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sanger-tol
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readmapping
Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
https://pipelines.tol.sanger.ac.uk/readmapping
MIT License
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Make sure we are handling CRAM files correctly
#111
tkchafin
opened
2 weeks ago
10
Fix broken full CI test
#110
tkchafin
closed
2 weeks ago
0
1.3.0 Release
#109
tkchafin
closed
2 weeks ago
0
Version 1.3.0 pre-release
#108
tkchafin
closed
2 weeks ago
2
Give user control of output format and compression
#107
tkchafin
closed
2 weeks ago
1
Pacbio fastq
#106
tkchafin
closed
3 weeks ago
0
Implement chunking to speed up alignment
#105
reichan1998
closed
1 week ago
0
Replace BlastN by Minimap2 splice.
#104
reichan1998
opened
1 month ago
9
Update branding in template
#103
tkchafin
closed
1 month ago
0
merge bwamem_index and remove unneeded multiqc options
#102
tkchafin
closed
3 weeks ago
6
Allow fastq input for PacBio alignment
#101
BethYates
closed
3 weeks ago
1
Disable BWAMEM2 index when no short reads data
#100
reichan1998
closed
1 month ago
2
nf-core v2.14 update
#99
tkchafin
closed
1 month ago
3
Template update for nf-core/tools version 2.14.1
#98
tkchafin
closed
1 month ago
0
Implement minimap2-based Hi-C alignments
#97
muffato
opened
1 month ago
4
add input type `fastq.gz` and `fq.gz` for Illumina and HiC reads
#96
reichan1998
closed
1 month ago
8
Option to incorporate additional metadata from provided SAM header file
#95
tkchafin
closed
1 month ago
1
Removed unneeded patch
#94
muffato
closed
2 months ago
0
Embed the BAM headers from the insdcdownload pipeline
#93
muffato
closed
1 month ago
0
Merqury and Meryl
#92
BethYates
closed
2 months ago
1
Pipes
#91
muffato
closed
2 months ago
1
Fix when multiple PacBio files are given
#90
muffato
closed
3 months ago
3
Ci resource increase
#89
gq1
closed
4 months ago
3
cram input necessary?
#88
gbdias
closed
1 month ago
4
Production fixes
#87
muffato
closed
6 months ago
0
Correct the official DOI of this repository
#86
muffato
closed
2 weeks ago
2
Set use_work_dir_as_temp to true when running at the Sanger
#85
muffato
closed
8 months ago
1
Release 1.2
#84
muffato
closed
8 months ago
6
Updated the docs before release
#83
muffato
closed
8 months ago
1
Resource optimisation
#82
muffato
closed
8 months ago
6
Can't align PacBio/ONT reads on genomes > 4Gbp
#81
muffato
closed
8 months ago
2
New tolsoft details
#80
muffato
closed
1 year ago
0
Added the cleanup profile and use it for our Tower Sanger tests
#79
muffato
closed
1 year ago
0
Combine steps with pipes to reduce disk footprint and make the pipeline faster
#78
muffato
closed
2 months ago
3
Support multiple output options
#77
priyanka-surana
closed
3 months ago
1
Crumble compression for all aligned files
#76
priyanka-surana
closed
2 months ago
0
Implement chunking to speed up alignment
#74
priyanka-surana
opened
1 year ago
1
Add support for RNAseq data
#73
priyanka-surana
opened
1 year ago
1
Add support for Pacbio ULI reads
#72
priyanka-surana
opened
1 year ago
1
Calculate PacBio filtered data percentage
#71
priyanka-surana
opened
1 year ago
0
Implement nf-validation
#70
priyanka-surana
closed
1 month ago
0
Update pipeline template
#69
priyanka-surana
closed
1 month ago
0
Add read group back and crumble for HiFi
#68
priyanka-surana
closed
9 months ago
3
edits for ksenia - not for use
#67
priyanka-surana
closed
1 year ago
0
Try minimap2 splice
#66
priyanka-surana
opened
1 year ago
0
Disable BWAMEM2_INDEX when no short read data
#65
priyanka-surana
closed
1 month ago
0
Add multiple output options
#64
priyanka-surana
closed
2 weeks ago
1
Reorganise subworkflow execution
#63
priyanka-surana
closed
2 weeks ago
0
Add CRAM compression option
#62
priyanka-surana
closed
3 months ago
0
Syncing main to dev
#61
priyanka-surana
closed
1 year ago
0
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