Jasmin F
b8386c42a7
Merge branch 'nf-core:master' into antismashlite
2022-05-02 17:58:19 +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
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
jasmezz
0fc352188b
Fix conda antismash path
2022-05-02 14:40:35 +02:00
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
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
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
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
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 )
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* update to new cli args
* remove bam index from tuple, not needed by program
* bump picard version
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-29 09:32:32 +02:00
Matthias De Smet
00467ac64a
update command line syntax for all tools
2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8
bump picard version across the board
2022-04-29 07:47:24 +02:00
Matthias De Smet
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
Jasmin F
c740853874
Antismash db output patch 1 ( #3 )
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* Update main.nf
* Update meta.yml
* Update test.yml
2022-04-28 16:42:44 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX ( #1579 )
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* Added: csi output to TABIX
* Added: tests for csi
* Fix tiddit/sv (#1580 )
* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
* Fix: prettier issues
Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:41:01 +02:00
JIANHONG OU
cdefbec669
add kimporttext module ( #1560 )
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* add kimporttext module
* fix the Prettier error.
* fix the Prettier error.
* fix the test.yml
* fix the test.yml
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update the test files;
simplify the main script of krona/ktimporttext.
* update the test file url for krona ktimporttext
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-28 08:16:26 -04:00
Daniel Cooke
57cb730e78
Fix tiddit/sv ( #1580 )
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* 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 )
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* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.
* Apply suggestions from code review
* Update modules/gatk4/haplotypecaller/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 13:41:20 +02:00
Harshil Patel
1b5d3f5ac2
Bump STAR version to 2.7.10a for RSEM modules ( #1573 )
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* Bump STAR version to 2.7.10a for RSEM modules
* Fix tests
2022-04-27 19:21:26 +01:00
Harshil Patel
2134031879
Bump SAMtools version for custom/getchromsizes ( #1572 )
2022-04-27 19:15:11 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads ( #1571 )
2022-04-27 16:03:44 +02:00
Jasmin F
61e740f79c
Add antismash download DB: missing container folders as output channels ( #1567 )
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* 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
Jasmin F
259f993df7
Update tool name
2022-04-27 10:06:58 +02:00
Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads ( #1568 )
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* 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 )
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* 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 )
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* 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
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge
2022-04-24 10:08:29 +02:00
