Commit graph

2439 commits

Author SHA1 Message Date
Matthias De Smet
d85f9c7011 add subworkflow bam_qc_picard 2022-04-21 13:16:23 +02:00
Jasmin F
d07d270743
Antismashlite download databases (#1426)
* Create module antismashlitedownloaddatabases

* Corrected user-specification of database directory

* Updated test.yml

* Apply suggestions from code review

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

* Fix typo in test.yml

* Feed database files via docker/singularity mount)

* Add external db file mounts to the containers

* Fixed docker command in main.nf

* Apply prettier

* Apply prettier and add PWD

* Add more output to test.yml

* Add more output paths to test.yml

* Fixed test.yml

* Apply suggestions from code review

Add documentation of why we need to mount files to the containers.

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

* Fix code linting errors (remove trailing whitespaces)

* Fix code linting error (remove trailing whitespace)

* Fix errors from Prettier linting

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 10:38:17 +02:00
Maxime U. Garcia
37bf3936f3
add decompress possibilities to bgzip (#1540)
* add decompress possibilities to bgzip

* spacing
2022-04-20 16:26:56 +02:00
louperelo
6c45773c0b
add module AMPlify (#1498)
* add module AMPlify

* Apply suggestions from code review

Thanks for the review!

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* removed trailing whitespaces

* Apply suggestions from code review

Thanks again!

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

* Apply suggestions from code review

Thank you for the suggestions!

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Apply suggestions from code review

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* including review suggestions

* fix versions.yml

* add model_dir input

* add model_dir to meta.yml

* complete faa pattern in meta.yml

* add fa.gz to pattern

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-20 11:53:26 +02:00
Maxime U. Garcia
705f8c9ac4
Add samtools/collatefastq module (#1536)
* add samtools/collatefastq module

* update yml file

* improve output
2022-04-20 10:05:17 +02:00
Maxime U. Garcia
7630e278f3
update gatk4 yml for spark (#1538) 2022-04-19 16:51:59 +02:00
Matthias De Smet
bddb88dfaf
Merge branch 'master' into tool/bamtools-split 2022-04-19 15:33:49 +02:00
Matthias De Smet
07982d6cb1 fix command line, fix meta.yml 2022-04-19 15:31:39 +02:00
Matthias De Smet
b35264e919 bugfixes 2022-04-19 15:11:37 +02:00
Matthias De Smet
6723ca7f90 bump version, add merge before split 2022-04-19 15:05:02 +02:00
Matthias De Smet
553c1bcf9d
Merge branch 'master' into tool/elprep-merge 2022-04-19 11:28:04 +02:00
Matthias De Smet
ad15d1b792 update label 2022-04-19 11:27:55 +02:00
Matthias De Smet
ccef7f8579 alignment 2022-04-19 11:26:01 +02:00
Anders Jemt
a6cb75174b
Add variant catalog ch to stranger (#1508)
* Add optional variant catalog input

* fix for no variant catalog test

Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com>
Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
2022-04-19 10:53:39 +02:00
James A. Fellows Yates
87005786e0
Update modules/motus/downloaddb/main.nf 2022-04-17 21:18:55 +02:00
James A. Fellows Yates
ec23ebc7c5
Update modules/motus/downloaddb/main.nf 2022-04-17 21:17:59 +02:00
JIANHONG OU
9a158acb50 Merge branch 'motus_downloaddb' of github.com:jianhong/modules into motus_downloaddb 2022-04-17 11:22:25 -04:00
JIANHONG OU
407d0bb752 update motus_downloaddb 2022-04-17 11:22:23 -04:00
JIANHONG OU
51214d655b
Update modules/motus/downloaddb/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:19:58 -04:00
JIANHONG OU
32d5257def
Update modules/motus/downloaddb/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:12:08 -04:00
JIANHONG OU
d247ef4a0d
Update modules/motus/downloaddb/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:10:54 -04:00
JIANHONG OU
2551201f43
Update modules/motus/downloaddb/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:10:48 -04:00
JIANHONG OU
f1f1df984c
Update modules/motus/downloaddb/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:06:06 -04:00
JIANHONG OU
ee04fc2737 add module motus_downloaddb 2022-04-14 12:56:42 -04:00
Matthias Hörtenhuber
c7def8707b
fix incorrect yaml formatting. (#1264) 2022-04-14 13:35:01 +02:00
FriederikeHanssen
4ea5499d7a
Merge branch 'nf-core:master' into master 2022-04-14 12:06:26 +02:00
Sofia Stamouli
be4ae28c3c
Add centrifuge_kreport module (#1514) 2022-04-13 15:33:51 +02:00
Maxime U. Garcia
e04970b7d2
typo in command line (#1523) 2022-04-13 15:15:44 +02:00
Sofia Stamouli
8856f127c5
Update input in kaiju_kaiju module (#1522) 2022-04-13 14:53:08 +02:00
Maxime U. Garcia
4f5274c3de
feat: remove read_group which should be set up with task.ext.args (#1521)
* feat: remove reat_group which should be set up with ext.args

* fix: simplify dragmap command
2022-04-13 14:30:34 +02:00
Sofia Stamouli
39b4b45ba0
Update test_data.config to include kaiju.tar.gz (#1520) 2022-04-13 13:31:32 +02:00
Matthias De Smet
0f7c046477 first commit 2022-04-13 12:51:17 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins (#1459)
* feat: code polishing

* Apply suggestions from code review

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

* code polishing

* more code polishing

* code polishing

* tests for applybqsrspark

* fix typo

* no need to check md5sum for versions.yml

* fix: use correct syntax

* code polishing again

* add tests for markduplicatesspark

* simplify mergevcfs tests

* add tests for baserecalibratorspark

* fix: path to entry

* code polishing

* fix linting

* simplify module

* update meta.yml

* fix pair mode

* fix: MITO mode

* more tests

* fix command

* bad copy paste

* fix typos

* fix tests

* fix test

* update meta.yml

* correct versions.yml in all test.yml

* code polishing

* code polishing

* more code polishing

* fix args

* add tmpdir for all

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
Matthias De Smet
b59713e623
Tool/snap aligner single (#1510)
* first commit

* add tool

* fix tests

* fix indents

* Update modules/snapaligner/single/meta.yml

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

* fix comments

* fix versions

* prettier

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:20:35 +02:00
Matthias De Smet
09125979cc
Tool/snap aligner paired (#1509)
* first commit

* edit main.nf

* edit tests

* run prettier

* fix test

* indent script

* Update modules/snapaligner/paired/meta.yml

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

* Update modules/snapaligner/paired/meta.yml

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

* fix version nr

* update meta

* fix versions

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:02:10 +02:00
FriederikeHanssen
ffedf09b6e
Revert manta changes (#1518)
* Fix typo

* Revert to have target bed matched with sample info

* Add comment on design decision
2022-04-12 10:40:06 +02:00
FriederikeHanssen
7e4b04be7c
Merge branch 'nf-core:master' into master 2022-04-12 10:26:26 +02:00
James A. Fellows Yates
2d38566eca
Add MEGAN/RMA2INFO (#1513)
* fix: remove left-over unnecessary code

* Add megan/rma2info

* Attempt at fixing test

* Right yml formatting

* Get the versios reporting correct
2022-04-12 08:35:36 +02:00
FriederikeHanssen
897c33d5da
Samtools version update (#1507)
* Fix typo

* update version to 1.15.1

* Fix md5sums

* update mulled containers

* update md5sums

* update md5sums
2022-04-11 14:26:28 +02:00
James A. Fellows Yates
9d69c58897
Merge branch 'nf-core:master' into master 2022-04-10 07:30:45 +02:00
Michael L Heuer
8dc680d3b3
Update dsh-bio to version 2.0.8. (#1483) 2022-04-09 11:13:47 -05:00
Matthias De Smet
d4160c669b
Tool/crosscheckfingerprints (#1505)
* first commit

* first commit

* update test.yml

* update test.yml

* Update modules/picard/crosscheckfingerprints/main.nf

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

* Update modules/picard/crosscheckfingerprints/main.nf

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

* add support for vcf haplotype maps

* update test

* update test data config, use test data

* fix exit code

* Update modules/picard/crosscheckfingerprints/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/crosscheckfingerprints/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* remove unused stub

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 10:02:10 -04:00
Matthias De Smet
e19a9a2474
new tool: staden_io_lib (#1499)
* new tool: staden_io_lib

* update docker containers

* add test.yml

* add fai index input

* typo

* fix version.yml

* update md5sum

* omit md5sum for cram

* move scramble to submodule

* add missing in/output

* remove some comments

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 09:54:15 -04:00
Matthias De Smet
f57f085912
new tool snap-aligner/index (#1506)
* add snapaligner/index

* output fixes

* fix outputs

* fix tests

* update inputs

* fix more bugs

* fix linting

* Update modules/snapaligner/index/main.nf

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

* Update modules/snapaligner/index/main.nf

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

* fix comments

* fix indents

* fix escaping

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-08 14:41:08 +02:00
FriederikeHanssen
9ae34a01d1
Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts (#1504)
* Fix typo

* Add stub runs for testing input without matched normals

* Add missing -stub-run

* remove empty file checksum tests and change workflow names

* test controlfreec naming

* fix output file names

* fix output file names

* fix output file names

* fix conda and container path difference for R scripts

* update tar version to work with conda

* fix version number in docker

* try to fix path to script, pretty sure it won't work

* try new ways to set path with wildcard

* try which

* add which but with escape

* remove comment
2022-04-08 11:43:40 +02:00
Lucpen
f079367416
Picard liftover vcf (#1431)
* Building Picard liftovervcf module

* Building Picard liftovervcf module_test

* Building Picard liftovervcf pytest

* Module for picard liftover vcf created

* Fixed files after linting test

* Fixed trailing whitespace

* Checked files with prettier

* further formatting with prettier

* Fixed test.yml

* Fixed input variable names

* Changed contain test.liftef.vcf

* Changed contain in test.yml test.liftef.vcf

* Run prittier

* Going back to previous version of test.yml

* downgrading picard to 2.26.10 from 2.26.11

* Update modules/picard/liftovervcf/main.nf

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/main.nf

Print available memory

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Output from .vcf to .vcf.gz

* Added spaces to align emit

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Update modules/picard/liftovervcf/meta.yml

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>

* Removing md5sum test

Co-authored-by: jemten <jemten@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-04-07 07:50:58 -04:00
FriederikeHanssen
f8b56d1248
Merge branch 'nf-core:master' into master 2022-04-07 12:22:40 +02:00
Sofia Stamouli
d2726fcf75
Update centrifuge/centrifuge (#1495) 2022-04-07 11:46:34 +02:00
Matthias De Smet
dc95e67e15
New tool: biobambam/bamsormadup (#1478)
* add bamsormadup

* fix yaml

* add test.yml

* Update tests/modules/biobambam/bamsormadup/test.yml

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

* test meta.yaml: remove md5sums

* Tool bamsormadup:
- add (optional) reference input
- add bam index ouput
- add cram output option
- make metrics output: more general

* fix input and output formats

* update input file description

* drop sam output, goes against nf-core regs; add input check for cram files

* fix typo

* Update modules/biobambam/bamsormadup/main.nf

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

* improve ref fasta name

* fix if else shorthand

* fix syntax error

* kind of fix tests

* set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2

* fix command line

* update test.yml

* add support for multiple input bams

* Update modules/biobambam/bamsormadup/meta.yml

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

* Update modules/biobambam/bamsormadup/meta.yml

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

* Update tests/modules/biobambam/bamsormadup/test.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-06 08:18:23 +02:00
Matthias De Smet
797ce3254e
Update: biobambam/bammarkduplicates2 to v2.0.183 (#1493)
* bump version, remove md5sums from test

* re-add md5sums
2022-04-05 11:06:46 +02:00