926516
Update intervals (#1278)
* Match target bed to input files

* Intervals in getpileupsumamries

* more interval updates

* change targets in strelka

* remove leftover channel

* fix checksums

* add new test vcfs

* add new test vcfs

* Update modules/freebayes/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 10:34:22 +01:00
Ramprasad Neethiraj
fc4bd3a2d2
Add svdb/query (#1249)
* first commit

* add test data
2022-02-01 20:46:10 +01:00
Michael L Heuer
c9587d76e2
Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format

* fix ci failures

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-17 09:24:40 +00:00
Simon Heumos
4cc3921efb
Add pangenome test data set keys (#1170)
* Update seqwish to version 0.7.2

* seqwish can work with a comma-separated list of PAFs

* level with nf-core/modules master branch

* add pangenome test data keys

* the odgi test data lives in its own folder

Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-12 12:01:57 -06:00
FriederikeHanssen
50eafb19c6
Update version for log4j vulnerability (#1176)
* Update version for log4j vulnerability

* update checksums

* update checksums

* update checksums

* Remove todo string

* remove werid output paths

* remove werid output paths

* remove werid output paths

* Update various checksums

* Update various checksums

* Remove unstable md5sums

* Update md5sums

* Fix pileupsummary

* Fix genotypegvcfs

* Update test files mutect2

* hm genotypevcf updated again

* Update some mutect checksums and whatnot

* Fix last mutect checksum

* Apply suggestion to use mtochondria data instead
2021-12-20 17:10:49 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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