Abhinav Sharma
0954204f9e
Add bcftools/norm module ( #655 )
...
* Initial draft [ci skip]
* trigger first test
* update output file path
* Tests passing
* finishing touches for meta.yml and update checksum
* tweak checksum
* add threads to the module
* skip version info for matching test md5sum [ci skip]
* Add ref fasta and finalize the module
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-16 17:40:03 +02:00
JIANHONG OU
6e68c1af9a
update typos. change quote from ' to ". ( #652 )
2021-08-16 11:57:22 +02:00
Robert A. Petit III
653e9e05b1
add module for dragonflye ( #633 )
...
* add module for dragonflye
* fix tests for dragonflye
* Update test.yml
* Update meta.yml
* Update main.nf
* Update main.nf
* Update modules/dragonflye/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-16 11:51:30 +02:00
Abhinav Sharma
67cc3bd116
Add bcftools/concat module. ( #641 )
...
* draft for bcftools modules [ci skip]
* initial test for bcftools concat
* Update the params for testing
* fix tests
* Accomodate code review [ci skip]
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update the meta file and open PR for review
* Update the keyword
* Update the tags for module [ci skip[
* add threads
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-08-10 15:10:27 +02:00
Christian Mertes
28b023e6f4
Require r-base>=3.5 for RSeqC Conda envs ( #654 )
...
* require conda-forge::r-base>=3.5 for conda-envs
* have same conda requirements for all rseqc submodules
2021-08-05 18:59:56 +01:00
praveenraj2018
5de3f2c50e
Added PL tag in read group information for downstream analysis ( #649 )
...
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-08-04 11:16:51 +02:00
James A. Fellows Yates
292e8eceb9
module: MALT/RUN ( #646 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add MALT with incomplete tests
* Parameter typo fix
* Clean up test yaml
* Finish MALT module prior UNZIP and MALT_BUILD modiules
* Add required modules for tests
* Sync test out with malt-build
* Fix input parameters in tests based on final build module
* Update modules/malt/run/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-04 11:06:08 +02:00
James A. Fellows Yates
6913da9d2d
module: MALT/BUILD ( #645 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Start MALT-build
* Start MALT build (missing meta files and outputs specS)
* Local tests
* Correct test map_type
* Finished module, just waiting for UNZIP module to finalise tests
* Correct tests in preparation for Unzip
* Ouptut log file too
* Update meta.yml
* Rename log file
* Rename log file
* Remove debugging stuff
* Add Unzip module
* Linting update
* Linting update
* Fix input db
* Fix db file in cmd
* Update modules/malt/build/main.nf
* Update modules/malt/build/main.nf
* Update main.nf
2021-08-03 16:24:19 +02:00
James A. Fellows Yates
4f1c1601cf
module: bwa/sampe ( #625 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* Add sampe
* Fix container paths
* Update based on code review from @grst
* Update input docs
2021-08-02 15:37:48 +02:00
James A. Fellows Yates
8a2f01c416
module: bwa/samse ( #626 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* Add bwa samse
* Fix container paths
* remove TODO comment
* Updated based on code from from @grst on bwa/sampe
* Clarify output docs
2021-08-02 15:21:23 +02:00
James A. Fellows Yates
e01a98a704
module: unzip ( #642 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add unzip module
* Remove missing TODOs update mtea
* Apply changes after code-review from @grst
* Account for user trying to supply two input archives
* Remove debugging test
* Update modules/unzip/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Correct output path
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-08-02 09:40:57 +02:00
James A. Fellows Yates
2a7c60e965
Guidelines update: describe workaround for modules called build ( #647 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Update README.md
2021-07-31 11:30:26 +02:00
Harshil Patel
29c8474240
Update Nextclade to output all files by default ( #638 )
2021-07-28 19:49:50 +01:00
Harshil Patel
c5235a983d
nf-core modules bump-versions for all modules ( #630 )
...
* Add blacklist of modules that shouldn't be updated to .nf-core.yml
* nf-core modules bump-versions for all modules
* Remove TODO statements identified by linting
* Fix md5sums for failing tests
* Fix more tests
2021-07-28 09:10:44 +01:00
Michael L Heuer
e1951d54be
Update dsh-bio to 2.0.5 ( #628 )
2021-07-27 15:32:18 +01:00
James A. Fellows Yates
c41c9487e9
Specify more guidelines on input channels ( #615 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
2021-07-27 09:36:03 +02:00
James A. Fellows Yates
45dee96bdf
module: bwa/aln ( #624 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* fix container paths
* Sync bwa version samese/sampe
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-27 08:13:48 +01:00
Johnathan D
a21cc95c69
Add variantbam ( #618 )
...
* template created for variantbam (#616 )
* 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>
* fixed autogenerated biocontainter links
* variantbam module passing all tests/lints (#616 )
* Added an optional output junction channel in STAR (#621 )
* Added an optional output channel for chimeric junctions
* Fix in test.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* removed qcreport output
fixes #616
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>
2021-07-26 19:07:29 +01:00
praveenraj2018
df909015b6
Added an optional output junction channel in STAR ( #621 )
...
* Added an optional output channel for chimeric junctions
* Fix in test.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-26 19:03:30 +02:00
Johnathan D
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>
2021-07-23 22:24:19 +01:00
Johnathan D
6f561b3b41
enhance module fastp: add save_merged ( #598 ) ( #614 )
...
* enhance module fastp: add `save_merged` (#598 )
* removed md5sum checks from log and json
2021-07-23 10:44:00 +01:00
praveenraj2018
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>
2021-07-22 15:19:42 +01:00
James A. Fellows Yates
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>
2021-07-22 11:19:51 +01:00
James A. Fellows Yates
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>
2021-07-21 15:22:19 +01:00
James A. Fellows Yates
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>
2021-07-21 15:51:33 +02:00
Jose Espinosa-Carrasco
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>
2021-07-21 15:38:40 +02:00
James A. Fellows Yates
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
2021-07-21 14:34:21 +01:00
praveenraj2018
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>
2021-07-21 13:30:52 +01:00
James A. Fellows Yates
1a26d48104
module: picard sortsam ( #603 )
...
* 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
f892f273fe
Updated optional input definition ( #599 )
...
* Updated optional input definition
* Update README.md
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 11:03:49 +01:00
James A. Fellows Yates
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>
2021-07-21 10:00:48 +02:00
Svyatoslav Sidorov
06a8ac9b72
Merge branch 'nf-core:master' into master
2021-07-21 10:37:14 +03:00
Harshil Patel
e4df336294
Add hifiasm module ( #596 )
...
* 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 )
...
* 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 )
...
* 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
Johnathan D
8c294882d7
fix: lofreq/call test.yml md5sum ( #587 )
2021-07-19 08:53:27 +01:00
Harshil Patel
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
2021-07-16 14:21:08 +01:00
Maxime U. Garcia
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>
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 )
...
* 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 )
...
* 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
Svyatoslav Sidorov
95dfa7bc8d
Enhance bedtools ( #557 )
...
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* Generalized intersect and genomecov
* Finished subtract and tests for intersect and genomecov
* Finished up meta YAMLs
* Replaced functions.nf in subtract
* do not add "." in prefix when suffix is set (#550 )
when using the suffix option in the fastqc module it gets added with a "." to the ${meta.id}, this leads to sample name clashing when passing the fastqc output of raw and processed files suffixed with "trim" or "clean" to multiqc.
I suggest to remove the "." this would also be more consistent with the prefix def in most of the other nf-core modules.
##' Ref:
https://nfcore.slack.com/archives/CJRH30T6V/p1625129138043900
* Modules TLC (#551 )
* Modules TLC
* Fix all the tests
* Fix linting failures (#552 )
* Modules TLC
* Fix all the tests
* Fix linting failures
* Soft-link build files to bypass lint error
* Update software/rseqc/junctionannotation/main.nf
* Fix rsem (#555 )
* bump bcftools filter
* fix bcftools
* rsem/preparereference
* added calculateexpression
* meta.yml and pytest_software
* paired end
* add test.yml
* fix rseqc/junctionsaturation (#553 )
* bump bcftools filter
* junctionsaturation meta.yml and test
* pytest config entry
* bump bcftools version down again
* fix test
* fix bcftools
* Adapt linting action (#556 )
* bump bcftools filter
* fix bcftools
* adapt module linting
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/intersect/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/bedtools/subtract/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/genomecov/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update tests/software/bedtools/intersect/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Fixed variable names in intersect and genomecov
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: riederd <dietmar.rieder@i-med.ac.at>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-07-07 09:44:09 +01:00
Sviatoslav Sidorov
2c421b7a43
Merge branch 'master' of https://github.com/nf-core/modules
2021-07-06 22:58:28 +03:00
