James A. Fellows Yates
553f51d6bf
fix: picard filtersamreads input ( #610 )
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* 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>
2021-07-22 11:19:51 +01:00
James A. Fellows Yates
3cc43838e1
module: picard filtersamreads ( #602 )
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* 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>
2021-07-21 15:22:19 +01:00
James A. Fellows Yates
2d26b037a1
(another) fix: picard sortsam ( #606 )
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* 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>
2021-07-21 15:51:33 +02:00
Jose Espinosa-Carrasco
217303f5c1
Add option -p to set the # of cpus on stringtie ( #601 )
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* 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>
2021-07-21 15:38:40 +02:00
James A. Fellows Yates
a0019d4175
fix: picard sortsam ( #605 )
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* 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
2021-07-21 14:34:21 +01:00
praveenraj2018
f43778b0e6
Updated the version of STAR in align and genomegenerate modules ( #604 )
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* 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>
2021-07-21 13:30:52 +01:00
James A. Fellows Yates
1a26d48104
module: picard sortsam ( #603 )
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* Add picard/sortsam module
* Fix container links
* Changes after code review
* Input meta in the right place
2021-07-21 13:48:07 +02:00
James A. Fellows Yates
10502399ad
Replaced param with input val channel ( #595 )
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* 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>
2021-07-21 10:00:48 +02:00
Harshil Patel
e4df336294
Add hifiasm module ( #596 )
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* Add hifiasm module
* Tidy up module
* Add pacbio files to test_data.config
2021-07-20 21:50:22 +01:00
Johnathan D
2e619add87
Add samtools ampliconclip ( #590 )
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* 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>
2021-07-20 21:31:31 +01:00
Harshil Patel
e7e30b6da6
Bump Pangolin to 3.1.7 ( #593 )
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* Bump Pangolin to 3.1.7
* Update md5sum
* Update README
* Re-word
* Re-word again
* Use channels
2021-07-20 12:25:36 +01:00
Harshil Patel
5dd049047d
Fix tyop in output for rseqc/junctionannotation ( #592 )
2021-07-20 11:27:47 +01:00
Johnathan D
0b40798d1b
fix: lofreq/callparallel missing arg ( #562 ) ( #586 )
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-19 09:19:27 +01:00
Harshil Patel
2ade120249
Add --paired flag to umitools dedup and bump to 1.1.2 ( #583 )
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* Add --paired flag to umitools dedup and bump to 1.1.2
* paired not paired_end
* Fix ECLint
2021-07-16 14:21:08 +01:00
Maxime U. Garcia
adfb8a3d65
fix: update samtools_merge ( #582 )
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* 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>
2021-07-16 14:32:17 +02:00
Maxime U. Garcia
65ab646870
fix: update seqkit to 0.16.0 ( #581 )
2021-07-16 11:54:21 +02:00
Maxime U. Garcia
b3c4667732
fix: update to gatk4.2.0.0 ( #575 )
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* fix: update to gatk4.2.0.0
* fix: update md5sum
2021-07-16 11:26:28 +02:00
Maxime U. Garcia
d624336cc1
fix: update to gatk4.2.0.0 ( #580 )
2021-07-16 11:25:22 +02:00
Maxime U. Garcia
c8877835c2
fix: update to gatk4.2.0.0 ( #579 )
2021-07-16 11:24:29 +02:00
Maxime U. Garcia
e7be649029
fix: update to gatk4.2.0.0 ( #578 )
2021-07-16 11:23:08 +02:00
Maxime U. Garcia
9fb21e1a84
fix: update to gatk4.2.0.0 ( #577 )
2021-07-16 11:22:01 +02:00
Maxime U. Garcia
bee23ba899
fix: update to gatk4.2.0.0 ( #576 )
2021-07-16 11:18:27 +02:00
Harshil Patel
e937c7950a
Rename software/ directory to modules/ to re-organise module structure ( #567 )
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* 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
