bounlu

Repeated isomiRs in the `mirtop.tsv` output

1

The `mirtop.tsv` output contains repeated rows for some isomiRs with identical first 12 columns: ``` UID Read miRNA Variant iso_5p iso_3p iso_add3p iso_snp iso_5p_nt iso_3p_nt iso_add3p_nt iso_snp_nt iso-16-03170FE ACAGTAGTCTACACAT hsa-miR-199b-3p...

`BiopythonDeprecationWarning`: `Bio.pairwise2` has been deprecated, please consider using `Bio.Align.PairwiseAligner`

1

`mirtop --help` gives the below warning: ``` /opt/anaconda3/lib/python3.9/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider...

`fq lint` fails on large files

3

Hi, It seems `fq lint` fails on large FASTQ file due to below error: `fq lint XXX_1.merged.fastq.gz XXX_2.merged.fastq.gz > XXX.fq_lint.log.txt` ``` Command error: Error: I/O error Caused by: corrupt deflate...

Nextflow does not work with the latest version of Java (22): ``` ERROR: Cannot find Java or it's a wrong version -- please make sure that Java 8 or later...

Please add `samstat` to conda: conda install -c bioconda samstat Thanks.

`segment` function fails

3

When using `batch` command, `.cns` file is not generated and no error is thrown. However, when I run `segment` function separately, it gives the below error: ``` # cnvkit.py segment...

Add support for custom targeted panel

1

### Description of feature Currently the pipeline only supports `tso500` panel for the `targeted` analysis with the pre-computed reference files given in the `panel_data.config`. It would be nice to allow...

`Rscript` error when running `PURPLE`

2

`Purple` fails with the below error: ``` ERROR ~ Error executing process > 'NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE (220024755)' Caused by: Process `NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE (220024755)` terminated with an error exit status (1) Command executed: purple...

### Name of the tool pyTMB.py ### Tool homepage https://github.com/bioinfo-pf-curie/TMB ### Tool description Tool to calculate tumor mutational burden from VCF file ### Tool output [my_sample.tmb.log](https://github.com/user-attachments/files/16901840/my_sample.tmb.log) ### Log filename pattern...