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15 commits

Author SHA1 Message Date
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