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Author SHA1 Message Date
Simon Heumos
1d668eefa2
Bump seqwish/induce to v0.7.6 (#2083) 
* Update seqwish to version 0.7.2

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

* level with nf-core/modules master branch

* update seqwish/induce to v0.7.6

* add pangenome test data

* test seqwish/induce v0.7.6 with pangenomics test data

* we already have pointed to the pangenomics test data sets

* update paths to test data

* add path to bgzipped fa, gzi, fai

* remove one tab

* remove one tab

* actually execute the 2nd test

* try to fix versions.yml

* pangenomic tests can be run in their own subworkflow

* maybe the csv input is the problem

* remove space as suggested by Rike

* csv input was not the problem

* update test.yml

* typo

* enable pangenome tests

* add md5sum for pangenomic test

* Update tests/modules/seqwish/induce/test.yml

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* PAF input is a list of files

* beautify comment

Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
 2022-09-26 17:01:21 +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
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
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
Michael L Heuer
d95be1434f
Update seqwish reported version to match bioconda version. (#678) 2021-08-26 15:33:38 -05:00
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
Renamed from software/seqwish/induce/meta.yml (Browse further)