Commit graph

66 commits

Author SHA1 Message Date
Rike
e8221cf98e Merge remote-tracking branch 'origin' into gatk_cnnscore 2022-05-18 14:27:25 +02:00
Rike
afa0f2a995 update test 2022-05-17 22:53:41 +02:00
Rike
265fd882ca update test 2022-05-17 19:44:48 +02:00
Rike
5f63904a50 update test 2022-05-17 19:37:18 +02:00
Rike
e0fcbb428d Add CNNScoreVariants 2022-05-17 19:09:46 +02:00
Rike
eb841d4ea0 revert markduplciatespark changes 2022-05-16 10:33:01 +02:00
FriederikeHanssen
8b4d021189
Merge branch 'master' into gatk_426 2022-05-16 09:50:13 +02:00
Nicolas Vannieuwkerke
a72f06dfe8 removed versions checksum 2022-05-13 14:27:59 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e added gatk4/splitintervals 2022-05-13 13:46:34 +02:00
Rike
99880654bf add output default bam 2022-05-12 18:06:15 +02:00
Rike
8792d102ee fix test input 2022-05-12 17:37:06 +02:00
Rike
a694267b4b fix empty index input 2022-05-12 17:01:03 +02:00
Rike
b3bd55da76 getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
Rike
15fbf21b28 double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
Rike
fef5434c4c Update md5sums 2022-05-12 16:07:12 +02:00
Lucpen
971a17a3ab fix datatest for stubs 2022-05-06 15:34:18 +02:00
Lucpen
0fa36e6777 fix added correct entry workflow in test.yml 2022-05-06 15:26:34 +02:00
Lucpen
50cc136a78
Update tests/modules/gatk4/mutect2/main.nf
fix spelling mistake

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-05-02 15:14:05 +02:00
Lucpen
da82e06354 fix gatk4_mutect2 test 2022-05-02 14:16:07 +02:00
Lucpen
3a4e415fe2 chores adding dummy files for stubs 2022-05-02 13:30:18 +02:00
Lucpen
de40c1bf54 chore removing file from test 2022-05-02 13:15:01 +02:00
Lucpen
08d5acbeb6 feat added tests for stubs 2022-05-02 11:59:08 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads (#1571) 2022-04-27 16:03:44 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins (#1459)
* feat: code polishing

* Apply suggestions from code review

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

* code polishing

* more code polishing

* code polishing

* tests for applybqsrspark

* fix typo

* no need to check md5sum for versions.yml

* fix: use correct syntax

* code polishing again

* add tests for markduplicatesspark

* simplify mergevcfs tests

* add tests for baserecalibratorspark

* fix: path to entry

* code polishing

* fix linting

* simplify module

* update meta.yml

* fix pair mode

* fix: MITO mode

* more tests

* fix command

* bad copy paste

* fix typos

* fix tests

* fix test

* update meta.yml

* correct versions.yml in all test.yml

* code polishing

* code polishing

* more code polishing

* fix args

* add tmpdir for all

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
James A. Fellows Yates
e080f4c8ac
Untar unzip meta (#1408)
* fix: remove left-over unnecessary code

* Adds support for meta lists for unzip and untar

* Fix test inputs

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Fix MALTEXTRACT/AMPS

* Fix further modules

* Fix cellranger

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00
Edmund Miller
f080015754
Prettier (#1405)
* style: Add prettier config files

* build: Add prettier vscode extension

* ci: Replace markdownlint and yamllint with prettier

* style: Run prettier

* style: Use indent of 2 for markdown as well

https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358

* style: Fix indent

* style: Let editorconfig take over tab widths

* style: yaml => yml

* ci: Run prettier once

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2022-03-18 14:27:50 +01:00
Michael J Cipriano
6400317623
Gatk4 selectvariants (#1346)
* initial commit

* tested

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-24 09:51:48 +01:00
Sateesh
a25423dbb9
Gatk4 combinegvcfs (#1342)
* add gatk4/combinegvcfs module

* update gatk4/combinegvcfs

* loop to create a string adding -V to each vcf file

* add contains for variable md5

* rm whitespace

* meta in output

* fix indentations

* fix indentations

* move tmpdir to args and update conda version

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:29:29 +01:00
FriederikeHanssen
3f364e2f31
add mergemutectstats (#1314)
* add mergemutectstats

* correct md5sum

* Update modules/gatk4/mergemutectstats/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-18 09:38:55 +01:00
FriederikeHanssen
fcd483e1b5
intervallisttobed (#1312)
* intervallisttobed

* correct md5sum
2022-02-17 16:32:26 +01:00
FriederikeHanssen
8c8be7d7c6
Add gatherpileupsummaries (#1311)
* Add gatherpileupsummaries

* fix checksum

* Update modules/gatk4/gatherpileupsummaries/main.nf

* Add in when
2022-02-17 15:05:21 +01:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
FriederikeHanssen
967fb22ded
Update versions (#1292)
* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break
2022-02-15 11:29:36 +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
GCJMackenzie
08db860938
Update mergebam syntax and sample specific unmapped channel (#1238)
* 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

* updated to follow the new mergebam syntax, also made unaligned input sample specific

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-01-27 15:30:27 +00:00
FriederikeHanssen
598d7abdb2
Log4j again (#1202)
* Log4j again

* Update checksums
2022-01-12 13:55:54 +01:00
FriederikeHanssen
a6e0629e24
Change intervals to be part of sample specific input (#1189)
* Change intervals to be part of sample specific input

* Fix some tests

* Update checksum

* Update intervals

* Update intervals

* Try out gavins idea for adding the file

* update test line

* update test line

* update test line

* revert contains line
2021-12-23 12:58:20 +01:00
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
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
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
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
Harshil Patel
9d0cad583b
Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
* 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

* Change syntax from task.ext.suffix to tast.ext.prefix

* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix

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>
2021-12-02 12:39:55 +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
praveenraj2018
43a1c1c6d1
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
* Added vcf_index to vcf tuple; output to vcf.gz format.

* Fix: extra new line in meta.yml.

* addressed review feedback

* fix: editorconfig error

* fix: gatk memory flag

* fix: editorconfig error

* fix: Indentation 

fix: Indentation

* Fix: lint editorconfig error

Removed one extra space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-18 21:47:40 +01:00
praveenraj2018
691feeafdc
GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split into separate input channels (#1076)
* fasta_fai_dict tuple is now split into separate input channels

* fix: lint errors

* fix: pytest errors

* Update modules/gatk4/splitncigarreads/meta.yml

* Update modules/gatk4/splitncigarreads/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-16 15:09:30 +01:00
Maxime U. Garcia
3426834744
feat: fastaidx -> fai (#1073) 2021-11-15 18:03:02 +01:00
Maxime U. Garcia
5b1ce484b9
feat: _idx -> _tbi (#1074)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:49:20 +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
Maxime U. Garcia
3b600af50e
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 (#1059)
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0

* update md5checksum

* commit all files

* actually checksum was good, but I suspect something fishy with the tests
2021-11-11 08:58:59 +01:00