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Author SHA1 Message Date
Priyanka Surana
504028346b
samtools fasta module (#2128) 2022-09-29 08:10:44 +01:00
Matthieu Muffato
e9bc33485e
bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list (#2114) 
* bugfix: when there is a single input file, stageAs("?/*) returns the path directly, not in a list

* Added a test

* Added a test

* Added MD5 checksum

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
 2022-09-28 13:28:52 +01:00
Priyanka Surana
83b05a8dc0
add qname feature to samtools/view (#2115) 
* add qname feature to samtools_view

* update tests

* Update modules/samtools/view/meta.yml

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

* Update modules/samtools/view/meta.yml

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

* added filter tests

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-28 13:04:41 +01:00
Matthias De Smet
b5aa12ad3b
new module: samtools/getrg (#2123) 
* new module: samtools/getrg

* add output file to stub

* add missing config

* Intentionally break prettier linting

* [automated] Fix linting with Prettier

Co-authored-by: Phil Ewels <phil@seqera.io>
Co-authored-by: nf-core-bot <core@nf-co.re>
 2022-09-28 14:00:10 +02:00
Matthieu Muffato
f0a86eaf5b
Multithreaded samtools commands (#2080) 
* Multithreaded samtools commands

* Updated the checksums since the BAM files include the actual command line

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
 2022-09-26 17:44:36 +01:00
Priyanka Surana
09159edc9e
Update samtools view (#2098) 
* samtools view update

* remove csi output

* prettier

* update meta

* add index functionality

* prettier

* fixed test checks
 2022-09-23 16:52:01 +02:00
Priyanka Surana
402631fdaa
Update samtools view (#2096) 
* samtools view update

* remove csi output

* prettier

* update meta
 2022-09-23 13:03:59 +01:00
Priyanka Surana
22e144dc63
samtools markdup module (#2087) 2022-09-21 15:39:10 +01:00
Priyanka Surana
ab4c2e440d
samtools collate module (#2078) 
* samtools collate module

* prettier fix

* prettier fix

* added cram functionality
 2022-09-21 14:12:59 +01:00
Benedetto Polimeni
d5d785b3d8
[samtools] add optional csi output (#2064) 
* [samtools] add optional csi output, when applicable

* Remove empty line

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
 2022-09-20 21:08:29 +01:00
Matthieu Muffato
3eb99152ce
Added the optional .gzi output of "samtools faidx" (#1935) 2022-09-08 13:35:23 +01:00
FriederikeHanssen
5e7b1ef9a5
Reduce resource requests (#2021) 
use process_single

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-09-07 10:33:05 +02:00
Matthias De Smet
bbb99cb8d6
Fix/samtools flagstat (#1979) 
* fix samtools stats thread usage

* flagstat: fix threads
 2022-08-29 13:11:58 +02:00
Matthias De Smet
f4eab79459
fix samtools stats thread usage (#1975) 
* fix samtools stats thread usage

* fix checksums
 2022-08-29 12:05:47 +02:00
nickhsmith
454e0acc09
Mpileup intervals (#1955) 
* update tests

* update

* update

* make the manta inputs consistant for germline/somatic/tumoronly

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* include intervals

* update md5 with interval

Co-authored-by: Smith Nicholas <smith@in.tum.de>
 2022-08-16 14:16:35 +02:00
Matthieu Muffato
31409f5e72
Added the samtools/dict module (#1922) 
* Added the samtools/dict module

* samtools/dict is single-threaded
 2022-07-26 22:13:19 +01:00
Matthieu Muffato
ce06694af8
Added support for ext.args in samtools/faidx (#1919) 
ext.args was not used in the actual command-line

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-07-26 21:51:47 +01:00
nvnieuwk
720027275c
small update to samtools/merge (#1896) 2022-07-18 11:37:45 +02:00
Maxime U. Garcia
f48a24770e
more generic name because of multiple extension (#1880) 2022-07-14 11:42:00 +02:00
Aleksei Korzhenkov
848ee9a215
Improve descriptions for modules with missing 
Description and keywords

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-06 12:03:08 +02:00
Matthias De Smet
ecece498f1
samtools/*stats*: use prefix for outputs (#1788) 
* use prefix in flagstat

* use prefix in idxstats

* use prefix in stats

* update test.yml
 2022-06-16 13:42:01 +02:00
WackerO
24e05f6097
Update modules/samtools/mpileup/main.nf 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-13 09:35:34 +02:00
WackerO
dc6c09e083 samtools mpileup now bgzips mpileup files 2022-06-11 13:32:53 +02:00
Rike
da79396f06 rename aligned to alignment 2022-05-09 16:07:49 +02:00
Rike
5bd456e5e8 rename file_type to output extension 2022-05-09 16:06:22 +02:00
Rike
1de1c2253e Combine output after code review 2022-05-09 16:04:58 +02:00
Rike
24d5e7feed Code review suggestions 2022-05-09 15:42:55 +02:00
Rike
ef5f145342 Generalize Bam2Cram do either conversion 2022-05-09 15:22:54 +02:00
ljmesi
034352dbbf Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-03 15:18:12 +02:00
ljmesi
5510ea39fe Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:13:55 +03:00
ljmesi
5503903457 Add compression for output fastq file 2022-05-03 09:46:04 +02:00
Lucpen
6b64f9cb6c feat added stub to modules 2022-05-02 10:34:14 +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
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
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
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
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
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
FriederikeHanssen
1ad73f1b2a
update samtools version to 1.15 (#1358) 
* update samtools version to 1.15

* Update checksums
 2022-02-28 12:42:29 +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
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
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +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
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
Jose Espinosa-Carrasco
cde237e7ce
Fix error messages mentioning suffix (#1190) 2021-12-23 17:22:07 +00:00
Harshil Patel
0fafaeebf5
Revert PR #1147 (#1166) 
* Revert PR #1147

* Fix md5sum for crai file
 2021-12-13 16:15:20 +00:00
Maxime U. Garcia
37c5cb495d
feat: add original input as optional output channel (#1147) 2021-12-09 11:04:53 +01:00
Mahesh Binzer-Panchal
d473a247d2
Replace remaining task.ext.suffix with task.ext.prefix (#1117) 
* Replace remaining task.ext.suffix with task.ext.prefix
 2021-12-07 15:00:43 +01:00
Maxime Borry
e0aa89141f
Add meta information to samtools/faidx (#1114) 
* add meta to samtools/faidx
 2021-12-06 11:37:04 +01:00