nf-core genomeqc issues

nf-core / genomeqc

Compare the quality of multiple genomes, along with their annotations.

https://nf-co.re/genomeqc

MIT License

3 stars 8 forks source link

issues

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Gene overlap

#94 chriswyatt1 opened 4 days ago
0
New feature: Check for overlapping genes in GFF (bedtools intersect)

#93 chriswyatt1 opened 4 days ago
3
WIP: check `agat_sp_extract_sequences.pl` as an alternative to `GFFREAD`

#92 FernandoDuarteF closed 5 days ago
3
Ideograms do not have a key

#91 chriswyatt1 closed 5 days ago
1
ideograms plot all contigs

#90 chriswyatt1 opened 1 week ago
2
`AGAT_CONVERTSPGXF2GXF` on myriad needs more memory

#89 FernandoDuarteF opened 1 week ago
0
WIP: Add longest and nf-core GFFREAD modules

#88 FernandoDuarteF closed 5 days ago
2
Updated README

#87 FernandoDuarteF closed 1 week ago
0
``BUSCO_IDEOGRAM`` fails when using ``samplesheet.csv``

#86 FernandoDuarteF closed 6 days ago
2
BUSCO fails due to rate limiter

#85 chriswyatt1 opened 2 weeks ago
0
Fixed combine() not working when empty ch_fastq

#84 FernandoDuarteF closed 2 weeks ago
2
Pipeline fails if genome or gff are not gzipped

#83 chriswyatt1 closed 2 weeks ago
0
WIP: Busco ideograms

#82 chriswyatt1 closed 1 week ago
4
Make ``GENOME`` and ``GENOME_AND_ANNOTATION`` into workflows

#81 FernandoDuarteF opened 2 weeks ago
3
Run from GTF files (instead of GFF3)

#80 chriswyatt1 opened 2 weeks ago
0
Run from GCA genome only IDs

#79 chriswyatt1 opened 2 weeks ago
0
Check what needs to be in results

#78 chriswyatt1 opened 3 weeks ago
0
Using `FASTA_GXF_BUSCO_PLOT ` sub workflow

#77 GallVp opened 3 weeks ago
7
join merqury input to fasta not fastq fixes #75

#76 stephenturner closed 2 weeks ago
1
Merqury inputs should use database+assembly (fasta, not fastq)

#75 stephenturner closed 2 weeks ago
1
busco and quast added to mq report

#74 awanalk opened 3 weeks ago
4
Multiqc

#73 chriswyatt1 closed 3 weeks ago
0
decontamination workflow

#72 LaurenHuet opened 3 weeks ago
5
Extract meryl+merqury subworkflow into modules

#71 stephenturner opened 3 weeks ago
1
Conditional tidk flags

#70 chriswyatt1 closed 2 weeks ago
1
Input samplesheet with .meta operator instead of branch by size

#69 chriswyatt1 opened 3 weeks ago
0
Update README.md with merqury info

#68 stephenturner closed 3 weeks ago
0
Add new test_with_merqury profile

#67 stephenturner closed 3 weeks ago
0
Fix Script path issue

#66 chriswyatt1 closed 3 weeks ago
0
Added AGAT checking to GFF file

#65 fperezcobos closed 3 weeks ago
0
Scripts updated

#64 chriswyatt1 closed 2 weeks ago
1
Add meryl and merqury

#63 stephenturner closed 3 weeks ago
3
Optionally pass in reads

#62 stephenturner closed 3 weeks ago
1
GFFREAD fails

#61 fperezcobos opened 4 weeks ago
0
add meryl union sum

#60 stephenturner closed 3 weeks ago
0
Migrate to nf-schema

#59 FernandoDuarteF opened 4 weeks ago
0
Add meryl count

#58 stephenturner closed 3 weeks ago
0
Fixed genome only option not working

#57 FernandoDuarteF closed 2 weeks ago
5
Check schema_input.json

#56 FernandoDuarteF opened 4 weeks ago
0
Pipeline fails when running on input_myco_tiny.csv dataset.

#55 FernandoDuarteF opened 1 month ago
1
Check linting

#54 FernandoDuarteF opened 1 month ago
0
First PR on nf-core

#53 chriswyatt1 opened 1 month ago
0
Remove unused bin scripts (from excon)

#52 chriswyatt1 closed 1 month ago
1
Create tube map

#51 FernandoDuarteF opened 1 month ago
1
Logic for variable input types

#50 chriswyatt1 closed 2 weeks ago
4
Add a tree building method for genome only

#49 chriswyatt1 opened 1 month ago
1
Add nf-test

#48 chriswyatt1 opened 1 month ago
0
new plots organisation

#47 chriswyatt1 closed 1 month ago
1
Add ability to turn off specific modules

#46 chriswyatt1 opened 1 month ago
1
Modules and tools ideas

#45 FernandoDuarteF opened 1 month ago
0