4 commits

Author	SHA1	Message	Date
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
suzannejin	989fb7d5b7	modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382) ... * new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem * Module samtools/fastq: * output compressed fastq.gz file(s) * add if conditionals for single/paired reads * samtools/fastq: modified test.yml * samtools/fastq: modified main.nf to avoid duplicated part of the script section * fix README.md * modify test path gatk4 * fix config * Add new module gatk4/haplotypecaller * solve check issues * fix test.yml file * fix test.yml gz.tbi * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: suzannejin <suzanne.jin@crg.eu> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-03-26 12:46:46 +01:00
Harshil Patel	acb1a12a56	Re-organise all test data (#354) ... * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint	2021-03-24 09:53:41 +00:00
Nicholas Toda	53109d53c0	add gatk4/fastqtosam #198 (#311) ... * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-03-22 18:26:02 +00:00