Comments (6)
I think having a multi FASTA at 2.Genomes/all-consensus-sequences.fasta
that combines all the single FASTAs in that folder into one file should do the job? Of course, this might then still include reconstructed consensus that fail a later QC: but this can be checked in the report
from porecov.
i personally would object multi fasta files as they expect that all sequencing data are delivered to the same target folder.
They are much harder to split (recreating meaningful names) than single files are to fuse.
from porecov.
each samples consensus fasta file is located in this folder:
./<outputdirectory>/2.Genomes/<sample_name>/<samplename>_consensus.fasta
<outputdirectory>
can be changed via --output
flag. samplename is usually "barcode01" etc. if you start from basecalling
Multifastafiles (with QC passing) are only collected via the optional --rki
flag. maybe I misunderstood the question?
from porecov.
i personally would object multi fasta files as they expect that all sequencing data are delivered to the same target folder.
They are much harder to split (recreating meaningful names) than single files are to fuse.
Ah, okay now I get what you mean @oliverdrechsel . You just want to have all the single FASTAs (one per sample) in one single output folder, right? Instead of sub-folders like described by @replikation:
./<outputdirectory>/2.Genomes/<sample_name>/<samplename>_consensus.fasta
so something like:
./<outputdirectory>/2.Genomes/all/<samplename>_consensus.fasta
?
It's a minor thing but maybe we can simply publish the FASTAs also to
./<outputdirectory>/2.Genomes/all_consensus/<samplename>_consensus.fasta
Thus, we would have the per-sample folder structure to check for details (VCF, BAM, FASTA, PDF, ...) and another folder that just has all the FASTAs.
or do you want an additional output folder for all the consensuses that is outside of the
./<outputdirectory>/
structure? This would need an additional parameter e.g.
--output_consensus /some/other/path/tp/write/all/consensus/fasta
from porecov.
Hi @hoelzer
something like ./<outputdirectory>/2.Genomes/all/<samplename>_consensus.fasta
would be fine, i think.
It would be easier to distribute the data to somewhere else, if one just has to visit one folder and not iterate through various folders to get all output data.
from porecov.
Hi @hoelzer
something like./<outputdirectory>/2.Genomes/all/<samplename>_consensus.fasta
would be fine, i think.
It would be easier to distribute the data to somewhere else, if one just has to visit one folder and not iterate through various folders to get all output data.
Okay, I think this should be doable with e.g. an optional --collect <outputdirectory>
flag
from porecov.
Related Issues (20)
- "split-fasta"-process fails due to leading empty line
- Workflow failed at artic_medaka, no '2.Genomes' output, with test_fastq and actual sample HOT 1
- export variant file (vcf) HOT 1
- add skip scorpio parameter to pangolin HOT 1
- Only calculate NanoPlot after read filtering step HOT 5
- Add new V5 ARTIC primer BED HOT 5
- Medaka step fails in the -profile fastq_test HOT 3
- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- The pipeline fails in artic_ncov_wf_artic_medaka HOT 7
- new pangolin table columns HOT 1
- CovarPlot fails w/ custom BED HOT 5
- Process retry in slurm profile HOT 1
- Publish VCF files HOT 2
- Update medaka to get the latest models HOT 1
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from porecov.