Commit graph

1896 commits

Author SHA1 Message Date
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
Harshil Patel
b4c6b430d0
Remove params call in ivar variants module (#1203)
* Remove params call in ivar variants module

* Update main.nf
2022-01-12 16:43:26 +00:00
FriederikeHanssen
598d7abdb2
Log4j again (#1202)
* Log4j again

* Update checksums
2022-01-12 13:55:54 +01:00
Subazini TK
05ba4d901d
samtools subsampling (#1194)
Co-authored-by: Subazini Thankaswamy Kosalai <sth036@orcus.orebroll.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-11 21:39:21 +00:00
Mei Wu
30e64becaa
ucsc/wigtobigwig: add meta map (#1199)
* add meta info

* updated meta.yml

* Apply suggestions from code review

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-11 21:31:37 +00:00
Anthony Underwood
bdd8159c53
Add functionality to handle vbz compression (#1197)
* 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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-11 21:10:26 +00:00
Harshil Patel
e751e5040a
Bump software versions for viralrecon modules (#1198)
* Bump software versions for viralrecon modules

* Remove custom params.save_unaligned from bowtie2_align

* Unify samtools modules and error if input and output names are the same

* Fix ALL the tests
2022-01-07 17:52:39 +00:00
emnilsson
c4549c0ecd
Editing the CAT/CAT module to handle single files (#1196)
* Removed if-statement to only run on more than 1 file, now it will run on single files as well.

* Added a test for running the cat_cat module on a single file.

* Created a new test.yml with nf-core modules create-test-yml -t cat/cat

* Edited test.yml to not include paths and md5sums for versions.yml, and also removed sometimes variable md5sums
2022-01-06 16:41:36 +00:00
Gwenna Breton
2d4b0f7787
Bcftools sort new syntax (#1169)
* Added files for bcftools/sort

* Fixed output format and removed md5 checksum

* Change input to avoid identical in/output names

* Created rows for bcftools/sort in pytest_modules.yml
2022-01-05 12:15:54 +01:00
Robert A. Petit III
bf5edb8614
add module for mash dist (#1193)
* add module for mash dist

* fix lint

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-04 17:29:49 +01:00
Harshil Patel
e3285528ac
Fix modules warned or failed with nf-core modules lint (#1191) 2022-01-03 18:00:46 +00:00
Sébastien Guizard
c0e1489133
🐛 FIX: remove suffix option (#1188) 2021-12-24 11:32:30 +00:00
Jose Espinosa-Carrasco
cde237e7ce
Fix error messages mentioning suffix (#1190) 2021-12-23 17:22:07 +00:00
FriederikeHanssen
a6e0629e24
Change intervals to be part of sample specific input (#1189)
* Change intervals to be part of sample specific input

* Fix some tests

* Update checksum

* Update intervals

* Update intervals

* Try out gavins idea for adding the file

* update test line

* update test line

* update test line

* revert contains line
2021-12-23 12:58:20 +01:00
Robert A. Petit III
5320ab7e6c
Fix kleborate inputs (#1172)
* Fix kleborate inputs

* Update test.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-12-22 11:39:35 +00:00
FriederikeHanssen
50eafb19c6
Update version for log4j vulnerability (#1176)
* Update version for log4j vulnerability

* update checksums

* update checksums

* update checksums

* Remove todo string

* remove werid output paths

* remove werid output paths

* remove werid output paths

* Update various checksums

* Update various checksums

* Remove unstable md5sums

* Update md5sums

* Fix pileupsummary

* Fix genotypegvcfs

* Update test files mutect2

* hm genotypevcf updated again

* Update some mutect checksums and whatnot

* Fix last mutect checksum

* Apply suggestion to use mtochondria data instead
2021-12-20 17:10:49 +01:00
Simon Pearce
02218ab5a0
hmmcopy/mapCounter (#1175)
* 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>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-17 15:39:50 +00:00
Harshil Patel
ce8c781bb4
Provide BAI when running rseqc/tin (#1177)
* Provide BAI when running rseqc/tin

* Add md5sum

* Add proper md5sums

* md5sum not md5

* Add xls to meta.yml
2021-12-17 10:00:09 +00:00
Mahesh Binzer-Panchal
754701fb3a
Add Gitpod environment to modules to allow pytest-workflow testing. (#1151)
* Add Gitpod Env

* Add Gitpod Env

* Change Gitpod to install only Nextflow and pytest-workflow

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-17 09:32:33 +00:00