praveenraj2018 598ca152ec Intervallisttools (#491) ... * added intervallisttools module * add intervallisttools module * arguments are now supplied using options.args * removed java heapsize settings * changes in main.nf and it is tested * comment added * Update software/gatk4/intervallisttools/meta.yml Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update tests/software/gatk4/intervallisttools/test.yml Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * review comment on tags in bedtointerval * modified the test to get input from bedtointerval module * Update software/gatk4/intervallisttools/meta.yml * Apply suggestions from code review Co-authored-by: Kevin Menden <kevin.menden@live.com> * Apply suggestions from code review * Update tests/config/pytest_software.yml Co-authored-by: Kevin Menden <kevin.menden@live.com> * Apply suggestions from code review * Apply suggestions from code review Co-authored-by: @praveenraj2018 <praveen.raj.somarajan@ki.se> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Kevin Menden <kevin.menden@live.com>		2021-05-12 11:44:36 +02:00
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applybqsr	remove deprecated test tags (#440)	2021-04-13 18:03:09 +01:00
baserecalibrator	remove deprecated test tags (#440)	2021-04-13 18:03:09 +01:00
bedtointervallist	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
createsequencedictionary	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
fastqtosam	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
haplotypecaller	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
intervallisttools	Intervallisttools (#491)	2021-05-12 11:44:36 +02:00
markduplicates	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
mergebamalignment	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
mergevcfs	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
revertsam	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
samtofastq	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
splitncigarreads	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00
variantfiltration	Update functions.nf to be more flexible for publishing by meta keys (#423)	2021-04-09 17:23:56 +01:00