Commit graph

346 commits

Author SHA1 Message Date
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
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
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
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
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
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
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
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
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
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
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
Svyatoslav Sidorov
01dc6a289d
Feat seqtk update (#503)
* 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

* Added seqtk/subseq and checking for seed in seqtk/sample

* Separate authors in software/seqtk/sample/meta.yml

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

* Align commans in output channesl software/seqtk/subseq/main.nf

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

* Define prefix in software/seqtk/subseq/main.nf

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

* Use prefix in output file name software/seqtk/subseq/main.nf

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

* Define suffix in options in tests/software/seqtk/subseq/main.nf

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

* Change output file name in tests/software/seqtk/subseq/test.yml

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

* Remove a to-do point from tests/software/seqtk/subseq/test.yml

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

* Added --no-name into gzip commands

* Update samtools from 1.10 to 1.12 (#530)

* feat: remove social preview image to use GitHub OpenGraph

* feat: update samtools from 1.10 to 1.12

* fix: CI tests

* fix: add meta.yml file for samtools/merge

* Update software/samtools/merge/meta.yml

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

* Update software/samtools/merge/meta.yml

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

* 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

* Added seqtk/subseq and checking for seed in seqtk/sample

* 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

* Separate authors in software/seqtk/sample/meta.yml

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

* Align commans in output channesl software/seqtk/subseq/main.nf

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

* Define prefix in software/seqtk/subseq/main.nf

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

* Use prefix in output file name software/seqtk/subseq/main.nf

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

* Define suffix in options in tests/software/seqtk/subseq/main.nf

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

* Change output file name in tests/software/seqtk/subseq/test.yml

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

* Remove a to-do point from tests/software/seqtk/subseq/test.yml

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

* Added --no-name into gzip commands

* Replaced functions.nf in seqtk/subseq

* Refreshed tests for sample and subseq

* Corrected paired-end test and YAML description for sample

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-14 12:23:15 +01:00
JIANHONG OU
d9e48b70ca
Pairtools restrict (#522)
* add software/pairtools

* create a branch for pairtools/restrict

* fix the different output of conda and docker

* remove customized code.

* add newline to Frag.bed file.

* change the folder of frag.bed.

* change \n to \r\n

* Remove work.frag.bed

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-06-10 19:39:35 +02:00
JIANHONG OU
580d1e194a
Cooler digest (#517)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/digest

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-09 11:39:22 +02:00
JIANHONG OU
8d4c6de50d
Cooler dump (#516)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/dump

* remove the bin size from metadata.
2021-06-09 11:14:17 +02:00
aleksandrabliznina
0745213729
New last/mafconvert module to convert MAF alignments. (#527)
* New last/mafconvert module to convert MAF alignments.

The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5)
format and converts them in another format (axt, blast, blasttab, chain,
gff, html, psl, sam, tab).

This new module is part of the work described in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency.
We will upgrade it later.

* Delete white space.

* Update the function.nf file to the dev version.
2021-06-09 08:38:57 +02:00
Charles Plessy
ca321ce69d
New module last/postmask to filter alignment files (#526)
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
filters alignments in a MAF file to remove those with too many masked
(lower-case) positions compared with their score.

As other filter modules like `last/split`, its output file risks to
overwrite its input file as their names are constructed from the sample
ID when multiple filters are chained in the pipeline.  I added a check
that gives a clearer error message in this case.  Please let me know
what you think about; I can add this test to the existing LAST modules
as well.

This new module is part of the work discribed in Issue #464. During this
development, we fix the version of LAST to 1219 to ensure consistency.
We will upgrade it later.
2021-06-08 11:14:08 +02:00
Charles Plessy
f7ebc2fc48
New last/dotplot module for pairwise similarity plots (#529)
* New last/dotplot module for pairwise similarity plots

The `last-dotplot` tool takes a pairwise alignment in
[MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format,
possibly compressed with gzip, or in a tabular format produced by the
`maf-convert` tool, and produces a similarity dot-plot of the two
sequences in one of the graphical formats supported by the Python
Imaging Library.

A the tool guesses the output format by the file extension of the file,
which is constructed by the module at run time, I have used the `args2`
option to convey this information to the module.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence please ignore lint's version warning).

* Update the functions.nf file to the dev branch.

https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
2021-06-08 11:13:51 +02:00
Michael L Heuer
68c678de93
Remove docker.runOptions in favor of docker.userEmulation. (#525) 2021-05-27 18:29:17 +01:00
JIANHONG OU
a303c6ed5b
Pairtools sort (#524)
* add software/pairtools

* create a branch for pairtools/sort

* fix the different output of conda and docker.

* remove customized code.

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 18:25:23 +01:00
JIANHONG OU
9842a10833
Pairtools parse (#521)
* add software/pairtools

* create a branch for pairtools/parse

* fix the issue of bioconda output is different from docker.

* remove customized code from test.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 18:15:54 +01:00
JIANHONG OU
cc8439a167
Pairtools flip (#520)
* add software/pairtools

* create a branch for pairtools/flip

* fix the issue of PG line in output

* remove custom code from test.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 18:09:28 +01:00
JIANHONG OU
912f30e95a
Pairtools dedup (#519)
* add software/pairtools

* create a branch for pairtools/dedup

* remove dedup from the filename.
2021-05-27 17:51:27 +01:00
JIANHONG OU
18440df87a
add genmap/mappability (#509)
* add genmap/mappability

* Add index module.
Remove -w parameter from mappability module.

* change the output of genmap/index

* fix the lint error which can not handle stageAs.

* Apply suggestions from code review

* Update main.nf

* Update test.yml

* Update main.nf

* Update test.yml

* Update tests/software/genmap/mappability/main.nf

* Update software/genmap/mappability/main.nf

* Update software/genmap/mappability/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 22:12:10 +01:00
Charles Plessy
207930139a
New last/lastal module to align query sequences on a target index (#510)
* New last/lastal to align query sequences on a target index

`lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last)
suite.  It align query DNA sequences in FASTA or FASTQ format to a
target index of DNA or protein sequences.  The index is produced by
the `lastdb` program (module `last/lastdb`).  The score matrix for
evaluating the alignment can be chosen among preset ones or computed
iteratively by the `last-train` program (module `last/train`).  For
this reason, the `last/lastal` module proposed here has one input
channel containing an optional file, that has to be dummy when not used.

The LAST aligner outputs MAF files that can be very large (up to
hundreds of gigabytes), therefore this module unconditionally compresses
its output with gzip.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).

* Apply suggestions from code review

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

* Un-hardcode the path to the LAST index.

Among multiple alternatives I have chosen the following command to
detect the sample name of the index, because it fails in situations
where there is no index files in the index folder, and in situations
were there are two indexes files in the folder.  Not failing would
result in feeding garbage information in the INDEX_NAME variable.

    basename \$(ls $index/*.bck) .bck

In case of missing file, a clear error message is given by `ls`.  In
case of more than one file, the error message of `basename` is more
cryptic, unfortunately.  (`basename: extra operand ‘.bck’`)

Alternatives that do not fail if there is no .bck file:

    basename $index/*bck .bck
    find $index -name '*bck' | sed 's/.bck//'

Alternatives that do not fail if there are more than one .bck file:

    basename -s .bck $index/*bck
    ls $index/*.bck | xargs basename -s .bck
    find $index -name '*bck' | sed 's/.bck//'

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 22:10:48 +01:00
JIANHONG OU
34f555a26a
add software/pairix (#508)
* add software/pairix

* Update the functions.nf to new version.
Remove -p parameter and fix version output command.
fix the duplicated documentation.
2021-05-25 21:22:57 +01:00
aleksandrabliznina
4575e5455c
New last/split module to find split alignments. (#511)
* New last/split module to find split alignments.

The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
finds split or spliced alignments in a MAF file that is produced with, for
example, LAST `lastal` command.

This new module is part of the work discribed in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency. We will
upgrade it later.

* Update software/last/split/main.nf

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-24 20:15:57 +01:00
JIANHONG OU
ce68395240
add additional ucsc tools (#506)
* add additional ucsc tools

* Update software/ucsc/wigtobigwig/meta.yml

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Update the functions.nf and software name for ucsc/wigtobigwig and bigwigaverageoverbed.

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-05-20 15:39:33 -04:00
Charles Plessy
e75f88c68a
New module last/mafswap to reorder sequences in alignments (#500)
* New module last/mafswap to reorder sequences in alignments

The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reorders sequences in alignment files in Multiple Alignment Format.
When run without command-line arguments, it will swap the target and the
query sequences.  This is useful when turning a many-to-many alignment
into a many-to-one and then a one-to-one alignment in conjunction with
the `last-split` command (split, swap, split and swap again).

The LAST aligner outputs MAF files, but other tools also use this
format.  As MAF files can be very large (up to hundreds of gigabytes),
the module expects its input to be compressed with gzip and will
compress its output.

This new module is part of the work described in Issue #464.  During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence ignore lint's version warning).

* Update MD5 sum.

Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of
an empty file compressed with `gzip --no-name`…  This happened
because I forgot to update the config file after correcting the
module… sorry !

* Apply suggestions from code review

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

* Change name as suggested in pull request.

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 08:59:23 +01:00
aleksandrabliznina
b592cea30b
New last/train module to train alignment parameters. (#492)
* New last/train module to train alignment parameters.

The last-train command creates a parameter file that
will be used by last/lastal module for sequence alignment.
It takes indexed sequences and query sequences as input
and we use the metadata of both to create an id of the
parameter output file.

Submission of the LAST modules is discussed in more
details in the issue #464. For consistancy, we use LAST
version 1219 for this whole development and will upgrade later.

* Corrected files according to the nf-core v1.14 standards.

* Fixed function.nf file for the last-train module.

* Apply suggestions from code review

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

* Find index name.

* Correct after the input channels were changed.

* Use double underscore as a name separator.

Single underscores can happen in ids, therefore, we would like to keep two underscores.

* Remove extra spaces.

* Fixed the passing of the "score matrix" line.

* Apply suggestions from code review

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

* Update software/last/train/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 08:37:08 +01:00
praveenraj2018
598ca152ec
Intervallisttools (#491)
* added intervallisttools module

* add intervallisttools module

* arguments are now supplied using options.args

* removed java heapsize settings

* changes in main.nf and it is tested

* comment added

* Update software/gatk4/intervallisttools/meta.yml

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update tests/software/gatk4/intervallisttools/test.yml

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* review comment on tags in bedtointerval

* modified the test to get input from bedtointerval module

* Update software/gatk4/intervallisttools/meta.yml

* Apply suggestions from code review

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Apply suggestions from code review

* Update tests/config/pytest_software.yml

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Apply suggestions from code review

* Apply suggestions from code review

Co-authored-by: @praveenraj2018 <praveen.raj.somarajan@ki.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-05-12 11:44:36 +02:00
Jose Espinosa-Carrasco
cdff9a056d
Increase conda build time (#489)
* Add module description to yml

* Increase conda build time
2021-05-10 12:23:52 +01:00
MGordon09
1f465a63d0
Bbmap/bbduk (#487)
* bbmap/bbduk module created

* created bbmap/bbduk module

* updated main.nf

* changed test.yml tags

* removed whitespaces

* Adjusted main.nf spacing

* whitespace, tags

* fix optional files, tags, tidy code

* fix suffix

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-10 11:45:52 +01:00
Ravneet Bhuller
12ebce50f7
Request to review code for seqtk/sample module (#488)
* added files

* removed file

* added file

* changed files

* changed files

* edited file

* edited file

* edited files

* edited files

* edited files

* edited tags

* edited tags

* edited tags

* edited tags

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 23:55:35 +01:00
Jose Espinosa-Carrasco
f8ea9828cd
Add artic minion (#486)
* Add artic minion module

* Add fast5 to test data configuration

* Add test for artic minion
2021-05-07 16:37:35 +01:00
Harshil Patel
b6e4ecabba
Add Nextclade module (#484)
* Bump pangolin version

* Add nextclade to software list

* Add nextclade module

* Update md5sum for Pangolin due to version bump

* Adding some URL to meta.yml

* Adding new line at end of file

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-05-06 15:48:15 +01:00
Yuk Kei Wan
faf77d6fee
add nanolyse module (from nanoseq modules) (#471)
* add nanolyse modules

* add clean.fastq.gz path and md5sum

* fix errors

* remove unreproducible md5sum

* solve linting problem

* address PR suggestions

* GET_NANOLYSE_FASTA as a local module

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/main.nf

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

* Update software/nanolyse/meta.yml

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

* Update software/nanolyse/meta.yml

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

* Update tests/software/nanolyse/test.yml

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

* Update tests/software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* update to the version from nf-core/tools-dev

* input and output files cannot have the same names

* Update test.yml

* Update software/nanolyse/main.nf

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

* Update tests/software/nanolyse/main.nf

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

* Update test.yml

* revert

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-05 11:20:09 +01:00
Michael L Heuer
e3cf4c822c
Update dsh-bio modules to version 2.0.4 (#482)
* Update dsh-bio modules to version 2.0.4

* update docker tag

* update md5 checksums

* Update software/dshbio/filtergff3/main.nf

* Update software/dshbio/splitgff3/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 14:28:44 +01:00
Edmund Miller
bdee7804ca
build: Bump version to 21.04.0 (#481)
* build: Bump version to 21.04.0

Recent stable release https://github.com/nextflow-io/nextflow/releases/tag/v21.04.0

* Update README.md

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 00:38:29 +01:00
Kevin Menden
5e86245388
updated paths to test data (#478)
* updated paths to test data

* Update test_data.config

changed file names
2021-05-03 07:13:07 +01:00
Yuk Kei Wan
6ad50f8ec4
Add stringtie merge module (from nanoseq modules) (#475)
* add stringtie merge module

* add md5sum and path for stringtie.merged.gtf

* fix errors

* try fixing stringtie check error

* add tag

* remove unreproducible md5sum

* address PR suggestions

* hopefully fix linting error
2021-05-03 07:18:51 +02:00
Charles Plessy
16d20a7cc4
New last/lastdb module to index sequences before alignment. (#476)
* New last/lastdb module to index sequences before alignment.

The `lastdb` command creates a sequence index for the LAST aligner
(https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ
format, and compression is handled automagically.  DNA or protein
sequences can be indexed.

The sequence index is a collection of files sharing the same basename.
This module sets the basename to the sample identifier (`$meta.id`) and
creates the index in a directory always called `lastdb`.  The module's
output channel then conveys a copy of the metadata and the path to the
`lastdb` directory.

Other modules will follow (see Issue #464).  The LAST aligner can align
proteins to proteins, DNA to DNA and can translate DNA align to
proteins.

* Remove trailing whitespace.

* Apply suggestions from code review

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

* Update as suggested in PR.

* Attempt to pass linting.

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 11:36:31 +01:00
Harshil Patel
466ab67808
Fixes for nanoseq modules (#479)
* Fix minimap2 index module

* Fix minimap2 index tests

* Fix graphmap2 index module

* Fix graphmap2 module

* Fix ECLint

* Fix bedtools bamtobed module

* Fix tests for bedtools bamtobed module

* Add tag for graphmap2 align module

* Fix EClint

* Fix qcat module

* Add md5sum for graphmap2/align module

* Remove non-started test data file

* Remove md5sum for graphmap2 align
2021-04-30 15:57:43 +01:00
Yuk Kei Wan
05f479f03a
add qcat module (from nanoseq modules) (#469)
* add qcat module

* remove md5sum(nom-reproducible)
2021-04-30 13:20:56 +01:00
Yuk Kei Wan
3f804ee667
add bedtools bamtobed module (from nanoseq modules) (#466)
* add bedtools bamtobed module

* fix erros

* fix linting problem
2021-04-30 13:20:31 +01:00
Yuk Kei Wan
a8720463ac
add graphmap index and align modules (from nanoseq modules) (#468)
* add graphmap index module

* add graphmap2/index

* add graohmap2 align module

* remove graphmap2 align md5sum
2021-04-30 13:18:58 +01:00
Yuk Kei Wan
05b067e907
add minimap2 index module (#467) 2021-04-30 13:18:11 +01:00
Florian Wuennemann
88dda738ac
Added kallistobustools/count (#409)
* Basic kb-python count functionality for scRNA-seq quantification working.

* Added tests and test data for workflow kite.

* Removed trailing whitespace

* Changed output channels to tuples with meta

Based on suggestions by @KevinMenden.

* Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message.

* Update software/kallistobustools/count/main.nf

@KevinMenden fixed wrong path definition

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Increased version of kb-python

* Updated tests with raw links.

* Fixed subtool referencing: kallistobustools/count

* Added newline

* Update software/kallistobustools/count/main.nf

Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-04-30 07:27:17 +02:00
FriederikeHanssen
9ce4427275
Add gvcf index files (#472) 2021-04-28 20:23:10 +01:00
Daniel Lundin
d7a3286a9a
New module to use hmmalign from HMMER to align sequences (#470)
* Ignore vim tmp files

* Added hmmalign module, not yet tests

* Test output

* Replaced functions.nf for hmmalign with upstream

* Update software/hmmer/hmmalign/main.nf

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

* Update software/hmmer/hmmalign/main.nf

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

* Update software/hmmer/hmmalign/meta.yml

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

* Update tests/software/hmmer/hmmalign/main.nf

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

* Update tests/software/hmmer/hmmalign/main.nf

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

* Update tests/software/hmmer/hmmalign/test.yml

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

* Update tests/config/pytest_software.yml

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

* Update software/hmmer/hmmalign/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-28 11:21:24 +01:00
Jose Espinosa-Carrasco
d63ff4ba1b
Add artic guppyplex (#455)
* Adding artic guppyplex module

* Adding guppyplex tests

* Fix tests

* Correcting typo

* Fix lint

* Fix test

* Missing description

* Missing descriptions

* Update functions to last version as suggested

* Bump newest version of nanoplot
2021-04-27 15:57:34 +01:00
FriederikeHanssen
ae154b8c3f
Add human data paths (#458)
* Add new human data and fix sarscov paths

* Fix filename typo

* Apply code review

* replace index with to match sarscov data

* lower case

* indent everythin

* Adapt sarscov keys to new naming convention

* Update test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-19 15:30:43 +01:00
Kevin Menden
f7e3b8260c
change process.time for tests to 2h (#452) 2021-04-16 13:08:03 +01:00
Harshil Patel
defaca4f1b
Add ucsc/bedclip module (#450)
* Add ucsc/bedclip module

* Fix tests

* Fix nf-core lint
2021-04-15 22:04:59 +02:00
Anthony Underwood
2ed9b6ae28
Raxmlng (#443)
* new raxml module

* new raxml module

* pass in args for bootstrap and add test for support file

* remove unnecessary tag

* ensure tags meet guidleines

* Apply suggestions from code review

* Update to latest functions file

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-14 08:38:59 +01:00
Jose Espinosa-Carrasco
750bd8c3e3
Finish deeptools modules (#442)
* Adding bigWig and deeptools computeMatrix files to config

* Adding meta.yml for deeptools modules

* Add test for deeptools modules

* Fixing and reordering tags

* Fixing conda test that worked in local...

* Apply suggestions from code review

* Changing bigwig file pattern to include bigwig extension

* Saving after last change is a good practice

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 21:48:43 +01:00
Jose Espinosa-Carrasco
a9fcbd93cc
Move assembly test files from genome to illumina (#441)
* FIx plasmidid tests for new contigs.fasta file

* Fixing two md5sum hashes

* Update test path in config for illumina assembly files

* Update modules using assembly files

* Correctly setting path of assembly files

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 12:52:11 +02:00
Kevin Menden
1d874bb0d0
Finish rseqc modules (#439)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

* added rseqc/bamstat tests

* added tests/meta.yml for rseqc/inferexperiment

* added test/meta.yml for rseqc/inner_distances

* added meta.yml and tests/main.nf for junctionannotation (test not running)

* added test/meta.yml for rseqc/readdistribution

* finished test/meta.yml for rseqc/readduplication

* added entries to pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 08:49:32 +01:00
Harshil Patel
c99ab09f8d
Add kraken2 pigz multi-tool container for compressing output fastq files (#434)
* Add kraken2 pigz multi-tool container for compressing output fastq files

* Add untar to pytest config

* Add untar process to kraken2 tests

* Remove unneeded tags
2021-04-12 18:47:34 +02:00
Anthony Underwood
df8910de4e
Iqtree (#435)
* Resolve suggests after PR review

* add newline to functions

* need variable interpolation using double quotes; remove unnecessary tag

* add a more resilient link to raw github files

* remove trailing slash

* Update software/iqtree/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 17:01:26 +01:00
Jose Espinosa-Carrasco
3ac21ff0dc
Add abacas module (#431)
* Add abacas module

* Add test for abacas module

* Add Harshil to authorship

* Updating test with the data uploaded to nf-core/datasets

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 15:37:08 +01:00
Kevin Menden
0b402ffda8
Move test data to nf-core/test-datasets (#432)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

* fixing a bunch of module tests

* remove vscode

* fixed minia

* move test data directory to nf-core/test-datasets

* bump multiqc version

* remove the test data

* updated test data link

* update README

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 12:32:39 +01:00
Jose Espinosa-Carrasco
2c43c39ccc
Add pycoqc module (#424)
* Add pycoqc module

* Adding pycoqc module tests

* Update pycoqc wilth new functions.nf

* Update tests to check for json report content
2021-04-12 10:52:14 +01:00
Anthony Underwood
575df10781
add new iqtree module (#427)
* add new iqtree module

* Resolve suggests after PR review

* add newline to functions
2021-04-12 09:45:56 +01:00
Thanh Lee
ec15bae344
🏋️‍♀️ new submodule mash/sketch🕺 (#426)
* new submodule mash/sketch

* fixed submodule naming

* OK, tag is diff to keyword

* OK  another round 🤣

* removed TODO comments

* updated as per review comments 🙆‍♂️

* updated functions.nf 😁

* Update software/mash/sketch/main.nf

* Update main.nf

Removed blank line at the 12th

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-10 16:24:23 +01:00
Harshil Patel
5e18e36895
Update and check tests are running for all modules (#420)
* Fixes for PR 371

* Fix tags

* Add md5sum

* Add md5sums for stringtie

* Fix tests for modules where subtool = build

* Fix pytest_software name conflicts

* Change _ to / in test.yml tags

* Nope...that didnt work

* Fix sequenzautils/bam2seqz tests
2021-04-09 13:47:05 +01:00
Thanh Lee
5a59e61052
new module: rasusa (#413)
* new module: rasusa

* Removed blank line in software/rasusa/main

* updated code as per reviewcomments

* removed blank line as failed for lint

* updated as per review comments

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 13:10:32 +01:00
Anthony Underwood
ca776e76a2
add rapidnj module (#421)
* add rapidnj module

* remove trailing whitespace

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 13:04:54 +01:00
Florian Wuennemann
0f53c3b96b
Added kallistobustools/ref (#408)
* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me

* Removed trailing whitespace line 29

* Moved workflow from meta to options.

* Update main.nf

* Forgot to remove previous testing input channel for workflow.

* Apply suggestions from code review

Applied changes suggested by @drpatelh

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

* Added gtf to meta.yml.

* Apply suggestions from code review

Adding @drpatelh suggested changes.

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

* Moved workflow to input value. Fixed tests.

* Update tests/software/kallistobustools/ref/test.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 09:41:41 +01:00
Yuk Kei Wan
16e8d21477
Nanoplot and sequencing_summary.txt for Nanopore test data (#364)
* add nanoplot

* add Nanopore 100 read subset bam and fastq

* add nanoplot module and sequencing_summary.txt

* Update pytest_software.yml

* Update main.nf

* test directory path

* testing one output file

* Update main.nf

* fix typo

* remove path to test outputs (it worked locally)

* use test_data.config in test

* add meta.yml

* allowing either summary.txt or fastq.gz inputs

* fix linting and test.yml

* test whether github check can catch the output

* add summary.txt test output paths

* check Nanoplot-report.html output
2021-04-09 08:31:38 +01:00
Anthony Underwood
6927f1d086
New Snpsites module (#416)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* revert to gubbins test on upstream

* add new lines

* renove whitespace

* Apply suggestions from code review

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 08:00:33 +01:00
Anthony Underwood
63b3975292
Update gubbins module to use new files (#417)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

* new snpsites module

* new snpsites module

* new snpsites module

* new snpsites module

* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* use sars-cov-2 alignment

* remove old test alignment

* new snpsites module

* new snpsites module

* new snpsites module

* updated test file names

* new snpsites module

* remove snpsites from gubbins branch

* remove redundant test_fas alignment

* update md5 sums

Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 07:54:11 +01:00
Jose Espinosa-Carrasco
f90dde0d88
Add plasmidid module (#410)
* Adding plasmidid module

* Adding test for plasmidid module

* Update plasmidid version to 1.6.4

* Adding contigs.fasta file

* Update tests

* Adding output files on test.yml
2021-04-08 22:44:30 +01:00
Anthony Underwood
be390a25e5
adding fasttree module (#412)
* adding fasttree module

* correct trailing whitespace

* using sarscov2 as a test dir

* remove TODO

* update test data naming

* further test data naming updates

* remove options in favour of $options.args

* ensure non standard exit codes don't cause an issue

* update md5sum
2021-04-08 18:15:23 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389)
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 09:10:52 +01:00
avantonder
710ab76b90
new module: gubbins (#377)
* new gubbins module

* new gubbins module

* new gubbins module

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/main.nf

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

* Update software/gubbins/meta.yml

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

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* new gubbins module

* Update tests/config/test_data.config

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

* Update tests/software/gubbins/main.nf

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

* new gubbins module

* new gubbins module

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-07 16:31:24 +01:00
Robert A. Petit III
c9256616b9
update tests for new config (#384)
* update tests for new config

* fix quast, update more

* more updates!

* more tests updated

* fix tests, added tabix gff3.gz

* Delete main.nf

Removing SPAdes from PR to avoid merge conflicts with https://github.com/nf-core/modules/pull/396

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-01 20:22:06 +01:00
Nicholas Toda
f126d980d7
Add tests for subread #106 (#393)
* inital commit

* added meta.yaml info

* add initial logic for featurecounts test

* add args and change SE/PE to strandedness for featurecounts test

* added tests to pytest

* added test.yml

* removed GTF flag in options

* corrected test meta params

* meta yaml corrected tool info

* update test.yml

* fix lint errors meta.yml

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
2021-04-01 20:02:36 +01:00
Ravneet Bhuller
c5c59d44a1
PR for sequenzautils/bam2seqz (#395)
* added files

* edited files

* removed file

* README.md edited

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 07:08:27 +02:00
sruthipsuresh
983ba000c1
New modules: Fgbio callmolecularconsensusreads and sortbam (#352)
* Added fgbio callmolecularconsensusreads and sortbam modules

* Fixed naming issue in meta.yml

* fix: test.yml and config lint

* Revert "fix: test.yml and config lint"

This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail.

* style: Fix test names

* style: Remove trailing whitespace

* fixed test.yml

* fix: test data in sortbam

* fix: data format

* fix: test data for callmolecularconsensusreads

* Corrected with updated test data

* Apply suggestions from code review

Applied changes from code review, mainly syntactical changes

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

Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 20:38:50 +01:00
JJ
e50a525715
gatk4 markduplicates (#356)
* new module gatk4/markduplicates

* add tests

* add gatk4_markduplicates entry in pytest_software.yml

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update software/gatk4/markduplicates/main.nf

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

* Update tests/software/gatk4/markduplicates/main.nf

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

* Update tests/software/gatk4/markduplicates/main.nf

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

* Apply suggestions from code review

* Fix EC lint

* Update md5sum

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
suzannejin
989fb7d5b7
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem

* Module samtools/fastq:
	* output compressed fastq.gz file(s)
	* add if conditionals for single/paired reads

* samtools/fastq: modified test.yml

* samtools/fastq: modified main.nf to avoid duplicated part of the script section

* fix README.md

* modify test path gatk4

* fix config

* Add new module gatk4/haplotypecaller

* solve check issues

* fix test.yml file

* fix test.yml gz.tbi

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/main.nf

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update software/gatk4/haplotypecaller/meta.yml

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

* Update tests/software/gatk4/haplotypecaller/main.nf

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

* Apply suggestions from code review

Co-authored-by: suzannejin <suzanne.jin@crg.eu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 12:46:46 +01:00
Nicholas Toda
e526eae472
Add tests for hisat2 (#366)
* initial commit hisat2/build

* initial commit hisat2/build

* changed names for hisat2

* fixed directory structure and args

* added splice site test data

* added splice site inputs

* replaced list with individual args

* fixed removed commas

* added test yml file

* updated hisat2 conda version

* added meta.yml

* added meta.yml description

* added meta.yml inputs

* added meta.yml outputs

* update conda version for hisat2

* removed trailing whitespace meta.yml

* fixed version number for containers

* added test data to test config

* updated for new test logic

* fix pytest issue?

* fix pytest issue

* fixed wrong tool in meta.yaml

* updated tets.yaml name

* handle build bug for testing

* handle build bug for testing in yaml

* moved test folder to fix build bug

* use old hisat2 version to avoid conda giving inconsistent md5sum

* initial commit

* removed temp file

* added meta yaml

* add to pytest

* added tests

* added test yml

* add align meta yaml

* add hisat2 align to pytest

* remove need for splice data by calling process

* add hisat2 align se test

* add hisat2 align pe test

* update names hisat2 align

* update software pytest for using mutiple modules

* remove splice site test data since using module instead

* remove splice site from config since using module instead

* fixed extra brace

* added hisat2 align test.yml

* removed md5sum for bam files

* updated build md5sums

* Apply suggestions from code review

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 21:08:46 +00:00
kevbrick
fead37d57a
Add module: nf-core hackathon #207 : new module: msisensor/msi (#343)
* Add module: nf-core hackathon #207 : new module: msisensor/msi

* Add module: nf-core hackathon #207 : new module: msisensor/msi

* Fix 4-spacing issues (caught in PR linting)

* Code review fixes & update configs

* Code review: remove stray echo

* Code review: Add msisensor modules

* Slashes to underscores to get tests to run on github

* Update software/msisensor/scan/main.nf

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

* Update software/msisensor/scan/main.nf

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

* Update software/msisensor/msi/main.nf

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

* Update software/msisensor/msi/main.nf

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

* Add all outputs to meta.ymls

* Fixes from code review

* Fixes from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 16:46:00 -04:00
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data (#386)
* Adding tar.gz kraken2 db to test data

* Update test path files for untar module

* Update test path files for kraken2/run module

* Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
Alexander Peltzer
0337916f8a
Add YARA module (#353)
* Initial work on yara module

* Adding in index basics

* Updated the index stuff

* Adding in proper tests

* Fix editorconfig

* Odd paths

* that should do it

* Fix tests

* Fix tests

* FFS

* Once more

* Mapping is not deterministic
2021-03-24 17:14:52 +01:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests (#365)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint

* Initial commit for test data config

* Rename test data

* Include test config

* Update indents

* Update test for FastQC via config

* Remove quotes of bottom-level variables

* Use underscores in key names

* Get tests working for fastp

* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Gisela Gabernet
22eaefe583
Add module kallisto/index (#357)
* add kallisto index module

* update kallisto module

* add kallisto module tests

* update kallisto index test.yml

* update test data paths

* fix version

* fix kallisto index test yml

* remove TODOs

* Update software/kallisto/index/main.nf

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

* Update software/kallisto/index/main.nf

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

* output folder instead

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 12:25:39 +00:00
arontommi
86bb832fae
Strelka germline (#340)
* nf-core template created

* boilerplate and sarek_dsl2 code merged

* adding an option to give it args

* bai got away

* seperating vcf files and vcf index files into seperate streams

* some minor spacefixes

* adding standard information about the module

* removing typos

* some basic tests based on tiddit tests

* removed the bed parameter, should be provided via options.args instead

* removing typos

* adding indexed bam file instead

* Adding changing out fasta with reference to deal with empty fasta input

* adding the correct fasta

* removing the empty test

* adding the correct data to the testoutput and removing the md5sum since
it constantly changes

* adding  target_bed to input

* adding info on target bed

* adding target bed to test

* adding more files to the test

* adding meta for target bed test

* adding a test for target_bed

* typo

* fixing pytest with master
2021-03-24 05:07:29 +00:00
Erkison Ewomazino Odih
67b3e00f58
add flash module (#341)
* add flash module

* remove todo

* run tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 05:05:45 +00:00
Ravneet Bhuller
a70abc236b
PR for sequenzautils/gcwiggle (#345)
* added files

* edited files

* edited files

* edited file

* test(sequenzautils): Remove md5sum

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-24 05:03:03 +00:00
Robert A. Petit III
3f14b1fabe
Update shovill module (#337)
* add shovill module

* removed deprecated shovill module

* fix line ending in functions.nf

* fix yaml indentation

* reduce spades memory usage

* update md5sums

* remove non reproducible md5sum

* Update test.yml

Remove last non-reproducible md5sum.

* purely cosmetic order change

* proper process label, improve output readability

Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00
Yuk Kei Wan
af3bc225c0
ucsc_bed12tobigbed (previous pull request had conflicts) (#302)
* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Update pytest_software.yml

* Update main.nf

* fix linting error

* Delete test.yml

* Create functions.nf

* Update main.nf

* change test data

* revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
Mark-S-Hill
399b58043d
add vcftools module (#334)
* add vcftools module

* fix padding issue

* fix linting errors
2021-03-24 04:54:23 +00:00
Kevin Menden
fe8a783cef
Homer (#330)
* started with homer

* added tests for homer annotatepeaks

* fix md5

* remove md5 sum
2021-03-23 11:24:54 -07:00
Gregor Sturm
e33860a2e8
Prodigal (#333)
* WIP add prodigal

* Implement module and add tests

* Fix EC lint
2021-03-23 11:03:58 -07:00
yocra3
5e3c9dfbf0
Add gatk4/baserecalibrator (#327)
* Add gatk4 BaseRecalibrator

* Solve format in main.nf

* Correct functions

* Add pytest
2021-03-23 18:32:37 +01:00
Alexander Peltzer
d13e22dcbe
Add in OptiType (configbuilder, type) module(s) (#301)
* Adding in optitype prototype (To be worked on these days)

* I've tried my best 😆

* No idea

* Add in YML stuff

* Fix paths

* Ok, lets try this

* Adding proper options

* Replacec configbuilder thing

* Fix seq_type

* Adding human bam - sarscov doesnt work

* Fix a bunch of things

* -def

* Make this test run

* Fancy as fuck

* Update tests/software/optitype/test.yml

* Add proper tag

* Remove md5sums

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 16:48:05 +01:00
Anthony Fullam
3d720a24fd
Add alleleCounter module (#313)
* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Add allelecount module

* Add bed file input

* Added bai file

* Changed conda version

* Update main.nf

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Update pytest_software.yml

* Remove newline

* Fix pytest_software.yml

* Update pytest_software.yml

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-23 14:37:53 +01:00
yocra3
614d61dc13
Add gatk4/applybqsr (#331)
* Add applybqsr module

* Solve problem in functions.nf

* Add to pytest
2021-03-23 14:15:26 +01:00
suzannejin
9115c12f88
new module: samtools/fastq (#316)
* new module: samtools/fastq

* solve conflict: pytest_software.yml

* solve linting conflicts

* solved EditorConfig linting problem
2021-03-23 12:13:07 +01:00
Robert A. Petit III
c2aa95cb6c
add prokka module (#298)
* add prokka module

* adjust test outputs

* fix prokka command

* adjust test outputs

* handle optional input

* update pytest

* update pytest

* adjust test outputs

* adjust test outputs

* switch to lists for optional inputs, add md5sums for non-timestamped outputs

* add optional prodigal training file

* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module (#173)
* Normal bam file added

* Normal bam.bai file added

* Tumour bam bai files added

* human dir added

* annotation dir added

* cnvkit dir added

* cnvkit dir added

* Update software/cnvkit/main.nf

Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>

* Update software/cnvkit/main.nf

Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>

* Update software/cnvkit/main.nf

Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>

* changed input filenames

* edited main.nf

* edited main.nf

* edited meta.nf

* edited test.yml

* filters.yml

* edited main

* edited main

* edited meta

* edited meta

* edited main

* removed unwanted lines

* edited the path to the main.nf

* removed function.nf

* added functions.nf

* deleted 2 workflows and craeted a common workflow

* deleted paths for 2 workflows and created paths for a common workflow

* Deleted annotation dir

* deleted params.modules

* Edited meta.with_normal

* deleted normal_280_sub_chr21.bam

* deleted normal_280_sub_chr21.bam.bai

* deleted tumour_278_sub_chr21.bam

* deleted tumour_278_sub_chr21.bam.bai

* Edited input and script parts

* Edited input part

* Added

* Edited args

* Edited script

* Edited input

* Changed annotation to annotationfile

* Changed description of the tool

* edited singularuty container

* edited input

* line 44 removed trailing whitespace

* Edited addParams

* Deleted pdf output

* Deleted pdf output

* edited the path to main.nf

* edited path to the main.nf

* Added docker image version

* Removed extra ../

* added md5sums

* added md5sums

* Update software/cnvkit/main.nf

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

* Update software/cnvkit/main.nf

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

* Edited the script

* Edited the input

* Edited main.nf

* Edited main.nf

* edited md5sum for reference.cnn

* removed human fasta

* removed human fasta.fai

* added GRCh38 fasta

* added GRCh38 fasta.fai

* added hg19 fasta.fai

* added hg19 fasta

* Edited fasta file name

* Edited bed file names and md5sums

* Edited md5sums

* edited the input and script section

* edited input section

* added targetfile

* changed the files

* changed the output files

* added bam files

* added bam files

* remove files

* added md5sums

* replace file

* added files

* edited tests/software/cnvkit files

* edited tests/software/cnvkit files

* edited authors list

* removed files

* added files

* added files

* added files

* added files

* added file

* added file

* added file

* added file

* edited files

* edited files

* edited files

* edited files

* edited files

* edited files

* added new module

* added new module

* edited files

* edited file

* edited file

* edited file

* removed files

Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Nicholas Toda
53109d53c0
add gatk4/fastqtosam #198 (#311)
* Inital nf-core create

* remove TODO comments, input and output files defined

* add get version in script

* added flow control for single/paired end data

* added script main commands

* removed completed TODO messages

* removed completed TODO messages

* added software info

* added input reads description

* added output description

* added description and keywords

* added single end test

* added paired end test

* fixed sample name flag

* fixed reverse read variable

* added test yaml

* update for pytest_software

* order in pytest_software was different

* replaced functions.nf with copy from another module

* simplify read command line

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

Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
Maxime Borry
aa76c6d870
new module: AdapterRemoval (#309)
* add adapterremoval module

* fix indentations

* switch to process_medium

* update docker tests

* remove duplicated entry

* fix line ending

* Update software/adapterremoval/main.nf

* Update software/adapterremoval/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
Jose Espinosa-Carrasco
cfa8f64c4f
Adding unicycler module (#307)
* Adding unicycler module

* Do not forget to change default keywords on meta.yml
2021-03-22 18:14:24 +01:00
Patrick Hüther
7fe6f9fab2
bismark: remove underscores from process names (#303)
* sanitize process names

no underscores allowed

* remove underscores from process names
2021-03-22 17:46:11 +01:00
Florian Wuennemann
592002aa23
add picard_collectwgsmetrics (#304)
* Added new module picard/collectwgsmetrics.

* Removed unused outputs from meta.yml

* Added version.txt file back to meta.yml

* Updated test.yml

* Removed md5sum from test.yaml and added contain tests.

* Update functions.nf

Fixed missing newline formatting.

* Update main.nf

Fixed missing newline formatting.

* style(picard): Remove trailing whitespace

Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 17:05:59 +01:00
Patrick Hüther
eb9178970f
add bismark/summary (#295)
* add bismark/align module

* bismark/align: add tests

* bismark/align: update meta.yml

* bismark/align: skip checksum for alignment logs

they contain timestamps

* bismark/align: restore correct checksum

caused some mixup in the last commit

* bismark/align: add genome_preparation to filters

* Fix conda version pin

* change options to be a global var

* remove params from meta.yml

* add bismark/summary

* remove md5sum check for bismark_summary_report.html

it contains a timestamp

* fix tests

* update meta.yml

* remove mysterious index files
2021-03-22 14:58:54 +01:00
Yuk Kei Wan
134c8ef6ce
add samtools merge (#296)
* add samtools merge

* Update pytest_software.yml

* get it back to 20.11.0-edge

* Update test.yml

* Update test.yml

* Update test.yml

* Update test.yml
2021-03-22 13:48:23 +01:00
Patrick Hüther
f9ce8664ba
add bismark/report (#297)
* add bismark/align module

* bismark/align: add tests

* bismark/align: update meta.yml

* bismark/align: skip checksum for alignment logs

they contain timestamps

* bismark/align: restore correct checksum

caused some mixup in the last commit

* bismark/align: add genome_preparation to filters

* Fix conda version pin

* change options to be a global var

* remove params from meta.yml

* add bismark/report

* fix test filepaths

* remove mysterious index files
2021-03-22 13:38:08 +01:00
Patrick Hüther
04704c2034
add bismark/methylation_extractor (#274)
* add bismark/methylation_extractor

* add tests for bismark/methylation_extractor

* bismark/methylation_extractor: add genome_preparation to filters

* Apply suggestions from code review

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

* remove params from meta.yml

* pytest: remove md5sum checks for gzipped output

gzip stores timestamps in the file header, so the checksum will be different each time

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
Jose Espinosa-Carrasco
72e81d6e90
Add spades module (#277)
* Add spades module

* Reorder gatk4 modules alphabetically

* Update software/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
Jose Espinosa-Carrasco
313241749c
Add kraken2 run module (#266)
* Add kraken2 run module

* Add kraken2 run module

* Add coronavirus kraken2 db

* Adding kraken2 run tests

* Update software/kraken2/run/meta.yml

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

* Fixing files commited by mistake

* Remove params for meta.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
Harshil Patel
d1cb9a845f
Check for minimum NF version (#278) 2021-03-18 12:00:32 +01:00
Kevin Menden
a90332906b
add mergebamalignment (#259)
* add mergebamalignment

* fix test.yml

* update to latest gatk4 version

* Update software/gatk4/mergebamalignment/main.nf

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

* Update tests/data/README.md

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

* Update software/gatk4/mergebamalignment/main.nf

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

* Update software/gatk4/mergebamalignment/meta.yml

* fixed unmapped/unaligned

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 15:56:56 +01:00
Kevin Menden
3c4d9466f4
Adding minia for viralrecon (#267)
* initial 'modules create' of minia

* fixed tests

* finished meta.yml

* fixed filters.yml

* resolved issues in pytest_software.yml

* add newline

* Update software/minia/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 12:54:15 +01:00
Kevin Menden
17dbff52f4
added gatk4 variantfiltration (#265)
* added gatk4 variantfiltration

* replace merge with filter

* Update software/gatk4/variantfiltration/main.nf

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

* updated input

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 09:42:35 +01:00
Jose Espinosa-Carrasco
74ff11b07b
Fix bowtie builds (#273)
* Fix bowtie  build test

* Forgot to delete old bowtie_build

* Fix bowtie2 build tests

* Add initOptions include on hisat2 extractsplicesites
2021-03-15 15:39:42 +01:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml (#271)
* Rename pytest filters.yml

* Change filters.yml name

* Update resoures for ivar trim
2021-03-15 12:51:30 +00:00
MaxUlysse
4968458b6c chores: add cpus, memory and time requirements to limit resource consumption 2021-02-16 14:18:29 +01:00
drpatelh
fe3cb87f6d
Direct download Singularity containers 2021-02-03 20:03:45 -06:00
Edmund Miller
467d1595c4
test: Use docker image with singularity 2021-02-02 18:14:39 -06:00
Edmund Miller
72b4fb35aa
test: Fix profile logic order 2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:25:58 -06:00
Edmund Miller
6b675eef6d
ci: Set pull docker container to false
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:00:40 -06:00
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack
The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
2021-02-02 12:44:30 -06:00
Edmund Miller
b96f2d6a5e test(config): One config to rule them all
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 20:26:04 +00:00