Commit graph

66 commits

Author SHA1 Message Date
Maxime U. Garcia
64006e239a
fix: actually do the tests for multiple files (#1058) 2021-11-10 16:26:34 +01:00
GCJMackenzie
316aedaaa6
bug fixes: genomicsdbimport (#1035)
* 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

* bug fixes, multicalling samples and gendb emissions now fixed

* Update pytest_modules.yml

* Update meta.yml

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>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 15:51:15 +00:00
GCJMackenzie
bc8697b766
FIX: Createsomaticpanelofnormals add requested test changes (#983)
* 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

* temp commit to allow checkout

* updated createsompon tests to use tarred gendb

* resolve conflict

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

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

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-29 17:45:32 +01:00
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
ac1e6df076
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

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

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-10-29 13:01:05 +02:00
GCJMackenzie
71945a5b5f
Mutect2 add mitochondria mode and update tests (#967)
* new mitochondria mode added, tests updated to allow for temp fix for test data

* add cram test

* bam/bam_idx renamed to input and input_index

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
2021-10-29 11:27:56 +01:00
FriederikeHanssen
1662201102
Add gatk4/estimatelibrarycomplexity (#965)
* Add gatk4/estimatelibrarycomplxity

* forgot to add yml

* Fix placeholder
2021-10-28 17:49:27 +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
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
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
GCJMackenzie
3c4eaec52b
Update for mutect2: add output channel for stats file (#716)
* added output channel for stats file, updated meta yml with description and test yml with check for stats file

* Update modules/gatk4/mutect2/main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-17 09:56:56 +01:00
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
Maxime U. Garcia
b3c4667732
fix: update to gatk4.2.0.0 (#575)
* fix: update to gatk4.2.0.0

* fix: update md5sum
2021-07-16 11:26:28 +02:00
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