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3 commits

Author SHA1 Message Date
FriederikeHanssen
19035c99d1
Add thread option to samtools modules (#1069)
* add thread option to samtools modules

* fix tests

* fix tests

* fix tests

* Fix naming to fix tests

* cpus-1 to account for mainthread

* remove thread in ampliconclip, docu doesn't report this param

* add -1 to all other applicable samtools modules

* Update samtools version

* Update checksums

* retrigger GHA after update

* Update modules/samtools/fastq/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/fixmate/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/flagstat/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/index/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/merge/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/stats/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/view/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Fix md5sum fixmate

* Fix md5sums

* sth funny with the fixmate checksums

* more md5sums updates

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 22:24:47 +01:00
FriederikeHanssen
ac1e6df076
Update to allow cram + update needed to use the gatk4 modules in sarek (#976)
* Make samtools/merge cram compliant

* samtools/stats cram compliance

* update yml file

* samtools/view to deal with crams

* Update tests to make sure cram works

* also fix tmp dir and min mem in one go

* basequalityrecal test for cram + min mem + tmpdir

* update haplotypecaller for sarek

* update haplotype yml

* update markdup to allow multiple bams, take out params to be passed with options.args

* remove TODO statement

* Remove variable md5sum

* add emtpy input to stats module in subworkflows

* subworkflows seem to work now on my side

* Apply code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* replace bam with input to be more inclusive

* rename everywhere

* rename input

* remove variable checksum

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-10-29 13:01:05 +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
Renamed from tests/software/samtools/merge/test.yml (Browse further)