Commit graph

1914 commits

Author SHA1 Message Date
Moritz E. Beber
7560689375
feat: add sourmash sketch (#1287)
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 12:30:28 +01:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config (#1279)
* fix yml formatting

* allow fastq.gz and fq.gz as file input, add meta.yml and test

* fix yaml files

* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"

This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.

* prettier magic!

* fix comments for yamllint

* remove node version number

* fix linting errors

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
Harshil Patel
12b0bc5aa9
Bump Pangolin version to 3.1.20 (#1296)
* Bump Pangolin version to 3.1.20

* Fix md5sum
2022-02-15 10:46:20 +00:00
FriederikeHanssen
967fb22ded
Update versions (#1292)
* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break
2022-02-15 11:29:36 +01:00
Matthieu Muffato
04e82ec61a
First version of the biobambam/bammarkduplicates2 module (#1247)
* First version of the biobambam/bammarkduplicates2 module

* Fixed the path of versions.yml

* Regenerated the checksums as the previous files were generated with a single core

* Added the `when:` block, as per #1261

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-14 16:30:48 +00:00
James A. Fellows Yates
6a9aa977ef
Minor meta.yml typo fix for samtools fastq (#1288)
* fix: remove left-over unnecessary code

* Correct typo in output meta information for fastq channel
2022-02-14 11:02:03 +01:00
Simon Pearce
78e2e76b24
New module: ichorCNA (#1182)
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

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

* Update modules/hmmcopy/mapcounter/meta.yml

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

* Update tests/modules/hmmcopy/mapcounter/main.nf

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

* ichorCNA run

* Add panel of normals code

* Try and fix tests

* Edit string detection in tests

* Fix linting issues

* Just failing END_VERSIONS

* Fixed versions.yml

* Added DOI

* Optional name for file

* Add when command

* Updated when

* Update modules/ichorcna/createpon/main.nf

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-02-11 16:56:13 +01:00
Maxime U. Garcia
fafae11068
feat: nicer syntax (#1286)
* feat: nicer syntax

* feat: code polishing

* feat: code polishing
2022-02-11 16:07:52 +01:00
Jose Espinosa-Carrasco
d1f33be04f
Bump multiqc version 1.12 (#1282) 2022-02-11 09:44:13 +01:00
James A. Fellows Yates
a9050b8ab6
Fix test data paths for hmmer/hmmalign (#1272)
* fix: remove left-over unnecessary code

* Update main.nf
2022-02-10 13:14:44 +01:00
Ramprasad Neethiraj
d0240fee1e
update manta to enable jointcalling (#1218)
* update manta to enable jointcalling

* fix lint errors

* fix error

* update comment

* remove comment

* suggestions from code review

* add stub
2022-02-10 10:37:31 +01:00
FriederikeHanssen
f5d5926516
Update intervals (#1278)
* Match target bed to input files

* Intervals in getpileupsumamries

* more interval updates

* change targets in strelka

* remove leftover channel

* fix checksums

* add new test vcfs

* add new test vcfs

* Update modules/freebayes/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 10:34:22 +01:00
FriederikeHanssen
c8ebd0de36
Add msisensorpro (#1267)
* Add msisensorpro

* remove absolute paths

* fixing tests

* fix msisensorpro tests

* Update modules/msisensorpro/msi_somatic/main.nf

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

* Update modules/msisensorpro/msi_somatic/main.nf

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

* add when back in

* add when back in

* Update modules/msisensorpro/msi_somatic/main.nf

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

* update description

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-09 21:05:49 +01:00
Ramprasad Neethiraj
45acc79667
Update mosdepth (#1256)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* mosdepth update

* update md5sums

* add stub

* add stub

* remove svdb

* remove merge

* Add tests

* code linting fix

* undo previous commit

* revert code linting fix
2022-02-09 12:45:55 +00:00
Matthias Hörtenhuber
fcb1dce7b6
fix yml formatting (#1263) 2022-02-07 18:16:43 +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
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
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
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
Maxime Borry
7026122ec8
Freebayes: compress with bgzip (#1243)
* move to bgzip
* update freebayes test results
2022-01-31 10:11:39 +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
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
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
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
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
Edmund Miller
550df3b006
ci: Remove second python setup call (#1225)
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-21 07:57:57 +01:00
Gregor Sturm
55ea3f2061
CI: print out pytest logs on failure (#1220) 2022-01-21 07:51:28 +01:00
Jose Espinosa-Carrasco
9573e7e53d
Bump version 0.1.5 to chromap/chromap (#1223)
* Bump version 0.1.5 to chromap/chromap

* Bump conda samtools version to 1.14

* Get read of inconsistent md5sum in conda

* Bump version in conda and retry md5 checks

* genome index md5 hash removed, conda failed
2022-01-20 19:00:20 +01:00
Mei Wu
435ca4100a
New module/vcfanno (#1204)
* boilerplate

* tests passed

* fixed regex

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-20 08:46:31 +00:00
Harshil Patel
bb90e4fb78
Remove bcftools and ivar module customisations (#1217)
* Remove customisation from bcftools modules

* Add save_mpileup option to bcftools/mpileup

* Remove params.save_mpileup from ivar/consensus

* Update meta.ymls
2022-01-18 16:04:56 +00:00
Jose Espinosa-Carrasco
4e9cc84514
Bump chromap index version (#1216)
* Bump chromap version

* Update md5 hash

* Remove md5 check, variable with conda
2022-01-18 12:24:21 +01:00
FriederikeHanssen
1287ba48fe
Update version & add intervals usage (#1214)
* Update version & add intervals usage

* Fix config when passing intervals as file

* Use proper paths
2022-01-17 16:40:31 +01:00
Harshil Patel
796dbb573e
Add nextclade/datasetget and nextclade/run modules (#1210)
* Remove old nextclade module

* Add nextclade/datasetget and nextclade/run modules

* Fix ECLint

* Add reference and tag as inputs to datasetget module

* Fix tests

* Adjust spacing
2022-01-17 11:46:15 +01:00
Abhinav Sharma
6243c3792c
module: deepvariant (#572)
* Add stubs for deepvariant [ci skip]

* Update the stubs for deepvariant [ci skip]

* functional with google docker image

* cleanup

* consume docker container within singularity executor

* update the meta.yml file and ask for review

* tweak the input channel shape and test data

* tweak input data [ci skip]

* update for the new syntax

* remove the functions and rename meta vars

* Update the arguments mechanism

* update chr, region and checksum

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-17 12:25:36 +02:00
Michael L Heuer
c9587d76e2
Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format

* fix ci failures

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-17 09:24:40 +00:00
Harshil Patel
280712419d
Add new vcflib/vcfuniq module (#1208)
* Add new vcflib/vcfuniq module

* Rename module from vcfutils to vcfuniq

* Fix tests

* Compress output by default

* Fix ECLint
2022-01-14 18:18:11 +00:00
Harshil Patel
3f9a028581
Bump mulled containers for kraken2 and bowtie2 (#1201)
* Bump mulled containers for kraken2 and bowtie2

* Syntax update

* Update modules/bowtie2/align/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-13 11:59:33 +00:00
Anthony Underwood
104f896a26
Artic vbz compression (#1205)
* Add functionality to handle vbz compression

In order for nanopolish to be able handle the default compression  for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution

* Make the HDF5_PLUGIN_PATH more configurable

Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g

```
params {
    modules {
        .....
        'nanopore_artic_minion' {
            .....
            hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
        }
        ......
    }
}
```

* Update modules/artic/minion/main.nf

* Export HDF5_PLUGIN_PATH

The HDF5_PLUGIN_PATH variable should be exported for `artic minion` to use it

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-13 01:05:01 +00:00
Simon Heumos
4cc3921efb
Add pangenome test data set keys (#1170)
* Update seqwish to version 0.7.2

* seqwish can work with a comma-separated list of PAFs

* level with nf-core/modules master branch

* add pangenome test data keys

* the odgi test data lives in its own folder

Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-12 12:01:57 -06:00