erikrikarddaniel magmap issues

erikrikarddaniel / magmap

Nextflow (nf-core) workflow for mapping reads to large collections of genomes.

MIT License

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issues

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Anvio table

#25 erikrikarddaniel opened 3 years ago
0
Add CDS column to overall stats

#24 erikrikarddaniel closed 3 years ago
2
Consistent read number units in overall_stats.tsv

#23 erikrikarddaniel closed 3 years ago
1
BBMap module doesn't output the log

#22 erikrikarddaniel opened 3 years ago
0
Make sure all documentation is in place

#21 erikrikarddaniel opened 3 years ago
0
Lists of standard genomes

#20 erikrikarddaniel opened 3 years ago
0
Make sure the code lints

#19 erikrikarddaniel opened 3 years ago
0
Check that collect stats uses pivoting

#18 erikrikarddaniel closed 3 years ago
1
Document the double concatenation and move gff to subworkflow

#17 erikrikarddaniel closed 3 years ago
1
Fetch genomes from NCBI

#16 erikrikarddaniel closed 3 years ago
1
Start from input BBMap index

#15 erikrikarddaniel opened 3 years ago
2
Add usemodulo as parameter

#14 erikrikarddaniel closed 3 years ago
1
Output collected faa file?

#13 erikrikarddaniel opened 3 years ago
0
Overall statistics: How much mapped etc.

#12 erikrikarddaniel closed 3 years ago
0
Read GTDB metadata to get taxonomy and completeness info for genomes

#11 erikrikarddaniel opened 3 years ago
0
Run CheckM and GTDBtk for genomes missing all taxonomy information

#10 erikrikarddaniel opened 3 years ago
0
Read CheckM and GTDBtk files for genomes missing in GTDB

#9 erikrikarddaniel closed 3 years ago
1
Update modules to new software version handling

#8 erikrikarddaniel closed 3 years ago
1
Remove stable RNA

#7 erikrikarddaniel closed 3 years ago
1
Summary tables ready for analyses

#6 erikrikarddaniel closed 3 years ago
0
Subset GTDB phylogeny to selected genomes

#5 erikrikarddaniel opened 3 years ago
1
Run featureCount on BBMap output

#4 erikrikarddaniel closed 3 years ago
0
Map QCed reads to contigs

#3 erikrikarddaniel closed 3 years ago
0
Collect genome collection

#2 erikrikarddaniel closed 3 years ago
0
Trim and cut adapters

#1 erikrikarddaniel closed 3 years ago
1