issues
search
sanger-tol
/
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
11
stars
6
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Include FASTA parameter, stage REF_CACHE and export REF_PATH
#138
reichan1998
opened
1 month ago
1
Re-enable remote reference lookup for CRAM
#137
tkchafin
opened
1 month ago
0
Integrate filtering steps into map-reduce
#136
reichan1998
closed
1 month ago
0
Integrate filtering steps into map-reduce
#135
tkchafin
opened
1 month ago
0
merge patch 1.3.1 into dev
#134
tkchafin
closed
1 month ago
0
Correct tag link for 1.3.1 in changelog
#133
tkchafin
closed
2 months ago
1
prettier linting
#132
tkchafin
closed
2 months ago
0
prettier linting
#131
tkchafin
closed
2 months ago
0
Implement cram chunking for PacBio and Nanopore
#130
reichan1998
closed
1 month ago
2
BBtools citation
#129
tkchafin
closed
2 months ago
0
Patch 1.3.1
#128
tkchafin
closed
2 months ago
3
patch 1.3.1
#127
tkchafin
closed
2 months ago
0
Incorporate fromSRA channel factory to allow read_run accessions as inputs?
#126
tkchafin
opened
2 months ago
0
Illumina pre-alignment filtering
#125
tkchafin
opened
2 months ago
0
PB pre-alignment filtering
#124
tkchafin
opened
2 months ago
0
ONT pre-alignment filtering
#123
tkchafin
opened
2 months ago
0
Hi-C pre-alignment QC
#122
tkchafin
opened
2 months ago
0
nf-core/prodigal
#121
tkchafin
closed
2 months ago
0
Docs, CI, copyright update
#120
tkchafin
closed
2 months ago
4
Calculate mapped vs unmapped read percentages
#119
tkchafin
opened
2 months ago
1
bwa-mem configuration for HiC
#118
tkchafin
closed
2 months ago
8
Switch to nf-core samtools modules
#117
tkchafin
opened
2 months ago
1
Update the adaptor sequence database (TBC)
#116
muffato
opened
2 months ago
0
Added branched handling of ULI inputs in filter_pacbio
#115
tkchafin
opened
2 months ago
3
Replace blastn sub workflow
#114
tkchafin
opened
2 months ago
0
Implement cram chunking and minimap2-based Hi-C alignments
#113
reichan1998
closed
2 months ago
2
spoof REF_PATH to disallow remote lookup for cram
#112
tkchafin
closed
2 months ago
1
Make sure we are handling CRAM files correctly
#111
tkchafin
closed
2 months ago
10
Fix broken full CI test
#110
tkchafin
closed
3 months ago
0
1.3.0 Release
#109
tkchafin
closed
3 months ago
0
Version 1.3.0 pre-release
#108
tkchafin
closed
3 months ago
2
Give user control of output format and compression
#107
tkchafin
closed
3 months ago
1
Pacbio fastq
#106
tkchafin
closed
3 months ago
0
Implement chunking to speed up alignment
#105
reichan1998
closed
2 months ago
0
Replace BlastN by Minimap2 splice.
#104
reichan1998
closed
2 months ago
10
Update branding in template
#103
tkchafin
closed
3 months ago
0
merge bwamem_index and remove unneeded multiqc options
#102
tkchafin
closed
3 months ago
6
Allow fastq input for PacBio alignment
#101
BethYates
closed
3 months ago
1
Disable BWAMEM2 index when no short reads data
#100
reichan1998
closed
3 months ago
2
nf-core v2.14 update
#99
tkchafin
closed
3 months ago
3
Template update for nf-core/tools version 2.14.1
#98
tkchafin
closed
3 months ago
0
Implement minimap2-based Hi-C alignments
#97
muffato
closed
2 months ago
4
add input type `fastq.gz` and `fq.gz` for Illumina and HiC reads
#96
reichan1998
closed
4 months ago
8
Option to incorporate additional metadata from provided SAM header file
#95
tkchafin
closed
4 months ago
1
Removed unneeded patch
#94
muffato
closed
5 months ago
0
Embed the BAM headers from the insdcdownload pipeline
#93
muffato
closed
4 months ago
0
Merqury and Meryl
#92
BethYates
closed
5 months ago
1
Pipes
#91
muffato
closed
5 months ago
1
Fix when multiple PacBio files are given
#90
muffato
closed
6 months ago
3
Ci resource increase
#89
gq1
closed
6 months ago
3
Next