Comments (8)
We can base the report on the following script:
https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe/-/blob/master/ncov_minipipe.Rmd
and modify it according to the Nanopore needs.
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the report currently takes a bunch of files. I think we can either modify the report to have all files optional or butcher it and make a nanopore version
What i find quite important for the report output (html) is that figures and tables have a maximum size and implement scroll bars. This keeps the report short and easy to scroll, although each section might contain 100 samples.
*coverage.tsv
loads of 0's because it's a negative control as example
$ head NK-1xTE_1.coverage.tsv
NC_045512.2 1 0
NC_045512.2 2 0
NC_045512.2 3 0
NC_045512.2 4 0
NC_045512.2 5 0
NC_045512.2 6 0
NC_045512.2 7 0
NC_045512.2 8 0
NC_045512.2 9 0
NC_045512.2 10 0
fragment size
this is basically the fragment size column of the mapping bam file
$ head NK-1xTE_1.fragsize.tsv
0
102
-102
-121
121
102
-102
102
-102
93
mapping statistics
output from bwa mem
$ head NK-1xTE_1.bamstats.txt
794 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
2 + 0 supplementary
0 + 0 duplicates
718 + 0 mapped (90.43% : N/A)
792 + 0 paired in sequencing
396 + 0 read1
396 + 0 read2
526 + 0 properly paired (66.41% : N/A)
640 + 0 with itself and mate mapped
transformed for improved reading in R
$ head NK-1xTE_1.bamstats.pipe.txt
794|0|in total (QC-passed reads + QC-failed reads)
0|0|secondary
2|0|supplementary
0|0|duplicates
718|0|mapped (90.43% : N/A)
792|0|paired in sequencing
396|0|read1
396|0|read2
526|0|properly paired (66.41% : N/A)
640|0|with itself and mate mapped
version
$ cat pipeline.version
v2.0.4
pangolin (optional)
$ cat NK-TE_1_21-00101.lineage.txt
taxon,lineage,probability,pangoLEARN_version,status,note
NK-TE_1_21-00101_iupac_consensus_v2.0.4,None,0,2021-01-16,fail,N_content:1.0
kraken (optional)
kraken2 result of a run of reads against a human/SARS-CoV-2 database (https://zenodo.org/record/3854856)
kraken read filtering improved out mapping tremendously
$ head NK-TE_1_21-00101.kraken.report.txt
22.58 56 56 U 0 unclassified
77.42 192 0 R 1 root
77.02 191 0 D 10239 Viruses
77.02 191 0 D1 2559587 Riboviria
77.02 191 0 K 2732396 Orthornavirae
77.02 191 0 P 2732408 Pisuviricota
77.02 191 0 C 2732506 Pisoniviricetes
77.02 191 0 O 76804 Nidovirales
77.02 191 0 O1 2499399 Cornidovirineae
77.02 191 0 F 11118 Coronaviridae
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@oliverdrechsel @rekm welcome to the reporting issue! :)
So basically @replikation needs to know what are the inputs (and formats) for the different parts https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe/-/blob/master/ncov_minipipe.Rmd already provides so he can generate the inputs.
Maybe we can start basic and try to implement the Rmd
script with support for
- some raw read metrics
- consensus coverage
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yep basically either an example "of input" to this script or a summary of what the script needs to function properly
from porecov.
@oliverdrechsel thanks ill prepare the information on my end and check if I can add all the mandatory items so you don't need to change anything.
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@oliverdrechsel thanks ill prepare the information on my end and check if I can add all the mandatory items so you don't need to change anything.
Thanks a lot. I don't know if things like fragment size make sense as minION is not performing paired end sequencing.
from porecov.
@oliverdrechsel just checked its 0 everywhere. so this might be good as an optional parameter or do you have another idea that I can supply here instead?
€ not sure how the final report looks like (e.g. can I supply some more nanopore relevant things here)
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@oliverdrechsel looking at your report script i tend to rewrite it as nextflow is more "file" oriented. so using dirs and recursively looking for inputs is counter intuitive here. Would this be okay if I fork your script and adjust it to the workflow?
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Related Issues (20)
- Pangolin v4.0 HOT 11
- Include artic-tools "validate_scheme" HOT 1
- Runs fail at barcode22 HOT 8
- Private mutation from nextclade HOT 1
- Frameshift correction
- "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
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