Commit graph

2067 commits

Author SHA1 Message Date
Benjamin Wingfield
8e5eaf1fa4
Update plink2/vcf to output zstandard compressed data automatically (#1258)
* update plink2/vcf to output zstandard compressed data automatically

* update meta

* set plink CPU and memory usage

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-03-01 19:43:28 -05:00
Benjamin Wingfield
4ab098733a
set memory in MB (#1260)
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-03-01 13:13:05 -05:00
Lauri Mesilaakso
fe4eb459fb
Add stranger (#1360)
* Add stranger

* Add when clause

* Update paths

* Update modules/stranger/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-03-01 14:29:46 +01:00
James A. Fellows Yates
7ec09d0ef4
Fix: use actual tar conda environment for untar module (#1362)
* fix: remove left-over unnecessary code

* Update main.nf

* Update modules/untar/main.nf
2022-03-01 12:41:20 +01:00
James A. Fellows Yates
5a75c44ac3
Merge branch 'nf-core:master' into master 2022-03-01 11:40:01 +01:00
FriederikeHanssen
950700bcdc
Update samtools version (#1361)
* Update samtools version

* update checksums
2022-02-28 23:13:11 +01:00
FriederikeHanssen
c189835b1b
add controlfreec (#1333)
* add drafty controlfreec

* get sofatware version

* use maps in map

* update paths to new and soon-to-be merged test files, add more input docu

* Stab at documenting args map

* Update syntax

* Bit more description

* Make the linter happy

* tests pass locally

* Add outputs & docu

* tests are failing locally now :/ but cpn file can also be added

* All tests passing, need to update test data again to add folder

* Clean up files

* Clean up files

* Clean up files

* Don't know how to get the test to run with the direcotry for now. they pass locally though

* Make linter happy

* Name process back

* Update to use tar folder

* fix the checksum
2022-02-28 19:08:58 +01:00
Mei Wu
38ffbfdb63
bcftools/annotate follow up corrections (#1359)
* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

* using match instead of find

* bcftools/annotate refactored with complete test

* rm trailing white space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-28 10:16:29 -05:00
Mei Wu
ef811d952b
bcftools/annotate ready2go (#1291)
* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-28 14:23:12 +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
841c661cad
Add MAFFT module (#1351)
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-28 00:40:24 -07:00
Robert A. Petit III
9e0abcc443
add module for ssuisero (#1329)
* add module for ssuisero

* Update main.nf

* Update meta.yml

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-27 20:04:03 -07:00
Robert A. Petit III
55bee0b02e
add module for hpsuisero (#1331)
* add module for hpsuisero

* Update meta.yml

* Update main.nf

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-27 17:58:35 -07:00
James A. Fellows Yates
e0bf0a1689
Fix: Leehom meta output channel descriptions (#1356)
* fix: remove left-over unnecessary code

* Fix metayml docs of R2 output channels
2022-02-27 14:35:47 +01:00
James A. Fellows Yates
8d16261543
Merge branch 'nf-core:master' into master 2022-02-27 14:20:41 +01:00
Sateesh
8a20253f40
update args & convert to bam (#1355) 2022-02-25 11:06:39 -07:00
Sateesh
4c59984d7b
Seqkit pair (#1348)
* add seqkit pair module

* local tests

* local tests

* fix workflow name

* fix workflow name

* fix version indentation

* fix version indentation

* fix version indentation

* fix review comments

* fix review comments

* fix github usernames

* minor fix

* add meta unpaired output

Co-authored-by: Peri <rrx8@cdc.gov>
2022-02-24 15:07:35 +01:00
Michael J Cipriano
6400317623
Gatk4 selectvariants (#1346)
* initial commit

* tested

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-24 09:51:48 +01:00
Ramprasad Neethiraj
ee915a43e4
update svdb merge (#1274)
* update svdb merge

* fix undefined variable error

* remove prio join in the script block

* fix error

* fix error again

* update tests and refactor
2022-02-24 09:49:30 +01:00
Hunter Seabolt
1016c9bd1a
Seqtk seq (#1340)
* Initial commit of seqtk/seq module files

* pytest.yml

* updated module and tests code, need to finish modules/main.nf

* Initial commit of seqtk/seq module files

* pytest.yml

* updated module and tests code, need to finish modules/main.nf

* Adding code and configs for seqtk/seq module

* Re-tested module following minor code update

* removed trailing whitespace errors

* Changed variable name  to  following reviewer suggestions

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-23 17:02:51 +01:00
Michael J Cipriano
f144171ddc
Faqcs (#1339)
* Initial module creation

* Update test.yml

* Update test.yml

* Update test.yml

* Update meta.yml

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:30:22 +01:00
Sateesh
a25423dbb9
Gatk4 combinegvcfs (#1342)
* add gatk4/combinegvcfs module

* update gatk4/combinegvcfs

* loop to create a string adding -V to each vcf file

* add contains for variable md5

* rm whitespace

* meta in output

* fix indentations

* fix indentations

* move tmpdir to args and update conda version

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:29:29 +01:00
Moritz E. Beber
938387d10d
feat: add hmmsearch module and tests (#1273)
* feat: add hmmsearch module and tests

* chore: set medium resource requirements

* tests: look for correct output

* fix: add when condition

* Apply suggestions to meta.yml

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

* refactor: create gzip compressed output

* docs: describe compressed in-/output

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-23 15:32:33 +01:00
James A. Fellows Yates
f9d25aad7f
Switch to native mandatory gzipped reading for hmmalign (#1343)
* fix: remove left-over unnecessary code

* Update main.nf

* Update hmmer/hmmalign command to natively accept gzipped input

* Making @drpatelh happy

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

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-02-23 09:59:24 +00:00
James A. Fellows Yates
b0052ca6fa
Merge branch 'nf-core:master' into master 2022-02-23 10:10:21 +01:00
nickhsmith
2383d43a0f
update priority (#1334)
bumping the base resource label
2022-02-22 14:25:36 +01:00
Harshil Patel
4dbc166a7c
Change label for rseqc/tin to process_high (#1327) 2022-02-21 13:26:51 +00:00
Mei Wu
2597c31d6b
refactored vcfanno (#1266)
* final refactor: using tarball instead
2022-02-21 11:49:21 +01:00
Robert A. Petit III
15d39f841a
add amrfinderplus module (#1284)
* add amrfinderplus module

* Update test.yml

* Update main.nf

* Update main.nf

* Update test.yml

* Update test.yml

* Update test.yml

* Update main.nf

* Update meta.yml

* Update meta.yml

* Update main.nf

* Update test.yml

* Update test.yml
2022-02-19 23:02:23 +00:00
Sateesh
a0d91e4a93
Picard addorreplacereadgroups (#1305)
* add picard-addorreplacereadgroups

* add picard_addorreplacereadgroups

* add new line to main.nf

* remove trailing whitespaces

* remove trailing whitespaces

* change to output in test yml

* add when directive

* picard 2.26.10 -> 2.26.9

* picard 2.26.10 -> 2.26.9 test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:59:06 -07:00
Sateesh
927dbfed04
Picard cleansam (#1306)
* add picard-cleansam

* add picard/cleansam

* update test yml with output

* picard 2.26.10 -> 2.26.9

* add output to test yml

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 19:17:58 -07:00
Sateesh
62e5d1f0b3
Picard createsequencedictionary (#1310)
* add picard/createsequencedictionary module

* add picard-CreateSequenceDictionary

* add picard/createsequencedictionary/

* add contains to test yml

* update test yml contains

* update test yml contains

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 18:49:12 -07:00
Sateesh
f655e5dea2
Picard fixmateinformation (#1315)
* add picard-fixmateinformation

* add picard-fixmateinformation

* fix trailing whitespace

* fix trailing whitespace

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-18 18:18:05 -07:00
Robert A. Petit III
be798861c6
add module for abricate (#1280)
* add module for abricate

* rename abricate/abricate to abricate/run

* Update test.yml

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-18 18:00:21 -07:00
Robert A. Petit III
45466684e7
add mobsuite_recon module (#1270)
* add mobsuite_recon module

* Update main.nf

* Update nextflow.config

* Update test.yml

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-18 17:52:38 -07:00
Robert A. Petit III
425939a108
add module for legsta (#1319) 2022-02-18 17:42:18 -07:00
Robert A. Petit III
439763bf2c
add module for sistr (#1323)
* add module for sistr

* Update test.yml
2022-02-18 17:33:48 -07:00
Robert A. Petit III
8055c5d1c3
add module for rgi (#1321)
* add module for rgi

* fix extension

* fix test yaml

* Update main.nf

* Update main.nf
2022-02-18 17:23:44 -07:00
Harshil Patel
cab399507b
Patch fix artic/minion and ivar/variants modules (#1326) 2022-02-18 17:36:09 +00:00
James A. Fellows Yates
d0a1cbb703
fix fastp to allow exporting of only *.merged.fastq.gz (#1325)
* fix: remove left-over unnecessary code

* Update main.nf

* Update meta.yml
2022-02-18 15:38:05 +01:00
James A. Fellows Yates
c3b75cfc90
Merge branch 'nf-core:master' into master 2022-02-18 15:27:02 +01:00
FriederikeHanssen
e31f1ff3b1
add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320)
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-18 09:43:53 +01:00
FriederikeHanssen
3f364e2f31
add mergemutectstats (#1314)
* add mergemutectstats

* correct md5sum

* Update modules/gatk4/mergemutectstats/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-18 09:38:55 +01:00
FriederikeHanssen
fdb1664885
Add deeptools bamcoverage (#1316)
* Add deeptools bamcoverage

* remove todo string

* Add in when

* fix c&p version format error

* Fix md5sums

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-18 09:35:41 +01:00
Oliver Schwengers
9e9ff6a86d
Update Bakta module (#1257)
* bump Bakta version to v1.3.1

* add annotation summary file

* add/amend meta information

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-17 08:59:31 -07:00
FriederikeHanssen
fcd483e1b5
intervallisttobed (#1312)
* intervallisttobed

* correct md5sum
2022-02-17 16:32:26 +01:00
FriederikeHanssen
8c8be7d7c6
Add gatherpileupsummaries (#1311)
* Add gatherpileupsummaries

* fix checksum

* Update modules/gatk4/gatherpileupsummaries/main.nf

* Add in when
2022-02-17 15:05:21 +01:00
nickhsmith
8717792135
include intervals_index (#1308)
* include intervals_index

In order to run the GATK `GenotypeGVCFs` tool with an interval file (such as a .bed file) you need to have the corresponding index file. Otherwise you get the following error message
```
A USER ERROR has occurred: An index is required but was not found for file genome.bed.gz: work/6c/541fce2dc670597f62a571c72288c6/genome.bed.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.
```

including the index file fixes this problem

* Update meta.yml
2022-02-16 18:35:09 +01:00
Hunter Seabolt
a69faefee8
Seqtk rename (#1304)
* Added seqtk/rename module and tests code

* Updated files and testing code for seqtk rename

* Added meta map to seqtk/rename module def

* updated prefix parameter usage

* updated test.yml to remove local filepaths --> change to output

* Added empty line to main.nf
2022-02-16 17:28:08 +01:00
Moritz E. Beber
7560689375
feat: add sourmash sketch (#1287)
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 12:30:28 +01:00