Commit graph

396 commits

Author SHA1 Message Date
Carpanzano
20787514d9 modifiche per il test 2022-04-29 15:11:21 +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
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
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
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
Moritz E. Beber
879d42c5e2
Refactor adapterremoval (#1491)
* refactor: insert .fastq file extensions

* style: insert whitespace

* refactor: create paired output

* refactor: rename settings from log

Requested by @jfy133

* tests: correct expected output

* fix: remove settings option due to default

* chore: rename output patterns

* refactor: omit paired files in single-end

* refactor: rename output to settings
2022-04-04 21:40:35 +02:00
Sofia Stamouli
6a11c5a222
Fix untar for centrifuge (#1472) 2022-04-04 10:18:11 +02:00
James A. Fellows Yates
f1c5384c31
Add PRINSEQPLUSPLUS (#1481)
* fix: remove left-over unnecessary code

* Add prinseq++

* Remove last todo

* Fix tests due to variability of output FASTQs (reads can be ordered differently between runs)

* Apply suggestions from code review
2022-04-03 16:06:22 +02:00
Ramprasad Neethiraj
67c1bc9568
Add stubs to cnvpytor module (#1473)
* callcnvs stub and tests

* partition stub and test

* histogram stub and test

* importreaddepth stub and tests

* update module scripts

Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
2022-04-01 17:35:15 +02:00
James A. Fellows Yates
8ce6810787
Update DASTool to 1.1.4 (#1471)
* fix: remove left-over unnecessary code

* Update DASTool

* Fix tests

* Fix test.ymls

* Fix container build version

* Make tests less strict to account for variability

* Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Add missing description

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-04-01 11:33:07 +02:00
Jose Espinosa-Carrasco
5e7daa7b96
Add task.ext.args to phantompeakqualtools and finish the module (#1474)
* Add --max--ppsize option

* Add args to phantompeakqualtools and all the missing files (test, yml, ...)

* Fix tests

* Add the nextflow.config

* Fix tests
2022-03-31 22:59:21 +01:00
Sébastien Guizard
794f84534b
New Module: gstama/polyacleanup (#1468)
* 📦 NEW: Add gstama/polyacleanup

polyacleanup script remove remaining polyA tails from FLNC reads (Pacbio isoseq3)

* 🐛 FIX: Prettier: replace simple quote by double quote

* 🐛 FIX: Update TEMPLATE to nf-core 2.4

* 👌 IMPROVE: Compress outputs

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-31 09:11:51 -04:00
Ramprasad Neethiraj
eeda4136c0
Update cat module (#1469)
* fix cat stub

* add test

* commit suggestions

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-03-31 13:42:44 +02:00
Moritz E. Beber
0de6406217
feat: add module for seqkit stats (#1466) 2022-03-30 23:01:17 +02:00
Ramprasad Neethiraj
fd5f6f5f4f
Revert recent changes made to some of the modules (#1463)
* revert changes to modules

* fix tests

* fix kraken2

* fix untar

* fix cat

* add blank lines

* fix typo
2022-03-30 20:21:06 +02:00
Jose Espinosa-Carrasco
dbb46c9b63
Bump chromap version 0.2.1 (#1462) 2022-03-29 16:44:19 +02:00
Ramprasad Neethiraj
49b18b1639
add stub to modules used in raredisease pipeline (#1206)
* add stub section

* add stub for bcftools norm

* add stub to more modules

* fix expansionhunter tests

* revert changes -picard

* Update stub to write version no.s to a file

* add picard

* revert picard again

* add stubs to more modules

* fix bwamem2

* add bcftools view

* add stubs

* fix svdb query

* review suggestions
2022-03-28 17:48:39 +02:00
James A. Fellows Yates
240ee4328c
Dastool update to allow non-gzipped inputs (#1458)
* fix: remove left-over unnecessary code

* Make gzipping optional for DAS_Tool scaffolds2bin

* Add optional unzipping

* Make gunzip optional for DAS_Tool scaffolds2bin

* Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

* Update modules/dastool/scaffolds2bin/meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-03-28 16:29:46 +02:00
Tanja Normark
1f483d9203
Add kaiju_kaiju module (#1448)
* Added kaiju_kaiju module

* Update modules/kaiju/kaiju/main.nf

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

* Update modules/kaiju/kaiju/main.nf

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

* Update modules/kaiju/kaiju/meta.yml

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

* Update keywords

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

* Update output file naming

* Update output file naming

* update spacing for lint

* Update input file patterns

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-28 14:28:50 +02:00
Edmund Miller
5832fbc225
Fix homer/maketagdirectory output collision (#1456)
* fix(homer): Update tagdir to have a prefix

Otherwise they have a naming collision

* test(homer): Update paths

* style(homer): Align ,'s

* chore(homer): Update md5sums
2022-03-27 03:17:42 +00:00
FriederikeHanssen
5acf301ddd
add freec2circos script (#1454)
* add freec2circos script

* remove todo statements
2022-03-26 21:25:29 +01:00
FriederikeHanssen
28e5211b35
add makegraph script (#1452)
* add makegraph script

* allow renaming of output files

* allow renaming of output files
2022-03-25 20:49:08 +01:00
FriederikeHanssen
8a64e73af2
add freec2bed script (#1453) 2022-03-25 20:31:52 +01:00
FriederikeHanssen
4efa8da5c5
controlfreec significance (#1451)
* controlfreec significance

* move freec files to own subfolder

* Fix meta.yml naming

* Fix meta.yml naming

* Fix linting

* Forgot to refactor

* forgot more refactoring

* Too much refactoring on output paths

* Too little refactoring here

* update checksum
2022-03-25 18:22:17 +01:00
Edmund Miller
27936729f2
Add samtools to homer/maketagdirectory to use bam files (#1437)
* fix(homer): Update dependancies for maketagdirectory

Closes #1363

* test(homer): Add tests for bam usage

* style(homer): Rename meta test

* fix(homer): Update args order and add missing \\

* docs(homer): Add DESeq2 and edgeR

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

* test(homer): Update md5sum

* test(homer): bam => sam

* fix(homer): Use nextflow conda recipe instead of biocontainers with commas

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 17:13:30 +00:00
Edmund Miller
7111e571cc
Split preseq lcextrap and ccurve (#1440)
* fix(preseq): Update lcextrap file name

* chore(preseq): Bump lcextrap image

* feat: Initialize preseq c_curve

* docs(preseq): Update documentation
2022-03-25 17:11:40 +00:00
Simon Pearce
a066456735
Add tests for umitools extract and dedup (#1429)
* NGSCheckMate v1

* Add some tests for UMItools

* Added tests for dedup

* Include pytest

* Delete main.nf

* Delete meta.yml

* Delete main.nf

* Delete nextflow.config

* Delete test.yml

* add prettier

* Add direct test on bam

* Update tests/modules/umitools/dedup/main.nf

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* Update tests/modules/umitools/dedup/main.nf

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* Update tests/config/pytest_modules.yml

Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>

* Not ignore-umi

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
Edmund Miller
1fb1801dcb
refactor(homer): Update output path for bedGraph (#1438)
This allow for caching because otherwise it modifies the tag directory input
2022-03-25 13:54:09 +00:00
Edmund Miller
98ed71c8f6
feat(homer): Add pos2bed module (#1435)
* feat(homer): Add pos2bed module

* test(homer): Pass bed format

* test(homer): Add upstream dependencies to avoid regressions

* Update modules/homer/pos2bed/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 13:29:36 +00:00
FriederikeHanssen
3d31fa4d04
CAT: Use meta map and supply output file name via modules.config (#1446)
* Use meta map and supply output file name via modules.config

* Remove all def declarations to make it work

* update tests & remove extra .

* fix ze tests

* update meta.yml with meta map info

* add tag line now that meta is available
2022-03-25 14:01:57 +01:00
FriederikeHanssen
b5825fe6b3
Mpileup also likes intervals (#1445)
* Mpileup also likes intervals

* Also update meta yml with inclusive input and intervals

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-03-25 07:46:51 +01:00
Robert A. Petit III
d16f1ea4d7
add module for panaroo, fix pirate tests (#1444)
* add module for panaroo

* update pirate test yaml

* update panaroo test yaml

* update pirate test yaml md5s

* Update main.nf

* Update main.nf

* pin bioperl version
2022-03-24 20:11:04 -06:00
Edmund Miller
6806cd1de9
feat(bbmap): Initialize pileup module (#1441)
* feat(bbmap): Initialize pileup module

* test(bbmap): Update outputs

* test(bbmap): Add pileup tags

* style(bbmap): Add in when

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-24 17:38:24 -06:00
Robert A. Petit III
dfbb0bc17c
update bakta to latest version (v1.4.0) (#1428)
* update bakta to latest version (v1.4.0)

* Update test.yml

* remove empty file md5sums

* bakta was rebuilt to fix dependencies on bioconda

* trigger ci

Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
2022-03-24 10:49:17 -06:00
Moritz E. Beber
9c386c5dd8
Add bracken (#1423)
* feat: add template for Bracken

* chore: update version

* refactor: change command build

* refactor: rename report variable, change quotes

* docs: remove refactored input parameter

* fix: correctly assign arguments to options

* tests: set up single and paired end tests

* style: apply prettier

* chore: change data sources to official ones

* refactor: rename test workflows

* tests: use correct input to the new UNTAR module

* chore: update md5sums
2022-03-22 16:40:21 +01:00
James A. Fellows Yates
e080f4c8ac
Untar unzip meta (#1408)
* fix: remove left-over unnecessary code

* Adds support for meta lists for unzip and untar

* Fix test inputs

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Fix MALTEXTRACT/AMPS

* Fix further modules

* Fix cellranger

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00
James A. Fellows Yates
8c00897853
Add AdapterRemovalFixPrefix (#1424)
* Add AdapterRemovalFixPrefix

* Prettifying

Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2022-03-21 11:26:12 +01:00
Ramprasad Neethiraj
5297d27fbf
update svdb to version 2.5.2 (#1390)
* update svdb version and tests

* update link
2022-03-21 10:39:34 +01:00
Robert A. Petit III
16096aba17
Update test.yml (#1419) 2022-03-19 15:06:21 +00:00
James A. Fellows Yates
15c7190e22
Deeparg singularity container fix 2 (#1406)
* fix: remove left-over unnecessary code

* Switch to more portable solution for singularity container issue by using bind paths

* Fix input collision of dummy files

* Repalce dummy with which bash

* Remove dummy usage from tests

* Apply suggestions from code review

* Fix singularity typo
2022-03-18 16:21:55 +01:00
Sofia Stamouli
ea41a8a6f7
Add centrifuge module (#1410)
* Add centrifuge module

* Add centrifuge module

* Add centrifuge module

* Add centrifuge module
2022-03-18 15:39:27 +01:00