Matthias De Smet
9d0f03d96a
Update modules/elprep/merge/main.nf
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-29 15:07:09 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge
2022-04-29 14:32:12 +02:00
Matthias De Smet
0ec3dea37f
Merge pull request #1541 from matthdsm/subwf/bam_qc
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New subworkflow: bam_qc_picard
2022-04-29 14:31:38 +02:00
Matthias De Smet
7e391c3a3b
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:26:06 +02:00
Matthias De Smet
343c0ebe20
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:26:00 +02:00
Matthias De Smet
20e3767657
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:24:25 +02:00
Matthias De Smet
71ccf0e207
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:24:19 +02:00
Matthias De Smet
73600b0339
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-29 14:20:15 +02:00
Matthias De Smet
3997d28a77
Merge branch 'master' into subwf/bam_qc
2022-04-29 11:39:18 +02:00
Matthias De Smet
c55032d10e
Merge pull request #1584 from matthdsm/bump/picard
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bump picard version across the board
2022-04-29 11:38:21 +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
Matthias De Smet
b2e4342105
fix args in nextflow.config
2022-04-29 10:21:22 +02:00
Matthias De Smet
bda132191d
fix args in nextflow.config
2022-04-29 10:13:39 +02:00
CMGG ICT Team
0e01d703ea
remove version md5sum from fixmateinformation
2022-04-29 10:12:52 +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
b72ec05d69
drop md5sum from versions.yml
2022-04-29 08:19:42 +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
da94b776ef
Merge branch 'master' into subwf/bam_qc
2022-04-28 22:12:48 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge
2022-04-28 21:14:30 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX ( #1579 )
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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
Matthias De Smet
fdaef46c90
Merge branch 'master' into subwf/bam_qc
2022-04-28 14:00:30 +02:00
Matthias De Smet
4618c542e9
fix metrics output
2022-04-28 13:59:46 +02:00
Matthias De Smet
2fc857955f
fix index omission
2022-04-28 13:53:48 +02:00
Matthias De Smet
8ad861a645
add fasta index
2022-04-28 13:52:03 +02:00
Matthias De Smet
55dfe1d8ab
fix hsmetrics input
2022-04-28 13:43:59 +02:00
Matthias De Smet
e0a8af8693
fix outputs
2022-04-28 13:42:24 +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
Matthias De Smet
dee8ec9e91
fix typos
2022-04-28 12:53:17 +02:00
Matthias De Smet
b92efb7abf
add nextflow.config
2022-04-28 10:21:47 +02:00
Matthias De Smet
881e9db4bf
update tests
2022-04-28 10:19:30 +02:00
Matthias De Smet
3cbf5c63e5
Update subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 10:09:25 +02:00
Matthias De Smet
433aaece46
Update tests/subworkflows/nf-core/bam_qc_picard/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 10:05:31 +02:00
Matthias De Smet
8fb8199f31
fix copilot suggestion
2022-04-28 10:05:07 +02:00
Matthias De Smet
2b29ff5883
drop params.options
2022-04-28 10:03:02 +02:00
Matthias De Smet
8303c509fe
Merge branch 'master' into subwf/bam_qc
2022-04-28 08:57:24 +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
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
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
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge
2022-04-24 10:08:29 +02:00
