7 commits

Author	SHA1	Message	Date
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