Split R1 and R2 for smartseq2 `light_class_input.py`

[olgabot]

scripts/light_class_input.py expects two bam files -- one each for R1 and R2

python3 scripts/light_class_input.py --outpath /oak/stanford/groups/horence/Roozbeh/single_cell_project/output/mouse_brain_PNAS_Tasic_2018/SRR7311317/ --gtf /oak/stanford/groups/horence/Roozbeh/single_cell_project/SICILIAN_references/mouse/refseq_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.gtf --annotator /oak/stanford/groups/horence/Roozbeh/single_cell_project/SICILIAN_references/mouse/refseq_GRCm38.p6/refseq_mm10.p6.pkl --bams /oak/stanford/groups/horence/Roozbeh/single_cell_project/output/mouse_brain_PNAS_Tasic_2018/SRR7311317/1Aligned.out.bam /oak/stanford/groups/horence/Roozbeh/single_cell_project/output/mouse_brain_PNAS_Tasic_2018/SRR7311317/2Aligned.out.bam --paired

Check Documentation

I have checked the following places for your error:

• [x] nf-core website: troubleshooting
• [x] nf-core/sicilian pipeline documentation

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
2. See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

• [ ] The command used to run the pipeline
• [ ] The .nextflow.log file

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:
• Image tag:

Additional context

[olgabot]

Need to split R1 and R2 into separate bam files: https://github.com/czbiohub/nf-sicilian/issues/11 in STAR_ALIGN process

This is the code to add:

mv ${prefix}.Aligned.out.bam original.bam
samtools view -hbf 64 original.bam > ${prefix}.R1.Aligned.out.bam
samtools view -hbf 128 original.bam > ${prefix}.R2.Aligned.out.bam