Specify custom gtf but gene bed is not generated from that gtf?

[mavershang]

Hi there, I ran the pipeline in two different settings:
run1. using the default ref genome GRCh38 without specify gtf and
run2. using the defualt ref genome GRCh38 and specified a custom gtf GENCODE.v26.basic.gtf

According to the document, the gene bed will be generated from the custom gtf, but in run2 the log says it seems the pipeline still go staging the genes.bed from S3 bucket.
The run2 get to the end successful. In the reference genome folder, the generated genes.tss.bed is exactly the same as run1.

So I am wandering is this a bug in the code or did I miss something?
Thanks,
Lei

[drpatelh]

Hi Lei! Please can you send me the full commands you used for each run please.

[mavershang]

Edited as a markdown code block 😉

run1:

nextflow run nf-core/atacseq \
    -c atacseq_custom.config \
    -profile conda \
    --input /hpc/grid/wip_drm_targetsciences/projects/p013_TE_Expression/GSE100750/nf_ATACSeq_pipeline/Design.txt \
    --outdir /hpc/grid/wip_drm_targetsciences/projects/p013_TE_Expression/GSE100750/nf_ATACSeq_pipeline/Output/AllSampleOutput_GRCh38_defaultGeneModel/ \
    --genome GRCh38 \
    --skip_multiqc

run2:

nextflow run nf-core/atacseq \
    -c atacseq_custom.config \
    -profile conda \
    --input /hpc/grid/wip_drm_targetsciences/projects/p013_TE_Expression/GSE100750/nf_ATACSeq_pipeline/Design.txt \
    --outdir  /hpc/grid/wip_drm_targetsciences/projects/p013_TE_Expression/GSE100750/nf_ATACSeq_pipeline/Output/AllSampleOutput_GRCh38_GENCODE26/ \
    --genome GRCh38 \
    --gtf /hpc/grid/wip_drm_targetsciences/users/shangl02/RefLib/Human/GENCODE/gencode.v26.basic.annotation.gtf  \
    --skip_multiqc

[drpatelh]

Hi @mavershang This is a bug but there is a simple workaround. Please can you add the parameter --gene_bed false and the pipeline will regenerate the bed from the gtf and then generate the tss from the bed as expected. The gene bed and tss bed are only used for some basic QC so shouldnt really interfere with the actual results 🙂 Thanks for reporting this. Ill fix it in the next release.

[mavershang]

Thank you @drpatelh. Will try

[drpatelh]

Fixed here @mavershang. Thanks for reporting!