Closed
Milestone
V2.0
Next release:
- add first version of binning
- add functional annotation
- add automatic Singularity image generation
- add taxonomic matrix (contigs)
- add filtering of contigs + deduplication of reads
Unstarted Issues (open and unassigned)
0
Ongoing Issues (open and assigned)
0
Completed Issues (closed)
62
- New test data
- kaiju db
- add -S option samtools markdup
- too much copies of files into results
- Contigs rennaming
- Issue with skip_host_filter
- Process reads_deduplication: issue with bam file in input to bamtofastq
- Process desman_length: rename process + replace fasta_length.pl by samtools faidx
- Add --no-group in fastqc function
- FeatureCount
- Improve step parameter
- Test with Singularity containers into nextflow.config in working directory
- Check if input step exists
- Update help
- Change qc step name
- Kaiju: simplify name of html file
- Close annotation_eval branch?
- Steps: no_qc --> --skip_clean_qc
- assembly_filter process: add ${min_cpm} in output file names
- Functional tables: add sum
- Abundance of GO terms table: add link to amigo for GO terms
- Make the pipeline modular
- Table abundance of reads for annotations terms
- Add ref poster JOBIM 2020
- Add process merging quantifcation and annotation files
- Documentation
- kaiju
- Generate matrix taxon_id -> lineage -> quantification + others metrics.
- Update Singularity container
- Add kaiju and sickle to Multiqc report
- Add genologin test config file
- Process assembly_filter: add QUAST into process
- Manage contigs with low reads coverage
- Manage sequencing duplicates
- Change adaptor sequences
- Ajouter assemblathon après PROKKA (et donc uniquement sur les contigs >200bp)
- Binning of contigs
- "Merge" process cd-hit + process script cd_hit_produce_table_clstr.py
- MultiQC use ouput of different processes
- Add eggNOG-mapper process
- Add eggNOG-mapper to Singularity container
- Assemblathon: create a unique file for all samples
- Add BWA indexation in option
- Configuration profiles
- kaiju: make 1 file with results for each sample
- Test pipeline nf-core/mag
- Rename output directories
- Add process get_version
- Simplifie kaiju db parameter
- Check bamToFastq/bedtools bamtofastq zippable ?
- Recode fasta_extract / Improve process assembly_filter
- Remove 'Script' string in programs names
- Delete fastqc_function
- Delete assemblathon process
- Improve fastQC processes: make only 1 process
- taxonomy consensus contigs
- Kaiju: add merge of resume files
- Test pipeline Snakemake ATLAS
- MultiQC: make new modules (kaiju graphs, etc)
- Add "when directive" into alignment_filter process (human reads deletion)
- Tests with real files
- PROKKA: propose metagenome option to user ?
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