a813e2e3a6
Add bcftools reheader ( #585 ) ( #608 )
...
* local tests and linting passing (#585 )
* 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>
* Added module arriba (#611 )
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
* Added module arriba
* Changes in test configs
* Added module Arriba for fusion detection
* Fixed review comments
* Added an output option for discarded fusions
* Resolved some conflits
* conflicts
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* added test for new header
* enhance module fastp: add `save_merged` (#598 ) (#614 )
* enhance module fastp: add `save_merged` (#598 )
* removed md5sum checks from log and json
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
3 years ago
6f561b3b41
enhance module fastp: add `save_merged` ( #598 ) ( #614 )
...
* enhance module fastp: add `save_merged` (#598 )
* removed md5sum checks from log and json
3 years ago
3cabc95d0e
Added module arriba ( #611 )
...
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
* Added module arriba
* Changes in test configs
* Added module Arriba for fusion detection
* Fixed review comments
* Added an output option for discarded fusions
* Resolved some conflits
* conflicts
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
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>
3 years ago
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>
3 years ago
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>
3 years ago
217303f5c1
Add option -p to set the # of cpus on stringtie ( #601 )
...
* Add option -p to set the # of cpus on stringtie
* Bump version 2.1.7 to stringtie modules
* Output stringtie/merge version
* Fix padding
* Apply suggestions from code review
* Defining software variable
* Fix test, gff can't be md5 check, contains instead
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
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
3 years ago
f43778b0e6
Updated the version of STAR in align and genomegenerate modules ( #604 )
...
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
1a26d48104
module: picard sortsam ( #603 )
...
* Add picard/sortsam module
* Fix container links
* Changes after code review
* Input meta in the right place
3 years ago
10502399ad
Replaced param with input val channel ( #595 )
...
* Replaced param with input val channel
* Apply suggestions from code review
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review (missed one)
* YAML lint
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
e4df336294
Add hifiasm module ( #596 )
...
* Add hifiasm module
* Tidy up module
* Add pacbio files to test_data.config
3 years ago
2e619add87
Add samtools ampliconclip ( #590 )
...
* created template for `samtools/ampliconclip` (#584 )
* All tests passing (#584 )
* Linting fixed (#584 )
* Final linting fixed (#584 )
* Optional output flags moved to `input` (#584 )
* typo fix (#584 )
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
e7e30b6da6
Bump Pangolin to 3.1.7 ( #593 )
...
* Bump Pangolin to 3.1.7
* Update md5sum
* Update README
* Re-word
* Re-word again
* Use channels
3 years ago
5dd049047d
Fix tyop in output for rseqc/junctionannotation ( #592 )
3 years ago
0b40798d1b
fix: lofreq/callparallel missing arg ( #562 ) ( #586 )
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
2ade120249
Add --paired flag to umitools dedup and bump to 1.1.2 ( #583 )
...
* Add --paired flag to umitools dedup and bump to 1.1.2
* paired not paired_end
* Fix ECLint
3 years ago
adfb8a3d65
fix: update samtools_merge ( #582 )
...
* fix: update samtools_merge
* Update modules/samtools/merge/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
3 years ago
65ab646870
fix: update seqkit to 0.16.0 ( #581 )
3 years ago
b3c4667732
fix: update to gatk4.2.0.0 ( #575 )
...
* fix: update to gatk4.2.0.0
* fix: update md5sum
3 years ago
d624336cc1
fix: update to gatk4.2.0.0 ( #580 )
3 years ago
c8877835c2
fix: update to gatk4.2.0.0 ( #579 )
3 years ago
e7be649029
fix: update to gatk4.2.0.0 ( #578 )
3 years ago
9fb21e1a84
fix: update to gatk4.2.0.0 ( #577 )
3 years ago
bee23ba899
fix: update to gatk4.2.0.0 ( #576 )
3 years ago
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
3 years ago
Johnathan D