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Author SHA1 Message Date
Michael L Heuer
bc7b5b3a12
Add dsh-bio export-segments module (#631) 
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
 2021-08-17 15:53:41 +02:00
James A. Fellows Yates
6c633ef305
Specify in guidelines one should split CPUs when module has n > 1 tool (#660) 
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* Describe CPU splitting

* Update README.md

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>

* More CPU examples

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
 2021-08-17 15:43:25 +02:00
James A. Fellows Yates
69b21f0dc0
Update test.yml (#668) 2021-08-17 15:08:21 +02:00
Anders Jemt
b261c1f549
Expansionhunter (#666) 
Please enter the commit message for your changes. Lines starting

* adds expansionhunter module

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2021-08-16 17:47:42 +02:00
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