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Author SHA1 Message Date
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
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
Maxime U. Garcia
e0d820f9f4
Add snpeff (#546) 
* feat: add snpeff

* fix: linting

* fix: tests

* fix: add csv output

* fix: add params information

* fix: improve script

* Update software/snpeff/environment.yml

* Update software/snpeff/environment.yml

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

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

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-06 13:40:55 +01:00
Maxime U. Garcia
7b4a28b6e8
feat: add VEP module (#547) 
* feat: add VEP module

* fix: name

* fix: EC lint]

* feat: add info about params

* fix: params as params, not input

* fix: improve script

* Update software/ensemblvep/environment.yml

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

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-06 14:11:11 +02:00
Mei Wu
3f4eccbf0f
Delly/call (#565) 
* testing works but need to fix paths and add exclude list

* edited meta file and removed TODOs

* left over TODOs

* test passed, final push

* resolving initial comments

* Update software/delly/call/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-06 12:54:14 +01:00
Johnathan D
79f3a55f6e
Lofreq call (#564) 
* created templates

* updated functions.nf to the one on dev

* Created test main

* Fasta added and docker, conda, singularity passing

* Fixed output version lint
 2021-07-06 10:41:00 +01:00
Ravneet Bhuller
42adce7af1
Pull request for module: lofreq/callparallel (#562) 
* first commit

* updated file

* edited files

* Update test.yml

* Update software/lofreq/callparallel/main.nf

* Update test.yml

* Update tests/software/lofreq/callparallel/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-06 09:51:38 +01:00
Charles Plessy
45f2f1ee5f
Input a triple (id, fasta, params) to last/lastal (#563) 
The `last/lastal` submodule takes query sequences to align to a target
index, and optionally takes one set of alignment parameters (including a
score matrix) computed by the `last/train` module for each of the
sequences.

In the previous implementation the sequences and the alignment
parameters were provided in different channels, causing them to be
sometimes desynchronised.

In the patched implementation, `last/lastal` takes a 3-tuple as
input to ensure synchronicity.  To produce this tuple in a pipeline,
one can use the `join` command as in the following example.

     LAST_TRAIN  ( query,
                   target )
     LAST_LASTAL ( query.join(LAST_TRAIN.out.param_file),
                   target )

In case no parameter file is computed one can pass a dummy file
to the module as follows:

     LAST_LASTAL ( query.map { row -> [ row[0], row[1], [] ] },
                   target )
 2021-07-06 09:35:04 +01:00
Johnathan D
fbab00238f
Lofreq filter (#559) 
* Created module template (#558)

* Created meta and implemented main (#558)

* Conda test and lint passing (#558)

* Updated functions.nf to the one on dev (#558)

* Update software/lofreq/filter/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-05 10:24:45 +01:00
Ravneet Bhuller
cd8bacc90a
PR for lofreq/indelqual module (#539) 
* first commit

* edited functions.nf

* edited functions.nf

* version line updated

* Update software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update software/lofreq/indelqual/meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/lofreq/indelqual/test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Update tests/software/lofreq/indelqual/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* updated files

* updated file

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-07-05 10:17:57 +01:00
Kevin Menden
2395734492
Adapt linting action (#556) 
* bump bcftools filter

* fix bcftools

* adapt module linting
 2021-07-02 14:15:32 +02:00
Kevin Menden
b59e8054e4
fix rseqc/junctionsaturation (#553) 
* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools
 2021-07-02 13:31:09 +02:00
Kevin Menden
fce4e60864
Fix rsem (#555) 
* bump bcftools filter

* fix bcftools

* rsem/preparereference

* added calculateexpression

* meta.yml and pytest_software

* paired end

* add test.yml
 2021-07-02 13:09:48 +02:00
Harshil Patel
b5f6a1da79
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
 2021-07-01 19:50:14 +01:00
Harshil Patel
b3278a1e63
Modules TLC (#551) 
* Modules TLC

* Fix all the tests
 2021-07-01 16:13:01 +01:00
riederd
601bf5eb64
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
 2021-07-01 11:14:58 +01:00
James A. Fellows Yates
394273f173
damageprofiler (#545) 
* Add damageprofiler module

* Fix tests

* Bump container hopefully with font fix

* Following code review
 2021-06-30 09:46:24 +02:00
MGordon09
af4b8814b8
update muscle (#542) 2021-06-28 08:20:02 +02:00
Maxime U. Garcia
81aba5734c
Add modules bgziptabix (#544) 
* feat: add modules bgziptabix

* fix: add module to config

* fix: lint

* fix: tests
 2021-06-25 10:52:02 +02:00
MGordon09
4d711a1428
Add metaphlan3 module (#543) 
* Add metaphlan3 module

* remove whitespace
 2021-06-25 08:15:15 +02:00
JIANHONG OU
e0b7952b56
Pairtools select (#523) 
* add software/pairtools

* create a branch for pairtools/select

* fix the different output of conda and docker.

* rmove the md5sum for gzip files.

* Update software/pairtools/select/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* update test file and documentation.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2021-06-23 15:58:31 +02:00
Jose Espinosa-Carrasco
e621f78757
Update salmon/quant to provide '--libType A' option (#536) 
* Update salmon/quant to provide '--libType A' option

* Modify lib_type description to  be a string

* Update tests

* lyb_type can be explicitly overwrite

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-06-17 15:13:47 +02:00