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@Juke34
Juke34 authored Jan 31, 2025
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Expand Up @@ -501,37 +501,40 @@ tableout$values <- tableout$values |> stringr::str_remove_all("^\\.$")
tableout <- tableout |> pivot_wider(id_cols = ID , names_from = ind, values_from = values,
values_fn = \(x) paste(unique(x), collapse = ""))
# round each value to 4 decimals
tableout <- tableout |> mutate(across(-ID, ~round(as.numeric(.), 4)))
# print with nice output
knitr::kable(tmp)
knitr::kable(tableout)
```
You will get a table similar to this one:
```
|ID |Dups |GC |Seqs |Error rate |Non-primary |Reads mapped |% Mapped |Total seqs |
|:-----------------------------------|:-----------------|:--|:--------------------|:-------------------|:----------------------|:-----------------------|:------------------|:----------|
|yeast_R1 |73.01 |43 |0.01 | | | | | |
|yeast_R1_seqkit_STAR_sorted |73.22686241444302 |43 |0.010081 |0 |0.00008099999999999999 |0.000096 |0.96 |0.01 |
|yeast_R1_seqkit_bbmap_sorted |73.01 |43 |0.01 |2020.4080000000001 |0 |0.000099 |0.9900000000000001 |0.01 |
|yeast_R1_seqkit_bowtie2_sorted |73.01 |43 |0.01 |11.46977 |0 |0.00008599999999999999 |0.86 |0.01 |
|yeast_R1_seqkit_bowtie_sorted |73.01 |43 |0.01 |49.57576 |0 |0.000032999999999999996 |0.33 |0.01 |
|yeast_R1_seqkit_bwaaln_sorted |73.01 |43 |0.01 |0 |0 |0 |0 |0.01 |
|yeast_R1_seqkit_bwamem_sorted |72.98080767692923 |43 |0.010003999999999999 |0.37602579999999997 |0 |0.001914 |19.139999999999997 |0.01 |
|yeast_R1_seqkit_bwasw_sorted |73.0288797841511 |43 |0.010007 |0.2639272 |0 |0.0018369999999999999 |18.357149995003496 |0.010007 |
|yeast_R1_seqkit_graphmap2_sorted |73.01 |43 |0.01 |0 |0 |0 |0 |0.01 |
|yeast_R1_seqkit_hisat2_sorted |73.01 |43 |0.01 |0 |0 |0.000004 |0.04 |0.01 |
|yeast_R1_seqkit_kallisto_sorted |73.01 |43 |0.01 |0 |0 |0.00181 |18.099999999999998 |0.01 |
|yeast_R1_seqkit_minimap2_sorted |73.28848436881678 |43 |0.010107999999999999 |0.3211603 |0.000108 |0.000252 |2.52 |0.01 |
|yeast_R1_seqkit_nucmer.fixed_sorted |64.73988439306359 |42 |0.000173 |0.2809365 |0 |0.000169 |100 |0.000169 |
|yeast_R1_seqkit_sublong_sorted |45.26 |43 |0.01 |0 |0 |0.0012339999999999999 |12.34 |0.01 |
|yeast_R1_seqkit_subread_sorted |73.01 |43 |0.01 |0.1395645 |0 |0.00156 |15.6 |0.01 |
|ID | Dups| GC| Seqs| Error rate| Non-primary| Reads mapped| % Mapped| Total seqs|
|:-----------------------------------|-------:|--:|------:|----------:|-----------:|------------:|--------:|----------:|
|yeast_R1 | 73.0100| 43| 0.0100| NA| NA| NA| NA| NA|
|yeast_R1_seqkit_STAR_sorted | 73.2269| 43| 0.0101| 0.0000| 1e-04| 0.0001| 0.9600| 1e-02|
|yeast_R1_seqkit_bbmap_sorted | 73.0100| 43| 0.0100| 2020.4080| 0e+00| 0.0001| 0.9900| 1e-02|
|yeast_R1_seqkit_bowtie2_sorted | 73.0100| 43| 0.0100| 11.4698| 0e+00| 0.0001| 0.8600| 1e-02|
|yeast_R1_seqkit_bowtie_sorted | 73.0100| 43| 0.0100| 49.5758| 0e+00| 0.0000| 0.3300| 1e-02|
|yeast_R1_seqkit_bwaaln_sorted | 73.0100| 43| 0.0100| 0.0000| 0e+00| 0.0000| 0.0000| 1e-02|
|yeast_R1_seqkit_bwamem_sorted | 72.9808| 43| 0.0100| 0.3760| 0e+00| 0.0019| 19.1400| 1e-02|
|yeast_R1_seqkit_bwasw_sorted | 73.0289| 43| 0.0100| 0.2639| 0e+00| 0.0018| 18.3572| 1e-02|
|yeast_R1_seqkit_graphmap2_sorted | 73.0100| 43| 0.0100| 0.0000| 0e+00| 0.0000| 0.0000| 1e-02|
|yeast_R1_seqkit_hisat2_sorted | 73.0100| 43| 0.0100| 0.0000| 0e+00| 0.0000| 0.0400| 1e-02|
|yeast_R1_seqkit_kallisto_sorted | 73.0100| 43| 0.0100| 0.0000| 0e+00| 0.0018| 18.1000| 1e-02|
|yeast_R1_seqkit_minimap2_sorted | 73.2885| 43| 0.0101| 0.3212| 1e-04| 0.0003| 2.5200| 1e-02|
|yeast_R1_seqkit_nucmer.fixed_sorted | 64.7399| 42| 0.0002| 0.2809| 0e+00| 0.0002| 100.0000| 2e-04|
|yeast_R1_seqkit_sublong_sorted | 45.2600| 43| 0.0100| 0.0000| 0e+00| 0.0012| 12.3400| 1e-02|
|yeast_R1_seqkit_subread_sorted | 73.0100| 43| 0.0100| 0.1396| 0e+00| 0.0016| 15.6000| 1e-02|
```
## Integrating AliNe in another nf pipeline
In Nextflow it is possible to call external workflow like AliNe from another workflow.
This require to write a dedicated process that will call AliNe and get back the results.
A complete guide how to do so is axailable [here](https://github.com/mahesh-panchal/nf-cascade?tab=readme-ov-file)
A complete guide how to do so is available [here](https://github.com/mahesh-panchal/nf-cascade?tab=readme-ov-file)
## Contributing
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