Commit graph

1346 commits

Author SHA1 Message Date
Mahesh Binzer-Panchal
d83281eac9
Merge branch 'master' into kat_hist 2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal
9194fb845e Add module kat hist 2022-05-06 07:54:10 +00:00
Matthias De Smet
853b623969 new module: md5sum 2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj
313d76e005 update svdb version 2022-05-06 00:18:16 +02:00
Ramprasad Neethiraj
af73544010 update meta 2022-05-06 00:13:49 +02:00
Ramprasad Neethiraj
db56d80060 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj
e4e4f8090c combine multiple pytor 2022-05-05 23:59:12 +02:00
JIANHONG OU
e391c65510 fix the version issue for motus_profile. 2022-05-05 15:35:31 -04:00
JIANHONG OU
b8efa2ae7c
Merge branch 'master' into motus_profile 2022-05-05 13:41:54 -04:00
JIANHONG OU
fb5c5d310a update motus module. 2022-05-05 13:38:46 -04:00
Sateesh Peri
faf45edc5e
Merge branch 'master' into busco 2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj
db2acba71b
Merge branch 'master' into feat/update_cnvpytor 2022-05-05 17:31:10 +02:00
Ramprasad Neethiraj
c183d7b397 Merge branch 'feat/update_cnvpytor' of github.com:ramprasadn/modules into feat/update_cnvpytor 2022-05-05 17:28:59 +02:00
Ramprasad Neethiraj
ea1f5daf44 polish python script in view 2022-05-05 17:28:49 +02:00
Harshil Patel
1289626cc9
Update modules/busco/main.nf 2022-05-05 16:09:45 +01:00
Mahesh Binzer-Panchal
2542ae1823
Update modules/busco/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-05-05 16:33:32 +02:00
Sateesh Peri
3414d3aba3
Merge branch 'master' into busco 2022-05-05 10:08:55 -04:00
JIANHONG OU
c8f2c44e22 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
JIANHONG OU
a8bc386ea3
Merge branch 'master' into motus_downloaddb 2022-05-05 09:36:25 -04:00
JIANHONG OU
566c11dacc
Merge branch 'master' into motus_downloaddb 2022-05-05 08:28:10 -04:00
Francesco L
97f318eea6
Merge branch 'master' into firstbranch 2022-05-05 14:25:00 +02:00
Carpanzano
a700a9c15e Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch 2022-05-05 13:52:45 +02:00
Carpanzano
9083d3bb3d integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
jasmezz
47a95388c2 Remove trailing whitespaces (ECLint check) 2022-05-05 13:17:36 +02:00
jasmezz
24b9c397dd Apply suggestions from code review + add support for GFF annotations 2022-05-05 13:14:39 +02:00
MaxUlysse
40dd662fd2 update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
James A. Fellows Yates
e60c6f9bfd
Merge branch 'master' into firstbranch 2022-05-05 10:57:27 +02:00
Carpanzano
204dfba2d8 fixing ktupdatetaxonomy/meta.yml as suggested in PR 2022-05-05 10:51:22 +02:00
Mahesh Binzer-Panchal
865ad3447a Update meta.yml output files 2022-05-05 08:23:54 +00:00
jasmezz
6a7aec8b41 Remove prokka test workflow 2022-05-05 10:22:02 +02:00
Mahesh Binzer-Panchal
58ea709f7f
Merge branch 'master' into busco 2022-05-05 09:34:14 +02:00
James A. Fellows Yates
6393a085c5
Apply suggestions from code review 2022-05-05 08:23:51 +02:00
JIANHONG OU
29ee72c693 update meta.yml and remove the cleanup step. 2022-05-04 15:37:12 -04:00
JIANHONG OU
e9c82a5f48
Update modules/motus/downloaddb/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-04 15:29:06 -04:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb 2022-05-04 20:58:08 +02:00
James A. Fellows Yates
ec5bada3fc
Update modules/motus/downloaddb/meta.yml 2022-05-04 20:55:16 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
a6086f549d recovered process name 2022-05-04 17:28:24 +02:00
Nicolas Vannieuwkerke
3c07602443 Added the version.yml 2022-05-04 16:51:09 +02:00
Carpanzano
8b1711d8a1 recovering old module name 2022-05-04 16:38:10 +02:00
Simone Carpanzano
162f8edf54
Merge branch 'master' into firstbranch 2022-05-04 16:35:25 +02:00
Carpanzano
6b8ca501ed fixing suggestions from PR 2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke
f875aec46b Split the module into two parts 2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal
5986a3efbf
Merge branch 'master' into busco 2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke
505ab03803 fixed a description 2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke
177a7e49f2 Fixed a linting issue 2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke
000b8ee2e0 Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py 2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke
065a5d6a7f Fixed a linting issue 2022-05-04 14:05:21 +02:00
nvnieuwk
c9808cb97f
Merge branch 'master' into new-module-hap.py 2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke
37338ecee3 Finished the module 2022-05-04 14:00:02 +02:00
Ramprasad Neethiraj
6541e151bc
Merge branch 'master' into feat/update_cnvpytor 2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal
73a8df9522 Fix no genes found test and update test.yml 2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke
c517ce9b4d Added the module and some simple testing 2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal
8df20218bf Add more tests and capture summaries
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal
3bb0711b06
Merge branch 'master' into busco 2022-05-04 09:15:46 +02:00
Lauri Mesilaakso
530b5ac661
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 09:53:46 +03:00
Chris Cheshire
79e64cdd1f
Merge branch 'master' into expected_error_fix 2022-05-03 22:21:28 +01:00
JIANHONG OU
dc59ad0bf5 fix the version issue. 2022-05-03 12:27:39 -04:00
jasmezz
480c4ced78 Update meta.yml 2022-05-03 17:35:16 +02:00
jasmezz
fa9f0753de Apply review suggestions + add stub for prokka test workflow 2022-05-03 17:30:16 +02:00
Jill V. Hagey, PhD
f02cd618b8
Update meta.yml 2022-05-03 10:09:19 -04:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
Mahesh Binzer-Panchal
1c54c0b1ae
Apply suggestions from code review
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
2022-05-03 16:02:11 +02:00
Matthieu Muffato
6351ec745e
Update contributor list 2022-05-03 14:56:27 +01:00
Matthieu Muffato
4be754b008
It's a file, not a directory 2022-05-03 14:53:17 +01:00
Mahesh Binzer-Panchal
636abad8f1
Merge branch 'master' into busco 2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke
96d4a31cc1 Moved the BED file to the main tuple 2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal
5f4781adaa
Merge branch 'master' into busco 2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal
57db28386e Support batch fasta analysis 2022-05-03 13:26:49 +00:00
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
Ramprasad Neethiraj
26311aba2a fix minor errors 2022-05-03 15:04:37 +02:00
Ramprasad Neethiraj
be085c0173 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-03 14:55:42 +02:00
Ramprasad Neethiraj
19cfb4e951 update meta files 2022-05-03 14:53:56 +02:00
Ramprasad Neethiraj
3efa931bf6 view 2022-05-03 14:26:46 +02:00
Ramprasad Neethiraj
829c15c98b partition 2022-05-03 14:26:34 +02:00
Ramprasad Neethiraj
7cc47f6ba6 importrd 2022-05-03 14:25:20 +02:00
Ramprasad Neethiraj
07e026054a histogram 2022-05-03 14:24:54 +02:00
Ramprasad Neethiraj
2990dc8357 callcnv module 2022-05-03 14:20:05 +02:00
Lauri Mesilaakso
a65e76e3dd
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 14:30:54 +03:00
Chris Cheshire
6f35537d40
Merge branch 'master' into expected_error_fix 2022-05-03 12:21:51 +01:00
Chris Cheshire
829183ee84
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:16:54 +01:00
Chris Cheshire
6015478b72
Merge branch 'master' into add-slimfastq 2022-05-03 12:11:19 +01:00
Chris Cheshire
d7fb969a74
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:10:23 +01:00
Chris Cheshire
61f68913fe
Merge branch 'master' into expected_error_fix 2022-05-03 11:49:35 +01:00
Chris Cheshire
768073be63 bowtie2|Added support for large indexes 2022-05-03 11:46:19 +01:00
Mahesh Binzer-Panchal
012f085378 Prettier 2022-05-03 09:19:39 +00:00
Mahesh Binzer-Panchal
9eff38ff94 Update meta.yml 2022-05-03 09:15:45 +00:00
Mahesh Binzer-Panchal
ddbe6e8f40
Merge branch 'master' into busco 2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal
9a72548ee1 Update busco module 2022-05-03 08:42:56 +00:00
Lauri Mesilaakso
6367c6a1ad
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:41:25 +03:00
nvnieuwk
f85787b19e
Merge branch 'master' into vardict-java 2022-05-03 10:17:04 +02:00
nvnieuwk
8187641280
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:45 +02:00
nvnieuwk
11c6faf433
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:36 +02:00
nvnieuwk
01085b3e09
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:30 +02:00
nvnieuwk
1609dfc96d
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:20 +02:00
nvnieuwk
3cdbdf50fc
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:14 +02:00
nvnieuwk
2dff193b54
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:15:59 +02:00
nvnieuwk
7c89af359c
Update modules/vardictjava/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:15:51 +02:00
Nicolas Vannieuwkerke
49ba3adbde Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 10:15:33 +02:00
Nicolas Vannieuwkerke
d33253513f put the version on top of the file 2022-05-03 10:15:30 +02:00
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:13:55 +03:00
nvnieuwk
278d41b6bf
Merge branch 'master' into vardict-java 2022-05-03 09:59:05 +02:00
ljmesi
5503903457 Add compression for output fastq file 2022-05-03 09:46:04 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules 2022-05-03 09:43:16 +02:00
Lauri Mesilaakso
77054795fb
Merge branch 'master' into add_handling_of_alternative_fn_suffix_for_metaphlan3 2022-05-03 09:38:51 +03:00
Nicolas Vannieuwkerke
71c5d21374 ran prettier 2022-05-03 08:34:12 +02:00
Nicolas Vannieuwkerke
9127f92ddd Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke
9a10e5beb5 Added the missing inputs in meta.yml + correct notation 2022-05-03 08:29:46 +02:00
Matthias De Smet
1687bfcb85
Merge branch 'master' into add-slimfastq 2022-05-03 08:22:49 +02:00
Matthias De Smet
a67c06af81
Merge branch 'master' into vardict-java 2022-05-03 08:22:19 +02:00
Nicolas Vannieuwkerke
d8782d7976 Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 08:20:13 +02:00
Nicolas Vannieuwkerke
b8a59c2b17 Fixed version annotation 2022-05-03 08:20:10 +02:00
Moritz E. Beber
16aa3915e3 feat: add module for slimfastq 2022-05-02 23:16:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules 2022-05-02 18:31:55 +02:00
JIANHONG OU
5735f515f8 fix a typo in version export. 2022-05-02 12:25:48 -04:00
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2 2022-05-02 12:13:11 -04:00
Jasmin F
b8386c42a7
Merge branch 'nf-core:master' into antismashlite 2022-05-02 17:58:19 +02:00
Carpanzano
c07ae8c483 fixed lint in ktimporttaxonomy 2022-05-02 17:47:45 +02:00
Simone Carpanzano
3d9c8a6bb1
Merge branch 'master' into firstbranch 2022-05-02 17:43:33 +02:00
Jasmin F
883b95bed6
Merge branch 'nf-core:master' into antismashlite 2022-05-02 17:31:43 +02:00
jasmezz
4a4de550b8 Simplify/reduce container mount volumes 2022-05-02 17:30:46 +02:00
jvhagey
24dc2d2113 added tests 2022-05-02 11:30:19 -04:00
Jasmin F
235944f797
Merge branch 'master' into antismash_db_output 2022-05-02 17:11:51 +02:00
Jasmin F
8db0b754c0
Fix commented-out command 2022-05-02 16:56:39 +02:00
jasmezz
6a9f2077cf Fix unbound variable crash 2022-05-02 16:41:59 +02:00
Lucpen
62c6123ec4 fix gatk4_mutect2 test by changing main.nf 2022-05-02 15:11:57 +02:00
JIANHONG OU
250d64dfde fix the typo of motus_downloadb. 2022-05-02 08:52:54 -04:00
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb 2022-05-02 08:42:09 -04:00
JIANHONG OU
31dd31079d update teh versions.yml 2022-05-02 08:41:41 -04:00
jasmezz
0fc352188b Fix conda antismash path 2022-05-02 14:40:35 +02:00
JIANHONG OU
0f24e4dcff add input database and intermediate bam file. 2022-05-02 08:37:12 -04:00
Jasmin F
5cd517e759
Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-02 14:31:40 +02:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules 2022-05-02 14:20:03 +02:00
ljmesi
ed4dd1a928 Add additional handling of fq.gz file name suffix 2022-05-02 14:16:12 +02:00
Lucpen
f231291e77 fix gatk4_reversam test 2022-05-02 12:58:12 +02:00
James A. Fellows Yates
575258332a
Merge branch 'master' into diamond-update 2022-05-02 12:41:37 +02:00
James Fellows Yates
bd3bfe0817 Add warn of default being used 2022-05-02 12:41:24 +02:00
James Fellows Yates
67b074382e Fix tests 2022-05-02 12:29:00 +02:00
James Fellows Yates
58e5c6aece Make variables consistent 2022-05-02 11:55:43 +02:00
James Fellows Yates
6986975bc0 Fix output channels allow BLAST table customisation 2022-05-02 11:39:07 +02:00
Praveen
0511e7fbbf Changed BAI as optional output to handle large genome 2022-05-02 11:35:15 +02:00
Lucpen
8a5bcbc325 fix the stub of gatk4_revertsam 2022-05-02 11:06:08 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java 2022-05-02 10:43:47 +02:00
Lucpen
6b64f9cb6c feat added stub to modules 2022-05-02 10:34:14 +02:00
Ramprasad Neethiraj
d2004a2b76 update cnvpytor 2022-05-01 21:14:01 +02:00
James Fellows Yates
44ed38beb8 Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update 2022-04-29 21:06:09 +02:00
James Fellows Yates
39530b5ca7 Bump DIAMOND version to 2.0.15 2022-04-29 21:05:12 +02:00
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split 2022-04-29 16:38:59 +01:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge 2022-04-29 15:11:09 +02:00
Thiseas Christos Lamnidis
4317ad85ae Passing test 2022-04-29 15:07:32 +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
bdbf629d93
Merge branch 'master' into tool/bamtools-split 2022-04-29 14:33:28 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge 2022-04-29 14:32:12 +02:00
Thiseas Christos Lamnidis
bad832c2ea Add Sexdeterrmine module 2022-04-29 14:28:45 +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
Simone Carpanzano
2efa5a09ab
Update main.nf
$args line 28
2022-04-29 00:00:13 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split 2022-04-28 21:17:46 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge 2022-04-28 21:14:30 +02:00
Jill V. Hagey, PhD
218769d7df
Update modules/srst2/srst2/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-04-28 14:41:37 -04:00
Jill V. Hagey, PhD
842ae3982b
Update meta.yml 2022-04-28 14:39:02 -04:00
Jill V. Hagey, PhD
9e7e10305b
Update modules/srst2/srst2/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-28 14:02:28 -04:00
Sateesh Peri
f5c4aecde5
Merge branch 'master' into srst2/srst2 2022-04-28 13:49:51 -04:00
Jill V. Hagey, PhD
e29a69077d
add doi 2022-04-28 12:30:04 -04:00
Jill V. Hagey, PhD
5be6afd6b1
changed container 2022-04-28 12:29:39 -04:00
Robert A. Petit III
4b6ee6fc14
Merge branch 'master' into rp3-add-shigatyper 2022-04-28 09:51:36 -06:00
Jasmin F
c740853874
Antismash db output patch 1 (#3)
* Update main.nf

* Update meta.yml

* Update test.yml
2022-04-28 16:42:44 +02:00
Nicolas Vannieuwkerke
4b04ca22dd Variable name change for var2vcf conversion arguments 2022-04-28 16:38:49 +02:00
Nicolas Vannieuwkerke
d626a1dcd3 Removed a whitespace in meta.yml... 2022-04-28 15:41:43 +02:00
nvnieuwk
a6397fac8f
Merge branch 'master' into vardict-java 2022-04-28 15:34:46 +02:00
Nicolas Vannieuwkerke
bdff37c3d7 Added the statistical tests and conversion to vcf 2022-04-28 15:33:27 +02:00
Nicolas Vannieuwkerke
6678ad4426 Added a header to the VCF 2022-04-28 14:54:20 +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
nvnieuwk
c9404ed266
Merge branch 'master' into vardict-java 2022-04-28 14:30:19 +02:00
Nicolas Vannieuwkerke
40e6e5273d fix for a linting issue 2022-04-28 14:30:04 +02:00
Nicolas Vannieuwkerke
c6ea41948d Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-04-28 14:29:39 +02:00
Nicolas Vannieuwkerke
bf18604471 fix for a linting issue 2022-04-28 14:29:37 +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
JIANHONG OU
24fb7c89aa
Update modules/motus/downloaddb/main.nf
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-04-28 08:14:30 -04:00
Matthias De Smet
c7806e7bef
Merge branch 'master' into vardict-java 2022-04-28 14:12:07 +02:00
JIANHONG OU
61799e80ab
Merge branch 'nf-core:master' into motus_profile 2022-04-28 08:09:47 -04:00
Nicolas Vannieuwkerke
8c98a78d2a Fixed the issue with the BED file 2022-04-28 14:07:55 +02:00
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
Nicolas Vannieuwkerke
45b4a61a15 Some small updates 2022-04-28 13:31:37 +02:00
Nicolas Vannieuwkerke
9df830f79d Added the .bai and .fai files 2022-04-28 10:23:07 +02:00
Matthias De Smet
484c8f5dfa
Update meta.yml 2022-04-28 09:29:27 +02:00
Matthias De Smet
def580ddb7
Add gzip for compressed output 2022-04-28 09:28:57 +02:00
Nicolas Vannieuwkerke
db43095b1a Split the bed file into a seperate input 2022-04-28 09:18:15 +02:00
nvnieuwk
1fd4719e9d
Merge branch 'master' into vardict-java 2022-04-28 09:09:07 +02:00
Nicolas Vannieuwkerke
fc942e062a Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-04-28 09:08:03 +02:00
Nicolas Vannieuwkerke
85c49a971f Fixed an issue with wrong file order 2022-04-28 09:07:52 +02:00
Jill V. Hagey, PhD
ecd31fd3cd
remove whitespaces and prettier fix 2022-04-27 19:55:42 -04:00
Jill V. Hagey, PhD
5b6d4fdace
Merge branch 'nf-core:master' into srst2/srst2 2022-04-27 18:19:18 -04:00
jvhagey
839ee59ca1 adding srst2 module 2022-04-27 18:01:28 -04:00
Simone Carpanzano
a5e7943f2b
update krona module
add "$args" to the module
2022-04-27 22:43:31 +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
Robert A. Petit III
30bd93602f
Merge branch 'master' into rp3-add-shigatyper 2022-04-27 11:37:13 -06:00
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
Matthias De Smet
d9b2c6af1a
Merge branch 'master' into vardict-java 2022-04-27 14:04:05 +02:00
Nicolas Vannieuwkerke
7956d38e61 Fixed the test on nextflow level 2022-04-27 13:18:46 +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
Matthias De Smet
d57664b576
cleanup TODO's 2022-04-27 11:18:58 +02:00
nvnieuwk
dc62de1a78
Merge branch 'master' into vardict-java 2022-04-27 11:17:33 +02:00
Nicolas Vannieuwkerke
024c992ca7 created the module 2022-04-27 11:12:58 +02:00
Jasmin F
259f993df7
Update tool name 2022-04-27 10:06:58 +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
jasmezz
1acde9a7a1 Fix container volume mounts 2022-04-26 16:28:39 +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
Jasmin F
6467e23809
Merge branch 'nf-core:master' into antismashlite 2022-04-25 14:21:54 +02:00
JIANHONG OU
98d318c0e0 init 2022-04-24 07:55:17 -04:00
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
Matthias De Smet
c3f13fdaf6
Merge branch 'master' into tool/bamtools-split 2022-04-22 19:36:18 +02:00
Matthias De Smet
da56a2d509
Update modules/bamtools/split/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:08 +02:00
Matthias De Smet
2d32267fcd
Update modules/bamtools/split/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:01 +02:00
Matthias De Smet
7bcede7474
Update modules/bamtools/split/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:14 +02:00
Matthias De Smet
2a2ac290c3
Update modules/bamtools/split/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:00 +02:00
Robert A. Petit III
a83202e710
Merge branch 'master' into rp3-add-shigatyper 2022-04-22 08:49:50 -06:00
Robert A. Petit III
c2d2399107
Update modules/shigatyper/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-22 08:49:44 -06:00
jasmezz
1c1e813c67 Initial module creation 2022-04-22 16:47:48 +02:00
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
CMGG ICT Team
b4af3f1475 test fixes 2022-04-22 15:02:41 +02:00
Sateesh Peri
8f2561c07f
Merge branch 'master' into rp3-add-shigatyper 2022-04-22 09:01:36 -04:00
Matthias De Smet
7e883da904 Revert "make use of dependent on input array size"
This reverts commit 413980e93a.
2022-04-22 14:50:50 +02:00
Matthias De Smet
413980e93a make use of dependent on input array size 2022-04-22 14:33:16 +02:00
Matthias De Smet
a6e7ecb3a3
Merge branch 'master' into tool/bamtools-split 2022-04-22 13:07:16 +02:00
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
d9348f3714
Merge branch 'master' into tool/bamtools-split 2022-04-22 13:04:16 +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
20728acde6
Merge branch 'master' into tool/bamtools-split 2022-04-22 11:57:22 +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
Robert A. Petit III
0095bc91f7 add module for shigatyper 2022-04-21 18:49:42 +00:00
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
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
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
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
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
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
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
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
James A. Fellows Yates
ae48653bd2
DASTool output channels update (#1489)
* fix: remove left-over unnecessary code

* Make summary output optional as not generated if no sufficiently HQ bins found

* Make contig2bin optional as only generated if sufficient HQ bins found
2022-04-04 13:31:36 +02:00
Ramprasad Neethiraj
cb54d1ebd7
update stubs (#1488) 2022-04-04 13:18:02 +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
Maxime Borry
64b06baa06
Update PyDamage module (#1467)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

* add bacillus fragilis alignments

* add meta to samtools/faidx

* move to bgzip

* update freebayes test results

* bump pydamage version to 0.70

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-31 09:18:18 -04:00
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
Ramprasad Neethiraj
233f2e728b
fix cnvpytor links (#1470) 2022-03-31 10:53:26 +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
Ramprasad Neethiraj
a973b68200
svdb update to 2.6.0 (#1465) 2022-03-30 14:50:27 +02:00
FriederikeHanssen
1ec1868264
Fix typo (#1464) 2022-03-29 13:13:41 -04:00
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
Ramprasad Neethiraj
cc671a5f3c
Update svdb/merge (#1449)
* fix error

* fix input string
2022-03-27 14:15:43 +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
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
Maxime U. Garcia
e786457fb0
feat: add readgroup info + reorder samtools command line to mimic bwamem (#1447) 2022-03-25 11:26:47 +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
Edmund Miller
e3a5795652
Homer/findpeaks improvements (#1436)
* fix(homer): Update expected file path to improve caching

* docs(homer): Update findpeaks

* test(homer): Add maketagdirectory dependency

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-25 02:44:12 +00:00
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
Edmund Miller
fe088745e0
style(deeptools): Indent script (#1439) 2022-03-24 19:44:31 +00:00
Robert A. Petit III
608bb22598
Update dragonflye to latest version (#1442)
* Update dragonflye to latest version

* trigger ci
2022-03-24 14:56:32 -04:00
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
Annick Renevey
1dddf1ce94
update star/align to include an optional sam output (support for --chimOutType SeparateSAMold option) (#1378)
Co-authored-by: Praveen Raj S <43108054+praveenraj2018@users.noreply.github.com>
2022-03-23 13:13:58 +01:00
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
Harshil Patel
f425aa3cea
Add outputs for umitools dedup summary stats (#1422) 2022-03-18 20:21:41 +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
Edmund Miller
f080015754
Prettier (#1405)
* style: Add prettier config files

* build: Add prettier vscode extension

* ci: Replace markdownlint and yamllint with prettier

* style: Run prettier

* style: Use indent of 2 for markdown as well

https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358

* style: Fix indent

* style: Let editorconfig take over tab widths

* style: yaml => yml

* ci: Run prettier once

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>

Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2022-03-18 14:27:50 +01:00
nickhsmith
979e57b7ac
Manta consistancy (#1407)
* update tests

* update

* update

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

* match chromosomes to cram file (chr21)

* undo genotypegvfs

* undo genotypegvfs

* update manta input structure to match strelka. tuple(relevant input), path(fasta), path(fai)

* update tests

* fix typos

* fix typos

Co-authored-by: Smith Nicholas <smith@in.tum.de>
2022-03-18 13:30:03 +01:00
James A. Fellows Yates
f469045a95
Fix DeepARG depenency issue with singularity containers (#1397)
* fix: remove left-over unnecessary code

* Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency

* Update modules/deeparg/downloaddata/main.nf

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

* Update modules/deeparg/predict/main.nf

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

* Apply suggestions from code review

* Update main.nf

* Update main.nf

* Update main.nf

* Update main.nf

* Go back to original logic

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-03-17 13:08:51 +01:00
Lasse Folkersen
df60a58426
round the < to ( to make markdown work for meta.yml (#1395)
* round the < to ( to make markdown work for meta.yml

* changing md5sums and stub output so it doesnt trigger the empty file linting error
2022-03-16 13:29:11 +01:00
Michael L Heuer
73aaecbc3a
Add BAM indexes as input for optitype module. (#1388) 2022-03-15 17:02:40 +01:00
Matthias Hörtenhuber
18e72fa0be
fix indent error, avoiding html tag confusion (#1393) 2022-03-15 11:56:42 +01:00
Lasse Folkersen
d6244b42f5
ASCAT (#1332)
* First commit

* putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it

* adding first try of relevant commands (not working yet, just took their basic pipeline example

* test commit

* remove test

* starting up work with module after 3.0.0 upgrade

* add ascat.prepareHTS statemet

* add location of docker for new mulled alleleCounter+ASCAT container

* first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam

* add notes on dropbox download

* use a newer pytest_modules.yml

* add outpit

* trying to align with current Sarek output

* adding in FH comments

* busy clearing up arguments and testing. Still WIP

* first working run, in nextflow, with sarek-like output. Still needs more work on input arguments

* cleaning up before writing up findings

* testing with putting in arguments in args

* draft for solution 3 style for arguments

* one more test added

* adding FH map

* finished testing maps for args

* wrap-up cram/crai test successfully

* updates to address ability to put in ref.fasta argument for cram running

* adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config

* first test with auto-downloading the s3-data (when not given as an argument)

* removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug

* adding mulled singularity container

* removing tests

* fix left padding lint issue

* lint failure in meta.yml

* more linting errors

* add when argument

* adding stub functionality

* add stub run

* correct md5sum for versions.yml

* more testing with -runstub

* stub code in pure bash - not mixed with R

* reformat version.yml

* get rid of absolute paths in test.yml

* correct wrong md5sum

* adding allelecount conda link

* rename normal_bam to input_bam etc

* let the pipeline dev worry about matching the right loci and allele files

* dont hardcode default genomebuild

* adding download instruction comment

* add doi

* fix conda addition bug

* add args documentation

* test new indent

* new test with meta.yml indentation

* retry with new meta.yml

* retry with new meta.yml - now with empty lines around

* retry with new meta.yml - remove trailing whitepsace

* trying to fix found quote character that cannot start any token error

* try with one empty line above triple-quote and no empty line below

* trying with pipe character

* checking if its the ending triple quote

* one more try with meta.yml

* test update bioconda versioning for linting failure

* test update bioconda versioning for linting failure 2

* testing allelecounter version error on conda

Co-authored-by: @lassefolkersen 
Co-authored-by: @FriederikeHanssen
2022-03-15 11:18:43 +01:00
Sima Rahimi
86ac223916
Cnvpytor (#1297)
* Added cnvpytor/importreaddepth module

* Corrected process name in meta.yml file

* added -chrom argument

* space correction

* Added complementary info

* fixed typo

* md5sum added

* modified the module to work on cram files as well

* Added cnvpytor/histogram module and test files

* Added cnvpytor/partition module and test files

* added cnvpytor/callcnvs module and tests

* modified by new modules

* Added test file and fixed input path in modules

* added when block

* little fixes

* skip tracking test.yml

* removed changes to test if conflicts get resolved

* updated outfile name

* corrected the version.yml content
2022-03-15 10:20:46 +01:00
Phil Ewels
50417f5f8c
Fix indentation in bwa/aln meta (#1392) 2022-03-15 06:22:44 +01:00
Nathan Spix
801240a971
Add core Biscuit tools (#1354)
* create files with nf-core command

* update meta.yml files

* starting to work on index main.nf

* prelim test for index

* index test working; not finding all output files

* index passing tests

* index and align passing tests

* prototyping biscuitblaster and pileup

* update containers

* updates to pileup

* pileup passing tests

* template creation for more biscuit tools

* tests passing on blaster,bsconv,pupsom

* epiread passing tests, but need to update SNP bed file path

* vcf2bed working; change test file

* all biscuit commands passing tests

* biscuitblaster rename

* try to fix permissions

* more permission fixes

* trying a couple more permission changes

* hopefully last permission fixes

* really last permission changes

* few more permissions

* add when blocks

* Remove read group meta

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

* remove read group meta

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

* changes for first round of review

* update meta.yml with more specific links

* Update modules/biscuit/biscuitblaster/main.nf

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

* Apply new version reporting

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

* Update modules/biscuit/pileup/main.nf

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

* Update main.nf

* Update modules/biscuit/pileupsomatic/main.nf

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

* update test file path

* Update modules/biscuit/align/main.nf

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

* Update modules/biscuit/align/main.nf

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

* tests passing again

* Update modules/biscuit/align/main.nf

* Update modules/biscuit/bsconv/main.nf

* Update modules/biscuit/epiread/main.nf

* Update modules/biscuit/index/main.nf

* Update test.yml

* Update modules/biscuit/pileupsomatic/main.nf

* remove module-specific extension/prefix

* remove module-specific extension/prefix

* add missing args

* switch pileup strategy

* update test.yml

* remove debug

* whitespace cleanup

* add in newline escapes

* requested changes

* Update modules/biscuit/pileup/meta.yml

Co-authored-by: Spix <nathan.spix@submit.cm.cluster>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Spix <nathan.spix@node107.cm.cluster>
Co-authored-by: njspix <nathan.spix@vai.org>
2022-03-14 09:34:22 -04:00
James A. Fellows Yates
625098a408
Adapterremoval glob fix (#1391)
* fix: remove left-over unnecessary code

* Partial fix for AR module output declarations

* Remove `def` for prefix so useable in output block

* Fix tests

* Add adapterlist support

* Fix tests after addition of adapter list
2022-03-14 07:32:21 +01:00
Simon Pearce
79a9d5e1ea
New module: NGSCheckMate (#1290)
NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected 

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-03-11 09:02:10 +00:00
Jose Espinosa-Carrasco
62da45b0e1
Bump chromap version 0.2.0 (#1374)
* Bump chromap version 0.2.0

* Temporary use the docker container until singularity container becomes available

* Temporary use the docker container until singularity container available

* Remove empty lines

* Update singularity container after became available
2022-03-10 09:23:45 +01:00
Michael J Cipriano
24f0bdd14e
added module seqkit replace (#1382)
* added module seqkit replace

* added when

* removed extra line

* Update modules/seqkit/replace/main.nf

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

* Updated meta

* updated indents

Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-09 10:36:05 -07:00
b82d7abe70
Decrease indent in seqtk/seq versions.yml output (#1384)
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-09 11:56:35 -05:00
James A. Fellows Yates
b78a4a4567
Fix for Maxbin2 emitting input files (#1376)
* fix: remove left-over unnecessary code

* Fix accidently emitting input

* Fix tests
2022-03-08 15:56:23 +01:00
Benjamin Wingfield
de0d57a562
implement plink2/score module (#1259)
* implement plink2/score module

* fix test yml

* fix typo :(

* set cpu

* set mem

* fix input process input block

* fix tests

Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-03-07 13:02:40 -05:00
Michael L Heuer
251015c8ba
Add samtools index to yara_mapper module (#1353)
* Add samtools index to yara_mapper module.

* samtools sort required for index

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-04 10:08:02 -05:00
James A. Fellows Yates
72b96f4e50
Add missing $prefix definition for MALT_RUN (#1373)
* fix: remove left-over unnecessary code

* Add forgotten prefix for the log

* Update meta.yml

* Update tests

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-03 17:58:04 +01:00
Ramprasad Neethiraj
d8028dc1c3
Add picard/sortvcf (#1370)
* sortvcf

* add files

* update meta

* update java mem

* update documentation link

* remove todo

* review suggestions

* fix test.yml

* fix conda error

* fix version code
2022-03-03 11:40:16 -05:00
James A. Fellows Yates
76cdd46f3f
Add meta to MALT/RUN (#1372)
* Add meta to MALT/RUN

* Update modules/malt/run/main.nf
2022-03-03 10:35:19 -05:00
FriederikeHanssen
c450b08a75
separate gvcf and vcf in output channels (#1371)
* separate gvcf and vcf in output channels

* regex not working, just using prefix now
2022-03-03 11:54:07 +01:00
James A. Fellows Yates
0816df1e8b
Fix: removes hardcoded flags and 'custom' file output for AdapterRemoval (#1357)
* fix: remove left-over unnecessary code

* Removes hardcoded flags and more explicit output

* Fix test md5
2022-03-03 10:01:39 +01:00
James A. Fellows Yates
61c88c6233
Add hamronization/summarize (#1366)
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add hamronisation/summarise

* Update test.yml

* Update modules/hamronization/summarize/meta.yml

Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>

* line up outputs

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-03-03 08:02:04 +01:00
Michael J Cipriano
2cd502a236
Faqcs patch (#1367)
* faqcs update to capture debug output

* change paths

Co-authored-by: Cipriano <rrn8@cdc.gov>
2022-03-02 08:27:38 -05:00
James A. Fellows Yates
4983f77796
Add hamronization/deeparg (#1364)
* fix: remove left-over unnecessary code

* Add hamronizer/deeparg

* Add when condition

* Apply suggestions from code review

* Update modules/hamronization/deeparg/meta.yml
2022-03-02 13:04:22 +01:00
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
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
Sateesh
8a20253f40
update args & convert to bam (#1355) 2022-02-25 11:06:39 -07:00
Priyanka Surana
3e6be50600 Adjusted Augustus Config Path settings. Suggested by @mahesh-panchal 2022-02-25 13:26:23 +00:00
Priyanka Surana
3cffa96efe Merge branch 'master' of https://github.com/nf-core/modules into busco 2022-02-25 13:12:53 +00:00
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
Priyanka Surana
c20f836450
Merge branch 'nf-core:master' into busco 2022-02-23 11:40:21 +00:00
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
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
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
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
Harshil Patel
12b0bc5aa9
Bump Pangolin version to 3.1.20 (#1296)
* Bump Pangolin version to 3.1.20

* Fix md5sum
2022-02-15 10:46:20 +00:00
FriederikeHanssen
967fb22ded
Update versions (#1292)
* Update versions

* update checksums + remove variables as input for applyvqsr

* sneak in removal of values and provide them via modules.config

* update another checksum

* more checksums

* move vairable to config

* remove controlfreec, wrong branch

* add line break
2022-02-15 11:29:36 +01:00
Matthieu Muffato
04e82ec61a
First version of the biobambam/bammarkduplicates2 module (#1247)
* First version of the biobambam/bammarkduplicates2 module

* Fixed the path of versions.yml

* Regenerated the checksums as the previous files were generated with a single core

* Added the `when:` block, as per #1261

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-14 16:30:48 +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
Simon Pearce
78e2e76b24
New module: ichorCNA (#1182)
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

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

* Update modules/hmmcopy/mapcounter/meta.yml

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

* Update tests/modules/hmmcopy/mapcounter/main.nf

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

* ichorCNA run

* Add panel of normals code

* Try and fix tests

* Edit string detection in tests

* Fix linting issues

* Just failing END_VERSIONS

* Fixed versions.yml

* Added DOI

* Optional name for file

* Add when command

* Updated when

* Update modules/ichorcna/createpon/main.nf

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-02-11 16:56:13 +01:00
Maxime U. Garcia
fafae11068
feat: nicer syntax (#1286)
* feat: nicer syntax

* feat: code polishing

* feat: code polishing
2022-02-11 16:07:52 +01:00
Priyanka Surana
e55664b0c3
Merge branch 'master' into busco 2022-02-11 10:43:56 +00:00
Jose Espinosa-Carrasco
d1f33be04f
Bump multiqc version 1.12 (#1282) 2022-02-11 09:44:13 +01:00
Ramprasad Neethiraj
d0240fee1e
update manta to enable jointcalling (#1218)
* update manta to enable jointcalling

* fix lint errors

* fix error

* update comment

* remove comment

* suggestions from code review

* add stub
2022-02-10 10:37:31 +01:00
FriederikeHanssen
f5d5926516
Update intervals (#1278)
* Match target bed to input files

* Intervals in getpileupsumamries

* more interval updates

* change targets in strelka

* remove leftover channel

* fix checksums

* add new test vcfs

* add new test vcfs

* Update modules/freebayes/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-10 10:34:22 +01:00
FriederikeHanssen
c8ebd0de36
Add msisensorpro (#1267)
* Add msisensorpro

* remove absolute paths

* fixing tests

* fix msisensorpro tests

* Update modules/msisensorpro/msi_somatic/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update modules/msisensorpro/msi_somatic/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* add when back in

* add when back in

* Update modules/msisensorpro/msi_somatic/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* update description

* Update main.nf

* Update main.nf

* Update main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-09 21:05:49 +01:00
Ramprasad Neethiraj
45acc79667
Update mosdepth (#1256)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* mosdepth update

* update md5sums

* add stub

* add stub

* remove svdb

* remove merge

* Add tests

* code linting fix

* undo previous commit

* revert code linting fix
2022-02-09 12:45:55 +00:00
veitveit
aa0e2fa752 nMerge branch 'maxquant' of github.com:veitveit/modules into maxquant 2022-02-09 10:42:17 +01:00
veitveit
918a7f0363 added when section 2022-02-09 10:42:07 +01:00
Veit Schwämmle
cb1f0b7fc3
Update modules/maxquant/lfq/main.nf
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-02-08 10:02:54 +01:00
Veit Schwämmle
360ac115f7
Update modules/maxquant/lfq/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-02-08 10:02:48 +01:00
veitveit
ad98111756 removed file 2022-02-08 09:50:33 +01:00
Veit Schwämmle
34dc4c181d
Merge branch 'master' into maxquant 2022-02-08 07:37:57 +01:00
Matthias Hörtenhuber
fcb1dce7b6
fix yml formatting (#1263) 2022-02-07 18:16:43 +01:00
Veit Schwämmle
ca8bca95cf
Merge branch 'master' into maxquant 2022-02-07 11:19:40 +01:00
Ramprasad Neethiraj
f44e6c74b4
Add svdb/merge (#1233)
* nf-core create

* svdb merge module and test

* remove to-do from test.yml

* version

* update meta.yml

* add stub

* add when
2022-02-04 15:29:44 +01:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block (#1261) 2022-02-04 09:53:32 +01:00
Veit Schwämmle
273d44f1f7
Update main.nf 2022-02-03 12:45:21 +01:00
Veit Schwämmle
ffdd7059b1
Update #main.nf# 2022-02-03 12:16:58 +01:00
Veit Schwämmle
53ebb374af
Merge branch 'master' into maxquant 2022-02-03 11:50:40 +01:00
Benjamin Wingfield
e687c7025a
New module: plink2/extract (#1228)
* add plink2_extract

* fix test yml path

* Update modules/plink2/extract/main.nf

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

* Update modules/plink2/extract/main.nf

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

* compress output

* add DOI

* make outputs less ambiguous

* update test for compressed output

* brain is dumb

* Update modules/plink2/extract/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-03 10:42:56 +00:00
Veit Schwämmle
bacf6165d0
Merge branch 'nf-core:master' into maxquant 2022-02-03 11:41:50 +01:00
veitveit
6385403a90 now with conda-based images 2022-02-03 11:39:08 +01:00
veitveit
6001db8aef now with conda-based images 2022-02-03 11:38:44 +01:00
Katarzyna Kamieniecka
f112e4d701
bamcmp (#1244)
* New module added bamcmp

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2022-02-02 16:38:41 +00:00
Harshil Patel
aa2eca6997
Bump versions for Pangolin and Nextclade (#1255) 2022-02-02 15:19:46 +00:00
Danilo Di Leo
aa97b1be3e
Transdecoder predict (#1251)
* create transdecoder/longorf module

* module transdecoder

* main.nf

* transdecoder/longorf ready to PR

* review comments update

* transdecoder/predict module create

* test transdecoder/predict module

* fix pytest

* pytest passed

* removed whitespace

* Update meta.yml

* Update meta.yml

Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-02-02 09:46:07 +01:00
Ramprasad Neethiraj
fc4bd3a2d2
Add svdb/query (#1249)
* first commit

* add test data
2022-02-01 20:46:10 +01:00
Felipe Marques de Almeida
53b324281f
Raven assembler (#1087)
Adding a new module for [Raven](https://github.com/lbcb-sci/raven), a De novo genome assembler for long uncorrected reads.
2022-02-01 11:47:01 +01:00
Danilo Di Leo
a74e8436cc
Transdecoder longorf (#1230)
* create transdecoder/longorf module

* module transdecoder

* main.nf

* transdecoder/longorf ready to PR

* review comments update

* transdecoder_longorf reviewed main.nf

* removed predict

* test.yml updated

* pytest run

Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
2022-01-31 13:34:38 +01:00
Maxime Borry
7026122ec8
Freebayes: compress with bgzip (#1243)
* move to bgzip
* update freebayes test results
2022-01-31 10:11:39 +01:00
Veit Schwämmle
b0e224f9f3
Merge branch 'master' into maxquant 2022-01-31 08:44:32 +01:00
Sébastien Guizard
080320765c
New module: bamtools/convert (#1219)
* 📦 NEW: Add bamtools/convert module

* 👌 IMPROVE: Update output channel name, Add tests for each output format

* 👌 IMPROVE: Add error test

* 🐛 FIX: Remove custom tags

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-28 09:58:25 +00:00
Antonia Schuster
a45e030166
Allow compressed input for prodigal (#1200)
* Allow compressed input for prodigal

* use pigz instead of gzip

* fix typo
2022-01-28 09:05:30 +01:00
GCJMackenzie
08db860938
Update mergebam syntax and sample specific unmapped channel (#1238)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* updated to follow the new mergebam syntax, also made unaligned input sample specific

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-01-27 15:30:27 +00:00
Priyanka Surana
8fdd5abe1d
Merge branch 'nf-core:master' into busco 2022-01-27 14:44:08 +00:00
Priyanka Surana
b412e6dabc Busco module commit with nf-core v2.2 c1 2022-01-27 14:36:18 +00:00
Harshil Patel
d70526c806
Bump Nextclade version to 1.10.1 (#1236) 2022-01-27 12:53:14 +00:00
James A. Fellows Yates
fc1e694e6e
fix: remove left-over unnecessary code (#1235) 2022-01-27 09:38:06 +01:00
James A. Fellows Yates
c3bacb9fdd
Add deeparg (#1234)
* Add deeparg download data

* Tweak downloaddata test.yml

* Add deeparg tests

* Apply suggestions from code review

* Fix output file paths in test

* Fix tests again md5sum to string
2022-01-26 15:19:16 +01:00
Regina Hertfelder Reynolds
1b24005f07
Add bcl2fastq2 to cellranger dockerfile (#1115)
* refactor: add bcl2fastq to cellranger dockerfile

bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.

* chore: add bcl2fastq zip to .gitignore

* style: fix code linting error

* test(cellranger): Add tiles to mkfastq

* additional dockerfile for mkfastq

* update readme and dockerfiles

* update readme

* fix: update container for mkfastq

* docs: correct typos in readme

* test: update md5sum following cellranger update

* test: update md5sum following cellranger update

* fix: new line for external args in mkfastq

* test: update mkfastq tiles argument

* test: comment out mkfastq tests until smaller test data found

* test: stub-run mkfastq test until smaller test data found

* test: fix incorrect file path for mkfastq

Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
2022-01-25 19:58:22 +01:00
Veit Schwämmle
3d0473fe48
Merge branch 'master' into maxquant 2022-01-25 15:18:55 +01:00
Annick Renevey
dcce431d51
Peddy update: delete png and add stub (#1180)
* delete png and add stub

* optional png file generation

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-24 10:28:55 +01:00
veitveit
0cb23e84ca Merge branch 'maxquant' of github.com:veitveit/modules into maxquant 2022-01-21 09:48:40 +01:00
veitveit
6fafefd007 now with working docker tests 2022-01-21 09:46:17 +01:00
Veit Schwämmle
4ba69d20fc
Merge branch 'nf-core:master' into maxquant 2022-01-21 08:55:28 +01:00
veitveit
ee3be7b8c4 now with working docker tests 2022-01-21 08:54:43 +01:00
Jose Espinosa-Carrasco
9573e7e53d
Bump version 0.1.5 to chromap/chromap (#1223)
* Bump version 0.1.5 to chromap/chromap

* Bump conda samtools version to 1.14

* Get read of inconsistent md5sum in conda

* Bump version in conda and retry md5 checks

* genome index md5 hash removed, conda failed
2022-01-20 19:00:20 +01:00
veitveit
77d2d83131 Merge branch 'maxquant' of github.com:veitveit/modules into maxquant 2022-01-20 18:02:45 +01:00
veitveit
98db2b9950 last checks 2022-01-20 18:02:30 +01:00
Veit Schwämmle
a862024a40
Merge branch 'nf-core:master' into maxquant 2022-01-20 12:11:22 +01:00
veitveit
2d48ca13ba corrected yaml version file 2022-01-20 12:10:49 +01:00
Mei Wu
435ca4100a
New module/vcfanno (#1204)
* boilerplate

* tests passed

* fixed regex

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-20 08:46:31 +00:00
Veit Schwämmle
2e13607a6a
Merge branch 'nf-core:master' into maxquant 2022-01-19 15:19:57 +01:00
veitveit
4770e84bf8 adjusted maxquant 2022-01-19 15:19:09 +01:00
Harshil Patel
bb90e4fb78
Remove bcftools and ivar module customisations (#1217)
* Remove customisation from bcftools modules

* Add save_mpileup option to bcftools/mpileup

* Remove params.save_mpileup from ivar/consensus

* Update meta.ymls
2022-01-18 16:04:56 +00:00
Jose Espinosa-Carrasco
4e9cc84514
Bump chromap index version (#1216)
* Bump chromap version

* Update md5 hash

* Remove md5 check, variable with conda
2022-01-18 12:24:21 +01:00
FriederikeHanssen
1287ba48fe
Update version & add intervals usage (#1214)
* Update version & add intervals usage

* Fix config when passing intervals as file

* Use proper paths
2022-01-17 16:40:31 +01:00
Harshil Patel
796dbb573e
Add nextclade/datasetget and nextclade/run modules (#1210)
* Remove old nextclade module

* Add nextclade/datasetget and nextclade/run modules

* Fix ECLint

* Add reference and tag as inputs to datasetget module

* Fix tests

* Adjust spacing
2022-01-17 11:46:15 +01:00
Abhinav Sharma
6243c3792c
module: deepvariant (#572)
* Add stubs for deepvariant [ci skip]

* Update the stubs for deepvariant [ci skip]

* functional with google docker image

* cleanup

* consume docker container within singularity executor

* update the meta.yml file and ask for review

* tweak the input channel shape and test data

* tweak input data [ci skip]

* update for the new syntax

* remove the functions and rename meta vars

* Update the arguments mechanism

* update chr, region and checksum

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-17 12:25:36 +02:00
Michael L Heuer
c9587d76e2
Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format

* fix ci failures

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-17 09:24:40 +00:00
Harshil Patel
280712419d
Add new vcflib/vcfuniq module (#1208)
* Add new vcflib/vcfuniq module

* Rename module from vcfutils to vcfuniq

* Fix tests

* Compress output by default

* Fix ECLint
2022-01-14 18:18:11 +00:00
Harshil Patel
3f9a028581
Bump mulled containers for kraken2 and bowtie2 (#1201)
* Bump mulled containers for kraken2 and bowtie2

* Syntax update

* Update modules/bowtie2/align/main.nf

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

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-13 11:59:33 +00:00
Anthony Underwood
104f896a26
Artic vbz compression (#1205)
* Add functionality to handle vbz compression

In order for nanopolish to be able handle the default compression  for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution

* Make the HDF5_PLUGIN_PATH more configurable

Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g

```
params {
    modules {
        .....
        'nanopore_artic_minion' {
            .....
            hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
        }
        ......
    }
}
```

* Update modules/artic/minion/main.nf

* Export HDF5_PLUGIN_PATH

The HDF5_PLUGIN_PATH variable should be exported for `artic minion` to use it

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-13 01:05:01 +00:00
Harshil Patel
b4c6b430d0
Remove params call in ivar variants module (#1203)
* Remove params call in ivar variants module

* Update main.nf
2022-01-12 16:43:26 +00:00
veitveit
5e81095694 maxquant 2022-01-12 16:58:30 +01:00
veitveit
af8e69c53a all files remote now 2022-01-12 16:44:28 +01:00
FriederikeHanssen
598d7abdb2
Log4j again (#1202)
* Log4j again

* Update checksums
2022-01-12 13:55:54 +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
Mei Wu
30e64becaa
ucsc/wigtobigwig: add meta map (#1199)
* add meta info

* updated meta.yml

* Apply suggestions from code review

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-11 21:31:37 +00:00
Anthony Underwood
bdd8159c53
Add functionality to handle vbz compression (#1197)
* Add functionality to handle vbz compression

In order for nanopolish to be able handle the default compression  for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution

* Make the HDF5_PLUGIN_PATH more configurable

Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g

```
params {
    modules {
        .....
        'nanopore_artic_minion' {
            .....
            hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
        }
        ......
    }
}
```

* Update modules/artic/minion/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-01-11 21:10:26 +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
emnilsson
c4549c0ecd
Editing the CAT/CAT module to handle single files (#1196)
* Removed if-statement to only run on more than 1 file, now it will run on single files as well.

* Added a test for running the cat_cat module on a single file.

* Created a new test.yml with nf-core modules create-test-yml -t cat/cat

* Edited test.yml to not include paths and md5sums for versions.yml, and also removed sometimes variable md5sums
2022-01-06 16:41:36 +00:00
Gwenna Breton
2d4b0f7787
Bcftools sort new syntax (#1169)
* Added files for bcftools/sort

* Fixed output format and removed md5 checksum

* Change input to avoid identical in/output names

* Created rows for bcftools/sort in pytest_modules.yml
2022-01-05 12:15:54 +01:00
Robert A. Petit III
bf5edb8614
add module for mash dist (#1193)
* add module for mash dist

* fix lint

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-04 17:29:49 +01:00
Harshil Patel
e3285528ac
Fix modules warned or failed with nf-core modules lint (#1191) 2022-01-03 18:00:46 +00:00
veitveit
994c0694e9 removed file 2022-01-03 11:27:27 +01:00
Gregor Sturm
240d08b32a
Merge branch 'master' into maxquant 2022-01-02 22:36:05 +01:00
Sébastien Guizard
c0e1489133
🐛 FIX: remove suffix option (#1188) 2021-12-24 11:32:30 +00:00
Jose Espinosa-Carrasco
cde237e7ce
Fix error messages mentioning suffix (#1190) 2021-12-23 17:22:07 +00:00
FriederikeHanssen
a6e0629e24
Change intervals to be part of sample specific input (#1189)
* Change intervals to be part of sample specific input

* Fix some tests

* Update checksum

* Update intervals

* Update intervals

* Try out gavins idea for adding the file

* update test line

* update test line

* update test line

* revert contains line
2021-12-23 12:58:20 +01:00
Robert A. Petit III
5320ab7e6c
Fix kleborate inputs (#1172)
* Fix kleborate inputs

* Update test.yml

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-12-22 11:39:35 +00:00
Veit Schwämmle
47f2da30dc
Merge branch 'master' into maxquant 2021-12-21 12:53:37 +01:00
FriederikeHanssen
50eafb19c6
Update version for log4j vulnerability (#1176)
* Update version for log4j vulnerability

* update checksums

* update checksums

* update checksums

* Remove todo string

* remove werid output paths

* remove werid output paths

* remove werid output paths

* Update various checksums

* Update various checksums

* Remove unstable md5sums

* Update md5sums

* Fix pileupsummary

* Fix genotypegvcfs

* Update test files mutect2

* hm genotypevcf updated again

* Update some mutect checksums and whatnot

* Fix last mutect checksum

* Apply suggestion to use mtochondria data instead
2021-12-20 17:10:49 +01:00
veitveit
14b661d3eb test 2021-12-20 09:53:47 +01:00
Simon Pearce
02218ab5a0
hmmcopy/mapCounter (#1175)
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

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

* Update modules/hmmcopy/mapcounter/meta.yml

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

* Update tests/modules/hmmcopy/mapcounter/main.nf

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

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-17 15:39:50 +00:00
veitveit
c3f8aca21b first working version of maxquant 2021-12-17 12:34:28 +01:00
Harshil Patel
ce8c781bb4
Provide BAI when running rseqc/tin (#1177)
* Provide BAI when running rseqc/tin

* Add md5sum

* Add proper md5sums

* md5sum not md5

* Add xls to meta.yml
2021-12-17 10:00:09 +00:00
SusiJo
3eff67f54d
Added new module snpsift/split (#1031)
* added new module snpsift/split

* added options.args

* added .vcf.gz to input

* removed test and updated to new NF DSL2 syntax

* Updated to new NF DSL2 syntax

* added option to join vcf files

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-17 09:08:14 +01:00
Harshil Patel
0d1e21686a
Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability (#1173)
* Bump picard version from 2.25.7 to 2.26.7 for log4j vulnerability

* Fix EC lint for unrelated hmmcopy module
2021-12-16 10:56:41 +00:00
GCJMackenzie
54e0ac4ed9
add module: Variantrecalibrator (#1088)
* committing to pull updated nf-core files

* saving changes to checout other branch

* committing progress so far, difficulty with test data

* uploading to be used as draft PR

* fix linting error in meta.yml

* attempt to group reference inputs together

* updated input format for resources

* meta.yml updated with new resource names

* added output channel for recal index

* module only takes single vcf file input now

* committing to checkout

* update to new syntax, remove indel test for now

* updated to use memory options and new test data

* Update modules/gatk4/variantrecalibrator/main.nf

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

* Update main.nf

* Update modules/gatk4/variantrecalibrator/main.nf

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

* remove duplicate test keys from test_data.config

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-16 10:54:49 +00:00
GCJMackenzie
9f8d9fb615
Add applyvqsr (#1101)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* add applyvqsr

* added memory options, new test data used

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-16 08:44:50 +00:00
Harshil Patel
67571c4e79
Add RSeqC tin.py module (#1174)
* Add RSeqC tin.py module

* Fix EC lint for unrelated hmmcopy module

* Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
Simon Pearce
ae92159762
New subtool: hmmcopy/generatemap (#1168)
* Initial structure

* Working with local singularity image

* Working generateMap.pl script

* Remote not working bioconda

* Working generateMap with biocontainer

* Lint changes

* Updated hmmcopy container version to be consistent

* Fix failing test

* Remove path to perl

* No hardpath to script

* Update main.nf

Moved version outside of process, add support for zipped fasta file

* Revert to not allowing gzip via pipe, as perl script can't cope

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2021-12-15 16:57:42 +01:00
GCJMackenzie
61376425fb
BugFix: add missing tbi output channel to genotypeGVCFs (#1153)
* initial commit to setup branch

* workflow finished

* Update nextflow.config

* tumour to tumor, getpileup passed as nomral and tumor

* paired_somatic renamed to tumor_normal_somatic

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* updated index names in meta.yml

* changed index file names in main script and test

* Apply suggestions from code review

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>

* Apply suggestions from code review

* fixed bug from changes

* Apply suggestions from code review

* modified yml to allow new subworkflow testing

* Update test.yml

* Update test.yml

* added output channel for tbi files, tweaked method of adding blank inputs for gendb tests

* Update main.nf

* Update main.nf

Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-14 16:10:08 +00:00
Mingda Jin
826a5603db
Stage fastq for concat in subfolders to avoid name collision issue (#1107)
* Stage fastq for concat in subfolders in task workdir

* Update main.nf

* Update test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-13 19:18:27 +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
Harshil Patel
47a9cf8ecb
Fix transcriptome staging issues on DNAnexus for rsem/prepareference (#1163) 2021-12-13 14:10:29 +00:00
Michael L Heuer
0bf40a26bd
Update seqwish to version 0.7.2 (#1144) 2021-12-09 11:07:47 -06:00
James A. Fellows Yates
be85289981
Update metabat2 output channels and compression (#1111)
* feat: each output type has dedicated channel replace bgzip with gzip can only zip one at a time

* Add condition moving of unbinned files

* fix: solution for moving sometimes non-existant files

* fix: update meta.yml to add the new channels

* fix: remove most of the checksums due to variability

* fix: tweaking of output

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Fix find commands

* Fix find commands

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-12-09 15:00:32 +01:00
Anan Ibrahim
1f3f2b18bb
Add new module macrel/contigs (#1109)
* Add new module macrel/contigs

* removed trailing whitespace

* removed whitespace

* linting cleanup

* Apply suggestions from code review

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

* Updated the test.yml

It didnt upload the updated version earlier for some reason :(

* Update test.yml

* Update test.yml

* Update test.yml as generated by pytest

* Update test.yml

* updated the version issue

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Update modules/macrel/contigs/main.nf

* Update pytest_modules.yml

* Update pytest_modules.yml

* Update modules/macrel/contigs/main.nf

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

* Zipped all fasta outputs

* Update main.nf

* Update test.yml

* Update test.yml

* Update main.nf

* Update main.nf (gzip -n)

* Update test.yml

* Update main.nf

* Update main.nf

* Update test.yml

* Update tests/modules/macrel/contigs/test.yml

* Update modules/macrel/contigs/main.nf

* Apply suggestions from code review

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

Co-authored-by: darcy220606 <ananhamido@hotmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-09 13:17:50 +01:00
Maxime U. Garcia
37c5cb495d
feat: add original input as optional output channel (#1147) 2021-12-09 11:04:53 +01:00
FriederikeHanssen
a9dd46f010
add gatk4/gatherbqsr (#1130)
* nf-core modules create

* add module files

* indent

* remove templte code

* manually revert pytest changes from tools

* manually revert pytest changes from tools

* add include statement back in

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 23:43:36 +01:00
Maxime U. Garcia
ca3ae9ff4f
feat: update dragmap to follow new bwa/mem + bwamem2/mem logic (#1146) 2021-12-08 23:19:37 +01:00
Maxime U. Garcia
1765225042
Add new boolean sort_bam as input to be able to chose between sort and view in bwamem and bwamem2mem (#1125)
* feat: view is now in args2 so we can use sort

* forgot one split_cpus

* feat: update with new logic

* fix: add more info

* fix: remove split_cpus logic
2021-12-08 14:31:27 +00:00
FriederikeHanssen
7389963d5c
Add memory stuff to all gatk4 modules (#1122)
* Add memory stuff to all gatj4 modules

* Add removed input line back in

* revert script section
2021-12-07 15:22:24 +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 U. Garcia
3b366c7c6a
greatly simplify syntax (#1121) 2021-12-07 11:18:12 +01:00
Maxime U. Garcia
6510a7ff4f
feat: add meta.id tag (#1116)
* feat: add meat.id tag

* fix: actually call the right container for singularity
2021-12-07 10:30:35 +01:00
FriederikeHanssen
7006699ff8
Update version & prefix (#1120)
* Update version & prefix

* Fix indentation
2021-12-07 10:22:32 +01:00
Maxime U. Garcia
e22966ce74
feat: emited channel should be gz_tbi and not only tbi (#1118) 2021-12-07 10:12:58 +01:00
Maxime U. Garcia
98b024c0e4
Fix syntax for extra containers for ensemblvep and snpeff (#1105)
* fix: correct syntax for task.ext.use_cache

* Apply suggestions from code review

* fix: simplify logic

* fix: update to new syntax
2021-12-06 12:59:49 +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
Edmund Miller
f3ffa69b8d
Dragmap (#1108)
* feat(dragmap): Add initial hastable module

* feat(dragmap): Add initial align module

* test(dragmap): Remove md5sum

Forgot sam files have a header. Might pipe this through samtools.

* build(dragmap): Add mulled container

* chore(dragmap): Update prefix

* feat(dragmap): Output a bam file

* feat(dragmap): Add log files

* Update modules/dragmap/align/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-12-06 09:56:41 +01:00
tamuanand
cd94731789
Update meta.yml by fixing html pattern expected (#1113)
Fixed html pattern typo:

Before: pattern: "*.thml"

After fix: pattern: "*.html"
2021-12-05 21:45:09 +00:00
Edmund Miller
e2ba70ed9a
Add Cell Ranger mkfastq, mkgtf, and count (#979)
* feat(cellranger): Add initial count module

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* feat(cellranger): Add mkgtf module

* test(cellranger): Fix count test with mkgtf

* fix(cellranger): Generalize gtf attribute filters

* chore: Add .gitignore for cellranger tar

* build(cellranger): Update dockerfile

https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/

* Apply suggestions from code review

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>

* Apply suggestions from code review

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

* Update modules/cellranger/mkgtf/main.nf

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

* style: Capitalize README

* test(cellranger): Update pytest_modules

* feat(cellranger): Add initial mkfastq module

* ci: Update pytest modules

* refactor(cellranger): Update modules to new syntax

* docs(cellranger): Update meta files

There is some terrible copy-pasting going on.

* fix(cellranger): Add args

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
Harshil Patel
9d0cad583b
Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

* Change syntax from task.ext.suffix to tast.ext.prefix

* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-12-02 12:39:55 +00:00
louperelo
1f8f86b793
takes gunzip out of fargene main.nf (#1090)
* takes gunzip out of fargene main.nf

* update definition of input

* options.args -> args

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-29 14:32:23 +01:00
Harshil Patel
20d8250d9f
Update all modules to new NF DSL2 syntax (#1099)
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
Annick Renevey
45985ff6f0
Peddy nf core2 2dev0 (#1048)
* Updated module to fit nf-core2.2dev0 templates

* Updated module to fit nf-core2.2dev0 templates

* Linked test files to nf-core/test-dataset branch:raredisease raw files

* Change order of input: vcf and tbi with meta, ped without

* Change order of input: vcf and tbi with meta, ped without/adapt test

* Change order of input: vcf and tbi with meta, ped without/adapt test, bugfix

* Indent and rename files

* Update modules/peddy/main.nf

Removed newline

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/meta.yml

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

* Update modules/peddy/main.nf

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

* Update modules/peddy/main.nf

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

* Update pytest_modules.yml

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 20:14:09 +00:00
Florian De Temmerman
1455498152
CNVkit: Make targets file optional when running in WGS mode (#1030)
* Make targets.bed optional when running in wgs mode

* added test for cram

* Update test_data_config with new reference.cnn

* Update main.nf to allow tumor-only running

Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn

* re-writing previous changes, but now it wont crash the entire CI-setup

* fixing overlooked merge conflict

* last overlooked merge-conflict

* move all files to batch subfolder

* adding an optional input for a reference file (needed when running germline and tumoronly)

* minor typo

* update meta.yml

* aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal

* Update pytest_modules.yml

Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 19:56:57 +00:00
Abhinav Sharma
15fd90ffe8
Add phyloflash module (#786)
* initial stubs [ci skip]

* remove comments and add main command [ci skip]

* design iteration [ci skip]

* add new standard functions.nf [ci skip]

* update the version string [ci skip]

* accomodate the db stubs and single/double ends [ci skip]

* add FIXME for missing info [ci skip]

* Accomodate the results folder [ci skip]

* Update main.nf

* Apply suggestions from code review

* Update main.nf

* Apply suggestions from code review

* Add version file to stubs [ci skip]

* Tweak the output dir pattern [ci skip]

* Update modules/phyloflash/main.nf

* Update modules/phyloflash/main.nf

* Update modules/phyloflash/main.nf

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-21 19:43:58 +00:00
Sébastien Guizard
c25c3fe466
Update: uLTRA (#1081)
* 👌 IMPROVE: Update .gitignore

* 📦 Add ultra module

* 👌 IMPROVE: Update test input

* 👌 IMPROVE: Update and clean code

- Update to last versions.yml file
- Update meta.yml
- Correct typos

* 👌 IMPROVE: Update output channels + Rename following subtool

* 👌 IMPROVE: Remove old ultre files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 👌 IMPROVE: Remove old ultra files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 🐛 Fix: add unsaved modifications

* 🐛 FIX: Remove one inconstant md5sum

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Remove md5sums for pickle files (not constant).

* Update modules/ultra/pipeline/main.nf

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

* Update modules/ultra/pipeline/main.nf

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

* 👌 IMPROVE: update output directory, update meta.yml

* 👌 IMPROVE: Use modules to gunzip and sort gtf

* 🐛 FIX: Set up channel correctly

* 👌 IMPROVE: Remove pickles files and databases

Those data might be useful in a debugging purpose.

* Apply suggestions from code review

* Update main.nf

* 🐛 FIX: Update uLTRA to version 0.0.4.1 + remove $(pwd)

* 👌 IMPROVE: Sort tags in test.yml

* align order of input between main.nf and meta.yml. Add ksahlin as co-author (he did update his package to overcome the pwd-problem

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-21 13:00:53 +00:00
James A. Fellows Yates
d30bf235b1
update: gunzip to include meta input tuple (#1082)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

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

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

* update: add (optional) meta to input tuple

* YAML linting

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-21 12:41:03 +00:00
Robert A. Petit III
29c669766d
add bakta module (#1085)
* add bakta module

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:17:25 +00:00
Robert A. Petit III
5ebe62612c
add ectyper module (#948)
* add ectyper module

* fix-lint

* try zcat

* Update main.nf

* fix lint

* Update main.nf

* Apply suggestions from code review

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>

* Update main.nf

* pass lint

* Update main.nf

* fix lint

Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:14:02 +00:00
veitveit
7e56e38f2a first maxquant 2021-11-21 10:47:16 +01:00
Maxime Borry
72c94dbed9
Add new module: Das Tool (#1004)
* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

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

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

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

* Update modules/pydamage/filter/meta.yml

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

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* Update modules/freebayes/main.nf

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

* add optional inputs

* Update modules/freebayes/main.nf

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

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/metabat2/meta.yml

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* add dastool/scaffolds2bin

* add dastool

* remove non reproducible md5sum check for compressed files

* Update tests/modules/metabat2/metabat2/main.nf

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

* Update tests/modules/metabat2/metabat2/main.nf

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

* split tests

* export env variable

* remove metabat2 from PR

* fix linting errors

* remove traling whitespace

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

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

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

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

* Update modules/metabat2/metabat2/main.nf

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

* Update modules/metabat2/metabat2/meta.yml

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

* answer PR comments and switch to bgzip

* PR review updates

* update from PR review

* update test files

* add bacillus fragilis alignments

* switch tests to bacillus fragilis

* add string check

* update test string

* add pr comment answer

* last fixes for PR review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 08:33:29 +01:00
FriederikeHanssen
19035c99d1
Add thread option to samtools modules (#1069)
* add thread option to samtools modules

* fix tests

* fix tests

* fix tests

* Fix naming to fix tests

* cpus-1 to account for mainthread

* remove thread in ampliconclip, docu doesn't report this param

* add -1 to all other applicable samtools modules

* Update samtools version

* Update checksums

* retrigger GHA after update

* Update modules/samtools/fastq/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/fixmate/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/flagstat/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/index/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/merge/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/stats/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Update modules/samtools/view/main.nf

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>

* Fix md5sum fixmate

* Fix md5sums

* sth funny with the fixmate checksums

* more md5sums updates

Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 22:24:47 +01:00
Jose Espinosa-Carrasco
4e5b6ed843
Fix picard markduplicates (#1084)
* Fix picard/markduplicates with new options syntax

* Delete md5sum for bam files and add contains for metrics.txt

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-18 21:54:14 +01:00
praveenraj2018
43a1c1c6d1
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. (#1083)
* Added vcf_index to vcf tuple; output to vcf.gz format.

* Fix: extra new line in meta.yml.

* addressed review feedback

* fix: editorconfig error

* fix: gatk memory flag

* fix: editorconfig error

* fix: Indentation 

fix: Indentation

* Fix: lint editorconfig error

Removed one extra space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-18 21:47:40 +01:00
praveenraj2018
691feeafdc
GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split into separate input channels (#1076)
* fasta_fai_dict tuple is now split into separate input channels

* fix: lint errors

* fix: pytest errors

* Update modules/gatk4/splitncigarreads/meta.yml

* Update modules/gatk4/splitncigarreads/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-16 15:09:30 +01:00
veitveit
d255e00f7a added maxquant 2021-11-16 13:26:55 +01:00
Michael L Heuer
b50f4e3d59
Update dsh-bio to 2.0.6. (#1075)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-16 11:37:27 +00:00
Robert A. Petit III
bc8899f1bf
[fix] hicap module allow optional outputs (#937)
* make hicap outputs optional

* update test data

* typo

* Update main.nf

* use mkfifo

* Update main.nf

Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-16 09:23:07 +00:00
Sateesh
d5f6985607
add new nucmer module (#945)
* add new nucmer module

* Apply suggestions from code review

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

* update tests with file produced by input

* Update main.nf

* Update meta.yml

Co-authored-by: Michael Cipriano <mcipriano@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 22:05:34 +00:00
JIANHONG OU
52c541b080
Cooler cload (#634)
* rebuild cooler cload.

* update test file path of cload.

* add pytest for cload

* update to version.yml

* update the test data path

* Update tests/modules/cooler/cload/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update modules/cooler/cload/main.nf

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update tests/config/test_data.config

Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>

* Update main.nf

Remove a lonely curly bracket.

* Update test.yml

Updated with new workflows.

* update the test files

* merge the conflicts.

* update the test.yml

* update for change of cooler/dump

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 21:43:55 +00:00
Robert A. Petit III
c2bba7a65d
add clonalframeml module (#974)
* add clonalframeml module

* Update main.nf

* try recommended gzip

* Update main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 19:43:53 +00:00
tamara-hodgetts
13b8a16f4a
Add module get_chrom_sizes (#1063)
* hifiasm copied from fastqc

* hifiasm tests init from fastqc

* meta.yml init; test.yml and main.nf for printing version

* Add hifiasm version printing

* Removed spaced on an empty line

* Reverted hifiasm from main

* init getchromsizes

* add tests for getchromsizes

* Included meta.yml

* removed whitespace

* Moved getchromsizes to custom folder

* Update modules/custom/getchromsizes/main.nf

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

Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 19:22:12 +00:00
Robert A. Petit III
2294ff7826
add ncbi-genome-download module (#980)
* add ncbi-genome-download module

* Update modules/ncbigenomedownload/main.nf

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:32:53 +00:00
SusiJo
ad46010385
Added new module csvtk/split (#1014)
* added module csvtk/split

* removed todo statement

* adjusted meta map names

* changed tests to use generic input files

* added module in pytest

* updated test-data paths

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:29:55 +00:00
avantonder
527ccdb419
Add Miniasm module (#962)
* add racon

* add miniasm module

* edit miniasm module

* edit miniasm module

* Update tests/modules/racon/main.nf

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

* Update tests/modules/racon/test.yml

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

* Update modules/miniasm/meta.yml

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

* Update main.nf

Add some spaces.

* Update meta.yml

Correct DOI

* Update main.nf

* Apply suggestions from code review

* Update tests/modules/miniasm/test.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:50:56 +00:00
mjakobs
466b964b37
add Kronatools KTImportTaxonomy (#928)
* created and initialised krona module

* Added kronatools/ktimporttaxonomy module

* removing previous redundant work

* added contains info for html

* edited contains in test.yml

* Update get versions

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

* remove old syntax

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

* rewording module description

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

* added detailed keywords

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

* update syntax and tool version

* fixed meta.yml issues

* remove contains line from test.yml

* re-wrote module after nf-core/tools update - should work now

* removed md5

* Update modules/kronatools/ktimporttaxonomy/main.nf

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

* update meta save

* removed typo

* double quotes to single quotes around html

* re-ran test, which updated md5

* removed md5

* 'classifier' removed to fix linting

* update version

* removed erroneous ktimporttaxonomy2

* Updated input to include meta and database

* fixed tab issues in yaml

* added `contains` to test.yml

* edited `contains` in test.yml

* trying another `contains`

* retrying `contains`

* contains with extra line

* removed classifier from tag

* Apply suggestions from code review

* Update meta.yml

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:40:46 +00:00
avantonder
8d9e8ae839
Add Medaka module (#992)
* add racon

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* add medaka module

* Indentation

* Apply suggestions from code review

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

* Update main.nf

* Update main.nf

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:26:37 +00:00
JIANHONG OU
4398056204
Macs2 calllpeak (#1038)
* Add tests and yml file for macs2/callpeak

* add format option for macs2

* update macs2/callpeak to accept format argument

* update test.yml

* update the container version.

* try to fix the issue in conda container.

* Update conda and containers

* Going back to previous container versions

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-11-15 18:17:40 +01:00
Maxime U. Garcia
3426834744
feat: fastaidx -> fai (#1073) 2021-11-15 18:03:02 +01:00
Maxime U. Garcia
5b1ce484b9
feat: _idx -> _tbi (#1074)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:49:20 +01:00
James A. Fellows Yates
632587a7fc
Add bamutil/trimbam (#1060)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add bamUtil trimBam

* Update modules/bamutil/trimbam/main.nf

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

* Update modules/bamutil/trimbam/main.nf

* Changes after code-review

* YAML lint

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-11-15 16:44:12 +00:00
louperelo
eff515891d
new module fargene (#1068)
* new module fargene

* Update main.nf

* Update modules/fargene/main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 16:42:48 +00:00
JIANHONG OU
7ad42eae1b
Cooler zoomify (#514)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/zoomify

* Apply suggestions from code review

* update functions.nf to new version.

* update the test file to test-datasets.

* update the test method of zoomify

* update dump test file.

* update version.txt to version.yml

* Update modules/cooler/dump/main.nf

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

* fix the output bug of versions update to pytest_modules.yml

* update the test file path and fix the output versions.

* Update modules/cooler/dump/main.nf

* indent

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:18:02 +01:00
mjakobs
f93c2f2604
add Krona_db module (#995)
* add Krona_db module

* removed md5 sum

* Update tests/modules/kronatools/kronadb/main.nf

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

* added input information

* removed trailing white spaces

* changed krona version to 2.7.1

* Apply suggestions from code review

* Update modules/kronatools/kronadb/meta.yml

* Update modules/kronatools/kronadb/main.nf

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
2021-11-15 16:01:46 +00:00
Sébastien Guizard
4a9bfec61d
New module: Ultra (#871)
* 👌 IMPROVE: Update .gitignore

* 📦 Add ultra module

* 👌 IMPROVE: Update test input

* 👌 IMPROVE: Update and clean code

- Update to last versions.yml file
- Update meta.yml
- Correct typos

* 👌 IMPROVE: Update output channels + Rename following subtool

* 👌 IMPROVE: Remove old ultre files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 👌 IMPROVE: Remove old ultra files

* 👌 IMPROVE: Update of pytest_modules.yml

* 👌 IMPROVE: Update test.yml

* 👌 IMPROVE: Keep md5sum as much as possible

* 🐛 Fix: add unsaved modifications

* 🐛 FIX: Remove one inconstant md5sum

* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}

* 🐛 FIX: Remove md5sums for pickle files (not constant).

* Update modules/ultra/pipeline/main.nf

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

* Update modules/ultra/pipeline/main.nf

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

* 👌 IMPROVE: update output directory, update meta.yml

* 👌 IMPROVE: Use modules to gunzip and sort gtf

* 🐛 FIX: Set up channel correctly

* 👌 IMPROVE: Remove pickles files and databases

Those data might be useful in a debugging purpose.

* Apply suggestions from code review

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 15:57:58 +00:00
Michael J Cipriano
0754d49db8
Initial commit mummer module (#940) 2021-11-15 16:53:41 +01:00
santiagorevale
1a4c7cec1b
New modules added: issues #200 and #310 (#884)
* New modules added: issues #200 and #310

* Update main.nf

* Update meta.yml

* Update tests/modules/gatk4/genotypegvcfs/main.nf

* Apply suggestions from code review

* Update main.nf

* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config

* Some minor changes on one of the test files I forgot to include

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
JIANHONG OU
a6ca2b006b
Cooler merge (#515)
* add software/cooler

* fix the wrong files uploaded.

* create a branch for cooler/merge

* remove the bin_size from metadata.

* update the test_data to test-datasets

* update pytest_modules.yml

* update the test file from single input file to two input file.
update the output file from hdf5 to bedpe.

* update the version.txt to version.yml and functions.nf

* change version.yml to versions

* update the test file path and fix the output versions.

* Update meta.yml

Correct "version" to "versions"

* Update main.nf

Fix typo

* Update main.nf

Remove some spaces

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-15 15:18:43 +00:00
Robert A. Petit III
73a09850fb
Update agrvate version (#970)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 16:06:02 +01:00
Robert A. Petit III
51f2d9a806
Update main.nf (#938)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:47:41 +01:00
Robert A. Petit III
b5b3ff16ce
add module for fastq-scan (#935)
* add module for fastq-scan

* change fastq to reads

* remove uncompressed support

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:41:36 +01:00
Robert A. Petit III
7be60774b6
add module for tbprofiler (#947)
* add module for tbprofiler

* Update test.yml

* Update meta.yml

Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:35:55 +01:00
James A. Fellows Yates
2c3c87a10f
Add leehom module (#1052)
* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

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

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

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

* fix: pigz formatting

* Apply suggestions from code review

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

* Apply suggestions from code review

* Add leeHom module

* Update modules/leehom/main.nf

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

* Update modules/leehom/main.nf

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

* Update modules/leehom/main.nf

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

* Update modules/leehom/main.nf

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

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:26:06 +01:00
Benjamin Wingfield
b012b349c1
New module: plink2/vcf (#1006)
* implement plink2 VCF import

* fix yaml indentation

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 13:55:18 +00:00
Ilya Pletenev
c48244b677
Add new module 'ataqv/ataqv' (#998)
* Add new module 'ataqv/ataqv'

* Update main.nf

* Update main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 12:51:40 +00:00
Daniel Straub
661bdb645e
Change Spades input (#1039)
* Change spades module

* correct meta map description

* adjust memory handling

* remove trailing whitespace

* fix hmm input

* Update modules/spades/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:53:07 +00:00
Daniel Straub
171a2a2dbf
Unicycler with long read input (#1041)
* Unicycler with long read input

* tests and md5sums

* remove unstable md5sums

* Update modules/unicycler/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:48:56 +00:00
JIANHONG OU
9475960928
Bwa index (#1040)
* fix a bug that the prefix is not handled by index.

* build the test.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:26:01 +00:00
alexandregilardet
94851901d5
add new module pmdtools/filter #847 (#963)
* commit but won't be used because pmdtools should have a submodule

* added submodule pmdtools/filter

* removed pmdtools module created before deciding to design two submodules

* oops forgot to remove a TODO

* removed white space meta.yml, removed v in version and manually added submodule /filter to test

* Update pytest_modules.yml

* Update main.nf

added split_cpus for multi-tools module resources

* Update test.yml

added .pmd extension to match modules/ main.nf

* Update test.yml

update md5sum

* Update singularity and docker build in main.nf

From build 4 to 5 in order to match the conda one

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/meta.yml

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

* Update modules/pmdtools/filter/main.nf

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

* Update modules/pmdtools/filter/main.nf

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

* Update main.nf adding samtools version

we need both pmdtools and samtools versions

* Update main.nf remove .pmd extension

* Update test.yml md5sum

Because file extension changed

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
Sébastien Guizard
001d5071c2
Update: gstama/collapse (#1057)
* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Remove junk files

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: Re add 10000 data test

* 👌 IMPROVE: Add some pbindex

* 🐛 FIX: Add pbi extension to files

* 📦 NEW: Add galgal6 chr30 test data

* 📦 NEW: Add gd-tama module

* 🐛 FIX (TEMP): Update singularity container address

* 📦 NEW: Add bamtools module

* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)

* 👌 IMPROVE: ignore test data

* 👌 IMPROVE: Update output

* 👌 IMPROVE: Add channel for publishing tama's metadata outputs

* 👌 IMPROVE: Update process label

* 🐛 FIX: Use depot.galxyproject.org url for singularity

* 👌 IMPROVE: autoselect running mode

* 🐛 FIX: correct gstama collapse bash test

* 👌 IMPROVE: Update to last templates version

* 👌 IMPROVE: Update tama package and label

* 👌 IMPROVE: Final version of test datasets config

* 👌 IMPROVE: Remove useless index + Fix Typos

* 👌 IMPROVE: Update test

* 👌 IMPROVE: delete unnecessary files

* 👌 IMPROVE: Update + clean

- Remove unnecessary files
- Update to new versions.yml file
- Better output channels

* 👌 IMPROVE: Update meta.yml and output channels

* 👌 IMPROVE: Remove useless files

* 👌 IMPROVE: Remove automatic MODE setup

* 👌 IMPROVE: Applied @jfy133 code modification suggestions

* Update modules/gstama/collapse/meta.yml

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

* 🐛 FIX: Add missing fasta option in meta.yml

* 🐛 FIX: Fix typo

* 🐛 FIX: Update package version

* Update main.nf

* Update meta.yml

* Update modules/gstama/collapse/meta.yml

* Apply suggestions from code review

* Update tests/modules/gstama/collapse/main.nf

* Update main.nf

* 👌 IMPROVE: Update to gs-tama 1.0.3

* Update modules/gstama/collapse/main.nf

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:57:55 +00:00
Sébastien Guizard
ec15d0f9fd
Update module: pbccs (#1018)
* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 📦 NEW: First commit of pbccs module

* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)

* 👌 IMPROVE: Move .pbi output  into report channel

* 🐛FIX: Correct code after --rq option removal from command line module

- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums

* 🐛FIX: Repair additionnal option usage

* 👌 IMPROVE: Add some pacbio test files

* 🐛 FIX: Add Pacbio index to test_data.config

* 👌 IMPROVE: CCS is run in parallel with --chunk option

* 👌 IMPROVE: Add Pbindex in bam ouput channel

* 👌 IMPROVE: Change label to process_low

* 👌 IMPROVE: Define reports files names + add json version of txt report

* 🐛 FIX: Add missing backslashes

* 🐛 FIX: Add missing gz extension

* 🐛 FIX: update ouput channel

* 🐛 FIX: output file name

* 👌 IMPROVE: .gitignore

* 👌 IMPROVE: Update function.nf to last version

* 👌 IMPROVE: Update saveAs in main.nf

* 👌 IMPROVE: Add pbccs module

* 🐛 FIX: Fix Broken test

* 👌 IMPROVE: Update test_data.config

* 🐛 FIX: Fix test

* 👌 IMPROVE: Update path of test dataset files

* 👌 IMPROVE: Remove useless index + Fix Typos

* 🐛 FIX: fill contains args

* 👌 IMPROVE: One output => One Channel

* 👌 IMPROVE: One input => One channel

* 🐛 FIX: Update tests

* 🐛 FIX: Remove TODOs from test.yaml

* 👌 IMPROVE: Revert and keep bam and pbi together

* 🐛 FIX: Remove old rq input from meta.yml

* 👌 IMPROVE: Update test to match input channels

* 👌 IMPROVE: use prefix for for output file name

* 👌 IMPROVE: Update to new versions.yml

* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2

* 👌 IMPROVE: Keep track of the former sample id in meta

* Update modules/pbccs/main.nf

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

* 👌 IMPROVE: remove former_id from meta

* 👌 IMPROVE: Use chunk number in output filename

* 🐛 FIX: Update meta.yml

* 🐛 FIX: Update reports filenames with chunk number.

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:19:26 +00:00