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rki-mf1
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clean
A nextflow pipeline for decontamination of short reads, long reads and contigs
BSD 3-Clause "New" or "Revised" License
30
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Duplicated entries in intermediate BAM file
#107
hoelzer
opened
9 hours ago
0
Summary file for number and proportion of mapped and unmapped reads
#106
ayoraind
opened
2 days ago
0
Summary file for number and proportion of mapped and unmapped reads
#105
ayoraind
opened
3 days ago
2
Add curl option for downloading available references
#104
ayoraind
opened
1 week ago
5
Add bwa
#103
MarieLataretu
opened
3 weeks ago
3
Replace minimap2 with another mapper for short-read data?
#102
hoelzer
opened
1 month ago
3
Increase ram
#101
hoelzer
opened
1 month ago
1
Dev
#100
hoelzer
closed
1 month ago
0
Add t2t hsa
#99
hoelzer
closed
1 month ago
7
Differences in MultiQC report between BBDUK and minimap2 runs
#98
hoelzer
opened
3 months ago
0
add RAM increase for mapping tools
#97
hoelzer
closed
1 month ago
5
Remove 'conda clean' from GitHub action to avoid random crashes
#96
matthuska
closed
3 months ago
0
Actions: keep conda and singularity jobs from running in parallel
#95
matthuska
closed
3 months ago
1
Bump github action versions for node 16 -> 20 change
#94
matthuska
closed
3 months ago
1
Fix intermittant conda-related failures of GitHub Actions
#93
matthuska
opened
3 months ago
0
Set default branch to 'main' instead of the Nextflow default 'master'
#92
matthuska
closed
3 months ago
1
Bump GitHub actions to handle warning re Node.js 16 to 20 transition
#91
matthuska
closed
1 month ago
0
Add --skip_qc to allow skipping fastqc/nanoplot/multiqc
#90
matthuska
closed
3 months ago
1
Provide an option to skip QC steps
#89
matthuska
closed
1 month ago
0
bam files instead of fastq?
#88
selmapichot
closed
5 months ago
1
add sc2 autodownload
#87
hoelzer
closed
6 months ago
0
Concat contamination error on SLURM/Singularity
#86
hoelzer
closed
6 months ago
3
Using user defined host genome
#85
haotianteng
closed
7 months ago
2
Improve output report/summary
#84
matthuska
opened
8 months ago
1
Add tests that use real sequencing data as input
#83
matthuska
opened
8 months ago
0
Increase memory when bbduk runs out
#82
MarieLataretu
opened
8 months ago
2
Dev
#81
MarieLataretu
closed
8 months ago
0
Change host genome index type (samtools --fai-idx) to work with IGV
#80
matthuska
closed
8 months ago
0
create an uncompressed index instead of a compressed one
#79
MarieLataretu
closed
8 months ago
0
Run dryrun action on PR against main or dev, and pushes directly to main
#78
matthuska
closed
8 months ago
0
Fix zcat problems on mac
#77
matthuska
closed
8 months ago
0
change zcat command to also work on MACs
#76
hoelzer
closed
8 months ago
1
Fix/reorganize results
#75
MarieLataretu
closed
8 months ago
0
FASTA host file does not work in IGV
#74
hoelzer
closed
8 months ago
15
GitHub Action: Bump setup-miniconda to v3, to support libmamba solver for conda
#73
matthuska
closed
8 months ago
0
Fix/results-orga-keep
#72
MarieLataretu
closed
9 months ago
0
Fix/update-repo-home
#71
MarieLataretu
closed
9 months ago
0
Marie lataretu/issue55
#70
MarieLataretu
closed
9 months ago
0
Add bed_samtools container
#69
matthuska
closed
9 months ago
0
Container for bedtools and samtools ("bed_samtools") is missing
#68
matthuska
closed
9 months ago
1
Reorganize the results directory
#67
matthuska
closed
9 months ago
15
Avoid zcat'ing *.gz when output file is also a .gz file.
#66
matthuska
closed
10 months ago
0
remove custom log file
#65
MarieLataretu
closed
10 months ago
0
Fixes a few issues in the ML/issue55 branch
#64
matthuska
closed
10 months ago
0
Add SARS-CoV-2 as an easy to use species
#63
matthuska
closed
11 months ago
0
Add SARS-CoV-2 as a species
#62
matthuska
closed
11 months ago
1
Dev
#61
MarieLataretu
closed
11 months ago
0
samtools error caused by ncurses version information
#60
imogen-foote
closed
11 months ago
5
Feature clean work dir
#59
MarieLataretu
closed
11 months ago
0
Reduce size of temp files and/or remove temp files
#58
mw55309
closed
8 months ago
7
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