2 commits

Author	SHA1	Message	Date
Lucpen	f434d0c671	Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) ... * feat added stubs to picard_liftovervcf * feat adding stubs to gatk4_mergevcfs * feat adding stubs to gatk4_filtermutectcalls * fix tests * fix output name filtermutectcalls * fix test * fix added missing [ * Update tests/modules/gatk4/mergevcfs/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/gatk4/filtermutectcalls/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/picard/liftovervcf/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Trying something on picard_liftovervcf * fix adding test data for stubs * fix added bracket and unindented workflow * fix picard 2.27.1 -> 2.27.0 to solve PaddingError * Update main.nf fix added tbi to stub Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>	2022-09-28 09:50:11 +02:00
Lucpen	f079367416	Picard liftover vcf (#1431) ... * Building Picard liftovervcf module * Building Picard liftovervcf module_test * Building Picard liftovervcf pytest * Module for picard liftover vcf created * Fixed files after linting test * Fixed trailing whitespace * Checked files with prettier * further formatting with prettier * Fixed test.yml * Fixed input variable names * Changed contain test.liftef.vcf * Changed contain in test.yml test.liftef.vcf * Run prittier * Going back to previous version of test.yml * downgrading picard to 2.26.10 from 2.26.11 * Update modules/picard/liftovervcf/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Print available memory Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Output from .vcf to .vcf.gz * Added spaces to align emit * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Removing md5sum test Co-authored-by: jemten <jemten@users.noreply.github.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>	2022-04-07 07:50:58 -04:00