Commit graph

41 commits

Author SHA1 Message Date
Matthias De Smet
63db63757c bump picard versions 2022-05-30 10:15:40 +02:00
Matthias De Smet
c390385cf5 revert wgsmetrics' 2022-05-22 06:44:17 +02:00
Matthias De Smet
a5a6973fcf picard: make reference sequence optional 2022-05-21 08:33:49 +02:00
Matthias De Smet
771d5a19f1 fix reference arg 2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9 update to long args 2022-04-29 10:52:40 +02:00
Matthias De Smet
e263f267a7
Merge branch 'master' into bump/picard 2022-04-29 09:48:15 +02:00
Matthias De Smet
ec10f98d55
picard CollectWgsMetrics: update to new cli args (#1578)
* update to new cli args

* remove bam index from tuple, not needed by program

* bump picard version

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-29 09:32:32 +02:00
Matthias De Smet
00467ac64a update command line syntax for all tools 2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8 bump picard version across the board 2022-04-29 07:47:24 +02:00
Matthias De Smet
35231d3949
update picard/collecthsmetrics (#1542)
* update picard/collecthsmetrics

* syntax fixes, bugfixes

* add tests

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-04-22 10:13:57 +02:00
Matthias De Smet
d4160c669b
Tool/crosscheckfingerprints (#1505)
* first commit

* first commit

* update test.yml

* update test.yml

* Update modules/picard/crosscheckfingerprints/main.nf

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

* Update modules/picard/crosscheckfingerprints/main.nf

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

* add support for vcf haplotype maps

* update test

* update test data config, use test data

* fix exit code

* Update modules/picard/crosscheckfingerprints/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/crosscheckfingerprints/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* remove unused stub

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 10:02:10 -04:00
Lucpen
f079367416
Picard liftover vcf (#1431)
* Building Picard liftovervcf module

* Building Picard liftovervcf module_test

* Building Picard liftovervcf pytest

* Module for picard liftover vcf created

* Fixed files after linting test

* Fixed trailing whitespace

* Checked files with prettier

* further formatting with prettier

* Fixed test.yml

* Fixed input variable names

* Changed contain test.liftef.vcf

* Changed contain in test.yml test.liftef.vcf

* Run prittier

* Going back to previous version of test.yml

* downgrading picard to 2.26.10 from 2.26.11

* Update modules/picard/liftovervcf/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/main.nf

Print available memory

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Output from .vcf to .vcf.gz

* Added spaces to align emit

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Removing md5sum test

Co-authored-by: jemten <jemten@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-04-07 07:50:58 -04:00
Ramprasad Neethiraj
49b18b1639
add stub to modules used in raredisease pipeline (#1206)
* add stub section

* add stub for bcftools norm

* add stub to more modules

* fix expansionhunter tests

* revert changes -picard

* Update stub to write version no.s to a file

* add picard

* revert picard again

* add stubs to more modules

* fix bwamem2

* add bcftools view

* add stubs

* fix svdb query

* review suggestions
2022-03-28 17:48:39 +02:00
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
Ramprasad Neethiraj
d8028dc1c3
Add picard/sortvcf (#1370)
* sortvcf

* add files

* update meta

* update java mem

* update documentation link

* remove todo

* review suggestions

* fix test.yml

* fix conda error

* fix version code
2022-03-03 11:40:16 -05:00
Sateesh
8a20253f40
update args & convert to bam (#1355) 2022-02-25 11:06:39 -07:00
Sateesh
a0d91e4a93
Picard addorreplacereadgroups (#1305)
* add picard-addorreplacereadgroups

* add picard_addorreplacereadgroups

* add new line to main.nf

* remove trailing whitespaces

* remove trailing whitespaces

* change to output in test yml

* add when directive

* picard 2.26.10 -> 2.26.9

* picard 2.26.10 -> 2.26.9 test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:59:06 -07:00
Sateesh
927dbfed04
Picard cleansam (#1306)
* add picard-cleansam

* add picard/cleansam

* update test yml with output

* picard 2.26.10 -> 2.26.9

* add output to test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:17:58 -07:00
Sateesh
62e5d1f0b3
Picard createsequencedictionary (#1310)
* add picard/createsequencedictionary module

* add picard-CreateSequenceDictionary

* add picard/createsequencedictionary/

* add contains to test yml

* update test yml contains

* update test yml contains

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 18:49:12 -07:00
Sateesh
f655e5dea2
Picard fixmateinformation (#1315)
* add picard-fixmateinformation

* add picard-fixmateinformation

* fix trailing whitespace

* fix trailing whitespace

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 18:18:05 -07:00
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
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
Harshil Patel
e751e5040a
Bump software versions for viralrecon modules (#1198)
* Bump software versions for viralrecon modules

* Remove custom params.save_unaligned from bowtie2_align

* Unify samtools modules and error if input and output names are the same

* Fix ALL the tests
2022-01-07 17:52:39 +00:00
Harshil Patel
0d1e21686a
Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability (#1173)
* Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability

* Fix EC lint for unrelated hmmcopy module
2021-12-16 10:56:41 +00:00
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
Jose Espinosa-Carrasco
4e5b6ed843
Fix picard markduplicates (#1084)
* Fix picard/markduplicates with new options syntax

* Delete md5sum for bam files and add contains for metrics.txt

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-18 21:54:14 +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
Kevin
3aacd46da2
Backfill software licenses meta (#876)
* backfilled modules with meta.yml that had no license identifier

* harmonized BSD license names

* whitespace linting at modules/unzip/meta.yml:12

* harmonized software from US NIH-NCBI/NIST to 'US-Government-Work'

* Update modules/bcftools/index/meta.yml

`bcftools` is dual-licensed, use associative array to allow for multiple licenses

Co-authored-by: Michael L Heuer <heuermh@acm.org>

Co-authored-by: Michael L Heuer <heuermh@acm.org>
2021-10-22 15:39:54 -07:00
Harshil Patel
49da864287
Update versions key in meta.yml for all modules (#787) 2021-10-03 08:20:26 +01:00
Harshil Patel
7b3315591a
Remove def software lines and emit versions channel as plural (#780)
* Remove def software line

* Replace version with versions in emit statement

* Fix default software names
2021-10-01 14:04:56 +01:00
James A. Fellows Yates
e971f538a9
Module new version reporting fixes (#753)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Fix IQ tree

* Fix picard markdup and merge sam

* Fix plink/vcf version

* Fix plink version output

* Fix prokka version command

* Fix pydamage

* Try fixing markduplicates

* Fix snpEff

* Fix vcftools version

* Fix pydamage and filtersamreads test run

* Fix MarkDuplicates tests

* Add missing unsorted checks

* Remove MD5 sym due to stochasicity in BAM file
2021-09-28 10:51:19 +01:00
Gregor Sturm
906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00
Mei Wu
b2a6f5409e
modify markduplicates module (#681)
* tested

* updated meta config and test config
2021-09-15 11:02:28 +02:00
Harshil Patel
c5235a983d
nf-core modules bump-versions for all modules (#630)
* Add blacklist of modules that shouldn't be updated to .nf-core.yml

* nf-core modules bump-versions for all modules

* Remove TODO statements identified by linting

* Fix md5sums for failing tests

* Fix more tests
2021-07-28 09:10:44 +01:00
James A. Fellows Yates
553f51d6bf
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>
2021-07-22 11:19:51 +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
2d26b037a1
(another) fix: picard sortsam (#606)
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place

* Correct output file suffix

* Define only `bam` in output tuple

* Correct output meta

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 15:51:33 +02:00
James A. Fellows Yates
a0019d4175
fix: picard sortsam (#605)
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place

* Correct output file suffix

* Define only `bam` in output tuple
2021-07-21 14:34:21 +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
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