Commit graph

2874 commits

Author SHA1 Message Date
James A. Fellows Yates
ab7d73f85d
Merge branch 'nf-core:master' into master 2022-02-09 10:58:57 +01:00
veitveit
aa0e2fa752 nMerge branch 'maxquant' of github.com:veitveit/modules into maxquant 2022-02-09 10:42:17 +01:00
veitveit
918a7f0363 added when section 2022-02-09 10:42:07 +01:00
Veit Schwämmle
8363559ba5
Update tests/config/test_data.config
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-02-08 10:03:02 +01:00
Veit Schwämmle
cb1f0b7fc3
Update modules/maxquant/lfq/main.nf
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-02-08 10:02:54 +01:00
Veit Schwämmle
360ac115f7
Update modules/maxquant/lfq/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-02-08 10:02:48 +01:00
veitveit
ad98111756 removed file 2022-02-08 09:50:33 +01:00
Veit Schwämmle
34dc4c181d
Merge branch 'master' into maxquant 2022-02-08 07:37:57 +01:00
Matthias Hörtenhuber
fcb1dce7b6
fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
veitveit
5b9313c2c5 corrected typos 2022-02-07 13:07:16 +01:00
veitveit
7df2fb74a3 Merge branch 'maxquant' of github.com:veitveit/modules into maxquant 2022-02-07 11:20:34 +01:00
veitveit
8f9f452a62 now with test data 2022-02-07 11:20:25 +01:00
Veit Schwämmle
ca8bca95cf
Merge branch 'master' into maxquant 2022-02-07 11:19:40 +01:00
Ramprasad Neethiraj
f44e6c74b4
Add svdb/merge (#1233)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* add stub

* add when
2022-02-04 15:29:44 +01:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
Veit Schwämmle
273d44f1f7
Update main.nf 2022-02-03 12:45:21 +01:00
Veit Schwämmle
ffdd7059b1
Update #main.nf# 2022-02-03 12:16:58 +01:00
Veit Schwämmle
53ebb374af
Merge branch 'master' into maxquant 2022-02-03 11:50:40 +01:00
Benjamin Wingfield
e687c7025a
New module: plink2/extract (#1228)
* add plink2_extract

* fix test yml path

* Update modules/plink2/extract/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/plink2/extract/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* compress output

* add DOI

* make outputs less ambiguous

* update test for compressed output

* brain is dumb

* Update modules/plink2/extract/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-03 10:42:56 +00:00
Veit Schwämmle
bacf6165d0
Merge branch 'nf-core:master' into maxquant 2022-02-03 11:41:50 +01:00
veitveit
6385403a90 now with conda-based images 2022-02-03 11:39:08 +01:00
veitveit
6001db8aef now with conda-based images 2022-02-03 11:38:44 +01:00
Katarzyna Kamieniecka
f112e4d701
bamcmp (#1244)
* New module added bamcmp

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2022-02-02 16:38:41 +00:00
Mahesh Binzer-Panchal
601c6e2023
Update gitpod config to use nf-core gitpod image and include extensions. (#1253) 2022-02-02 17:31:32 +01:00
Harshil Patel
aa2eca6997
Bump versions for Pangolin and Nextclade (#1255) 2022-02-02 15:19:46 +00:00
Danilo Di Leo
aa97b1be3e
Transdecoder predict (#1251)
* create transdecoder/longorf module

* module transdecoder

* main.nf

* transdecoder/longorf ready to PR

* review comments update

* transdecoder/predict module create

* test transdecoder/predict module

* fix pytest

* pytest passed

* removed whitespace

* Update meta.yml

* Update meta.yml

Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-02-02 09:46:07 +01:00
Phil Ewels
f207f6c870
Add repository_type to .nf-core.yml (#1252) 2022-02-01 22:33:25 +01:00
Ramprasad Neethiraj
fc4bd3a2d2
Add svdb/query (#1249)
* first commit

* add test data
2022-02-01 20:46:10 +01:00
Felipe Marques de Almeida
53b324281f
Raven assembler (#1087)
Adding a new module for [Raven](https://github.com/lbcb-sci/raven), a De novo genome assembler for long uncorrected reads.
2022-02-01 11:47:01 +01:00
James A. Fellows Yates
e25722d606
Merge branch 'nf-core:master' into master 2022-01-31 13:54:57 +01:00
Danilo Di Leo
a74e8436cc
Transdecoder longorf (#1230)
* create transdecoder/longorf module

* module transdecoder

* main.nf

* transdecoder/longorf ready to PR

* review comments update

* transdecoder_longorf reviewed main.nf

* removed predict

* test.yml updated

* pytest run

Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
2022-01-31 13:34:38 +01:00
James A. Fellows Yates
20f9dfde69
Merge branch 'nf-core:master' into master 2022-01-31 13:19:30 +01:00
Maxime Borry
7026122ec8
Freebayes: compress with bgzip (#1243)
* move to bgzip
* update freebayes test results
2022-01-31 10:11:39 +01:00
Veit Schwämmle
b0e224f9f3
Merge branch 'master' into maxquant 2022-01-31 08:44:32 +01:00
Sébastien Guizard
080320765c
New module: bamtools/convert (#1219)
* 📦 NEW: Add bamtools/convert module

* 👌 IMPROVE: Update output channel name, Add tests for each output format

* 👌 IMPROVE: Add error test

* 🐛 FIX: Remove custom tags

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-28 09:58:25 +00:00
Chris Cheshire
f3a405e4f2
Fix for version file output check when performing an expected error test (#1242)
* 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

* Ignores version file checking if testing for error

* Added comment

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk>
2022-01-28 10:32:36 +01:00
Chris Cheshire
70ea9ac9a8 Added comment 2022-01-28 09:27:28 +00:00
Chris Cheshire
1abcc93837 Ignores version file checking if testing for error 2022-01-28 09:14:47 +00:00
Chris Cheshire
b83db65f33 Merge remote-tracking branch 'nf-core/master' 2022-01-28 09:11:14 +00:00
Antonia Schuster
a45e030166
Allow compressed input for prodigal (#1200)
* Allow compressed input for prodigal

* use pigz instead of gzip

* fix typo
2022-01-28 09:05:30 +01:00
GCJMackenzie
08db860938
Update mergebam syntax and sample specific unmapped channel (#1238)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

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

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

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

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

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

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* updated to follow the new mergebam syntax, also made unaligned input sample specific

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-01-27 15:30:27 +00:00
Priyanka Surana
8fdd5abe1d
Merge branch 'nf-core:master' into busco 2022-01-27 14:44:08 +00:00
Priyanka Surana
b412e6dabc Busco module commit with nf-core v2.2 c1 2022-01-27 14:36:18 +00:00
Harshil Patel
d70526c806
Bump Nextclade version to 1.10.1 (#1236) 2022-01-27 12:53:14 +00:00
James A. Fellows Yates
fc1e694e6e
fix: remove left-over unnecessary code (#1235) 2022-01-27 09:38:06 +01:00
James A. Fellows Yates
21ecd68bfe
fix: remove left-over unnecessary code 2022-01-27 08:43:02 +01:00
James A. Fellows Yates
c3bacb9fdd
Add deeparg (#1234)
* Add deeparg download data

* Tweak downloaddata test.yml

* Add deeparg tests

* Apply suggestions from code review

* Fix output file paths in test

* Fix tests again md5sum to string
2022-01-26 15:19:16 +01:00
Regina Hertfelder Reynolds
1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115)
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 19:58:22 +01:00
Veit Schwämmle
3d0473fe48
Merge branch 'master' into maxquant 2022-01-25 15:18:55 +01:00
Annick Renevey
dcce431d51
Peddy update: delete png and add stub (#1180)
* delete png and add stub

* optional png file generation

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-24 10:28:55 +01:00