Commit graph

529 commits

Author SHA1 Message Date
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge 2022-04-29 15:11:09 +02:00
Matthias De Smet
9d0f03d96a
Update modules/elprep/merge/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-29 15:07:09 +02:00
Matthias De Smet
7de207f93f
Merge branch 'master' into diamond-update 2022-04-29 15:02:54 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge 2022-04-29 14:32:12 +02:00
Matthias De Smet
771d5a19f1 fix reference arg 2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9 update to long args 2022-04-29 10:52:40 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update 2022-04-29 10:28:38 +02:00
James Fellows Yates
42564565b9 Update diamond/blastx diamond/blastp to support all possible output formats 2022-04-29 10:26:17 +02:00
Matthias De Smet
e263f267a7
Merge branch 'master' into bump/picard 2022-04-29 09:48:15 +02:00
Lauri Mesilaakso
1a5a9e7b40
Fix typo (#1586) 2022-04-29 09:37:23 +02:00
Matthias De Smet
ec10f98d55
picard CollectWgsMetrics: update to new cli args (#1578)
* update to new cli args

* remove bam index from tuple, not needed by program

* bump picard version

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-29 09:32:32 +02:00
Matthias De Smet
00467ac64a update command line syntax for all tools 2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8 bump picard version across the board 2022-04-29 07:47:24 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge 2022-04-28 21:14:30 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX (#1579)
* Added: csi output to TABIX

* Added: tests for csi

* Fix tiddit/sv (#1580)

* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>

* Fix: prettier issues

Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:41:01 +02:00
JIANHONG OU
cdefbec669
add kimporttext module (#1560)
* add kimporttext module

* fix the Prettier error.

* fix the Prettier error.

* fix the test.yml

* fix the test.yml

* Update modules/krona/ktimporttext/meta.yml

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

* Update modules/krona/ktimporttext/meta.yml

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

* Update modules/krona/ktimporttext/meta.yml

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

* Update modules/krona/ktimporttext/meta.yml

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

* Update modules/krona/ktimporttext/meta.yml

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

* update the test files;
simplify the main script of krona/ktimporttext.

* update the test file url for krona ktimporttext

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-28 08:16:26 -04:00
Daniel Cooke
57cb730e78
Fix tiddit/sv (#1580)
* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:06:38 +02:00
Praveen Raj S
68f1c27169
Changed tbi as optional output in GATK4 HaplotypeCaller (#1576)
* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.

* Apply suggestions from code review

* Update modules/gatk4/haplotypecaller/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 13:41:20 +02:00
Harshil Patel
1b5d3f5ac2
Bump STAR version to 2.7.10a for RSEM modules (#1573)
* Bump STAR version to 2.7.10a for RSEM modules

* Fix tests
2022-04-27 19:21:26 +01:00
Harshil Patel
2134031879
Bump SAMtools version for custom/getchromsizes (#1572) 2022-04-27 19:15:11 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads (#1571) 2022-04-27 16:03:44 +02:00
Jasmin F
61e740f79c
Add antismash download DB: missing container folders as output channels (#1567)
* Add missing container folders as output channels

* Apply suggestions from code review

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

* Update tool name

* Update test output checksum

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-27 12:40:04 +02:00
Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads (#1568)
* Add Trimgalore output for unpaired reads

* Use glob instead of outprefix
2022-04-26 19:15:24 +01:00
Sofia Stamouli
1f77bc130b
Update minimap2/align module (#1537) 2022-04-26 16:32:20 +02:00
Jose Espinosa-Carrasco
6a46e7cf11
Allow to pass arguments to the phantompeakqualtools script itself (#1562)
* Allow to pass arguments to the script itself

* Place args2 correctly

* Define args2 aaaaarrrrgggg

* Testing locally before commiting is a good practice

* Update modules/phantompeakqualtools/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-25 19:07:43 +02:00
Maxime U. Garcia
569e07f0af
add samtools/bamtocram modules (#1561)
* add new samtools/bamtocram module

* fix md5sum

* remove md5sum

* Update modules/samtools/bamtocram/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-25 14:32:49 +02:00
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge 2022-04-24 10:08:29 +02:00
Sateesh Peri
378fa5fbb4
new module: GAMMA (#1532)
* initial version of gamma module

* remove trailing whitespace

* prettier fix

* hardcode version number

* Update modules/gamma/main.nf

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

* Update modules/gamma/main.nf

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

* Update modules/gamma/meta.yml

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

* update meta and prettier

* add whitespaces

* add fasta output and tests

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-23 10:12:06 -04:00
Jose Espinosa-Carrasco
b3e56c83c6
Remove task.cpus from the command (#1559) 2022-04-22 15:29:49 +01:00
Harshil Patel
6d88f2da8c
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546)
* Rename process from STRINGTIE to STRINGTIE_STRINGTIE

* Bump Stringtie version to 2.2.1 and remove empty files in tests

* Fix tests for stringtie/merge

Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 15:13:06 +01:00
Harshil Patel
9aadd9a6d3
Replace vanilla Linux Biocontainer with Ubuntu (#1557) 2022-04-22 14:50:07 +01:00
Matthias De Smet
d57024ddc0
Merge branch 'master' into tool/elprep-merge 2022-04-22 13:05:30 +02:00
Matthias De Smet
c17d1a7a7b
fix output glob (#1552) 2022-04-22 13:04:41 +02:00
Matthias De Smet
b1749445d7
fix output glob (#1551) 2022-04-22 12:50:17 +02:00
Matthias De Smet
fefffb9bb0 fix output glob 2022-04-22 12:36:32 +02:00
Matthias De Smet
2f6382168c update meta.yml 2022-04-22 11:51:54 +02:00
Matthias De Smet
c4072f274c fix formatting, fix code style 2022-04-22 11:39:22 +02:00
Matthias De Smet
b4d2e374a0
Merge branch 'master' into tool/elprep-merge 2022-04-22 11:35:48 +02:00
Sofia Stamouli
538dbac98b
Kaiju2table module (#1545)
* Add kaiju2table module
2022-04-22 11:26:30 +02:00
Matthias De Smet
4af5be8de3
Merge branch 'master' into tool/elprep-merge 2022-04-22 11:10:23 +02:00
Matthias De Smet
9e3daae8ef
New module: elprep filter (#1524)
* first commit

* syntax fix

* fix input

* output sam during test for md5sum

* replace md5sum with contains

* add new test data, add extra in/outputs

* cli fixes

* fix outputs

* Update modules/elprep/filter/main.nf

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

* Update modules/elprep/filter/meta.yml

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

* Update modules/elprep/filter/meta.yml

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

* fix suggestions by @jfy133

* Bit more verbose explanation for bool vals

* define variables

* fix prettier

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 11:08:03 +02:00
Matthias De Smet
a1757897cb
Merge branch 'master' into tool/elprep-merge 2022-04-22 10:20:59 +02:00
Matthias De Smet
90b203d3e9
Tool/elprep split (#1533)
* tool: elprep split

* fixes for testing

* fix tests

* fix test outputs

* create test-yaml

* fix suggestions by @jfy133

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 10:20:05 +02:00
Matthias De Smet
35231d3949
update picard/collecthsmetrics (#1542)
* update picard/collecthsmetrics

* syntax fixes, bugfixes

* add tests

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-04-22 10:13:57 +02:00
Ramprasad Neethiraj
c7329a3a57
add stubs for stranger (#1543) 2022-04-22 10:10:43 +02:00
Lucpen
12afb6b0fa
Update samtools view to add input path(index) (#1539)
* feat added index as input, to allow module to be used for subsampling

* fix test

* feat added index to meta.yml

* Update modules/samtools/view/meta.yml

feat corrected description of idea pattern file in meta.yml

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 10:01:47 +02:00
Matthias De Smet
f4c69bc427
Module/bclconvert (#1485)
* bclconvert: initial commit

* add most of tool

* attempt at adding testing stub

* add dockerfile + instructions

* add container to module

* update readme

* more attempts at making stubs work

* finish stub run

* fix ci issues

* more fixes to stub

* add read version check to stub

* fix some tests

* update readme

* fix version number

* syntax fix

* revert edit to output directory

* Update modules/bclconvert/meta.yml

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

* Update modules/bclconvert/meta.yml

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

* update meta.yaml

* update thread usage

* Update modules/bclconvert/main.nf

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

* Escape env variable

* Update modules/bclconvert/Dockerfile

Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>

* fix comments by @Emiller88

* fix task.cpus

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 15:39:22 +02:00
Francesco L
abe025677c
update to kraken2: breaking change - output channels renamed (#1525)
* updated kraken2 module to include optional classification of each input reads, and make fastq outputs optional
NB: this is a breaking change, because the output channels have been renamed as a consequence of changes

* updated yml

* pigz command made optional, in order to be executed only if fastq of classified/unclassified reads are saved

* updated test yaml file for kraken2

* fixed TODOs and renamed variables and outputs

* untar in conda cannot keep same md5sum of version, and therefore md5sum check removed

* improved description of the options

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 14:33:59 +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