Add test data for nf-core/pacsomatic

[HaidYi]

Add test data for nf-core/pacsomatic

Summary

This PR adds test data for the nf-core/pacsomatic pipeline, consisting of downsampled mitochondrial genome BAM files from GIAB HG008 (paired tumor-normal samples).

Contents

• Test data: Downsampled tumor/normal mitochondrial BAM files (testdata/)
• Reference files: MT genome FASTA and target BED file (reference/)
• Samplesheet: Input CSV following pacsomatic schema
• Documentation: Comprehensive README with dataset details and usage instructions

Checklist

• Test data is minimal size
• README follows nf-core standards
• Files follow naming conventions
• Samplesheet matches pipeline schema

[jfy133]

Overall really good documenation! I've made some suggestions just to make it really solid :)

[jfy133]

Could you provide a link to the original source files, and a descirption how they were downsampled?

[jfy133]

Could you include the a link to the originanal source?

[wzhang42]

The original data-HG008 are from GIAB (https://www.nist.gov/programs-projects/cancer-genome-bottle) I downloaded the normal and tumor data from GIAB ftp ( https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/PacBio_Revio_20240125/ )

[jfy133]

Note if you manually made it

[jfy133]

I would place this section with the description of the date itself (it's a bit out of context after you've deescibed how to run the test data)

[jfy133]

Describe how generated (which tool/command with version used for alignment, filtering) etc., to allow reconstruction in an 'emergency'

[wzhang42]

@jfy133. It's me responsible for generating the tiny HG008_Downsample_MT_xx.bam. Take the HG008 Normal as example. My procedure are the following:
1.) get the total read number of HG008 Normal sample
samtools view -c -f 4 ${HG008_Normal_hifibam}
2.) calculate the percentage to a 10K reads against total read. , e.g 0.01/66.8=0.00015
3.) Use the above percentage to generate the downsampled 10K unaligned bam.
samtools view -b -s 0.00015 ${HG008_Normal_hifibam} > ./HG008-N_Downsample_10K.bam
4.) Use pbmm2 align the above downsampled unaligned bam to reference hg38, and generate aligned bam, Patient_HG008_Downsample_10K_N.align.bam
5.) Get the MT region specific aligned bam
samtools view -b Patient_HG008_Downsample_10K_N.align.bam MT| samtools sort -@ 16 -T HG008_Downsample_10K_N.tmp -o HG008_Downsample_MT_normal.align.bam
6.). Use Picard to convert the above tiny MT region aligned bam to unaligned bam
java -jar ${PICARD} RevertSam INPUT=HG008_Downsample_MT_normal.align.bam OUTPUT=HG008_Downsample_MT_normal.bam
samtools/1.17, picard/2.9.4 are used for the above command. pbmm2 is from smrttools/25.1.

[HaidYi]

@jfy133 Thank you for the valuable comments. @wzhang42 Please check the comments and answer the data generation-related ones.

[wzhang42]

@HaidYi, Have replied as above.

[HaidYi]

@jfy133 The readme is updated based on the answers of @wzhang42 and your comments.

[jfy133]

Great thank you both!