11 commits

Author	SHA1	Message	Date
James A. Fellows Yates	7b1e84f7be	Add bcftools/index (#812) ... * feat: add bcftools index * Extend tests to also test gen for TBI * Update meta.yml * Update meta.yml	2021-10-13 10:40:04 +02:00
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
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
Abhinav Sharma	6ff995e93d	Add bcftools/query module (#670) ... * initial commit [ci skip] * add basic structure [ci skip] * finalized the bcftools/query module * add optional files [ci skip] * Add the vcf index file as param [ci skip] * update the md5sum for output file [ci skip] * all tests passing	2021-09-14 09:19:01 +02:00
Abhinav Sharma	c5634ba99b	Add bcftools/view module (#669) ... * initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters	2021-09-12 19:51:40 +02:00
Abhinav Sharma	0954204f9e	Add bcftools/norm module (#655) ... * Initial draft [ci skip] * trigger first test * update output file path * Tests passing * finishing touches for meta.yml and update checksum * tweak checksum * add threads to the module * skip version info for matching test md5sum [ci skip] * Add ref fasta and finalize the module Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>	2021-08-16 17:40:03 +02:00
Abhinav Sharma	67cc3bd116	Add bcftools/concat module. (#641) ... * draft for bcftools modules [ci skip] * initial test for bcftools concat * Update the params for testing * fix tests * Accomodate code review [ci skip] Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update the meta file and open PR for review * Update the keyword * Update the tags for module [ci skip[ * add threads Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2021-08-10 15:10:27 +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
Johnathan D	a813e2e3a6	Add bcftools reheader (#585) (#608) ... * local tests and linting passing (#585) * 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> * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>	2021-07-23 22:24:19 +01:00
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