--mod and --cnv output files seemingly missing or labelled incorrectly?

[fidibidi]

Ask away!

Hello,

I'm confused by what appears to be a number of files missing from in my final output.

Here is my command:

nextflow run epi2me-labs/wf-human-variation -w data/wf-human-var-A0485-cnv-5/workspace -profile standard --sv --sniffles_args '"--no-qc"' --cnv --bin_size 5 --mod --bam data/bams/A0485/021924_022224_P2_A0485/A0485.pass.bam --ref references/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac@v4.2.0 --sample_name A0485 --threads 16 --bam_min_coverage 0 --out_dir data/wf-human-var-A0485-cnv-5 -resume

with the --mod and --cnv; I'm expecting the following files as seen described in the readme:

for --mod: {{ alias }}.wf_mods.bedmethyl.gz

for --cnv {{ alias }}.wf_cnv.vcf.gz

The only files I see that seem to be related to these two parameters are:

A0485.bed.gz A0485.wf-human-cnv-report.html qdna_seq/ A0485_bins.bed A0485_calls.vcf A0485_cov.png A0485_noise_plot.png A0485_raw_bins.bed A0485_segs.seg A0485_calls.bed A0485_combined.bed A0485_isobar_plot.png A0485_plots.pdf A0485_segs.bed A0485_segs.vcf trace.txt

So just wondering is the documentation out of date or am I experiencing some sort of error?

I've done some digging and it does seem like modkit only generates the bedgraph file if you give the modkit command the --bedgraph option.

I've included the trace.txt as well. Thank you

[RenzoTale88]

Hi @fidibidi do you mind sharing the following:

1. workflow version
2. log files
3. list of the files in the directory

[fidibidi]

Hi Renzo,

1. I looked in the report.html for the workflow version Workflow repository https://github.com/epi2me-labs/wf-human-variation, revision master (commit hash 8f0c968c82dea66dbb492be2271f2beacc923184) I included the report.html as report.txt since I can't upload HTML here... if you'd like to view you should just be able to rename to HTML...

2. Unfortunately I've run samples since, and it seems like the nextflow logs for this run were overwritten. the log files are found at .nextflow.log right?

3. list of files:

   A0485.bed.gz
   A0485.mosdepth.global.dist.txt
   A0485.mosdepth.summary.txt
   A0485.readstats.tsv.gz
   A0485.regions.bed.gz
   A0485.thresholds.bed.gz
   A0485.wf-human-cnv-report.html
   A0485.wf-human-sv-report.html
   A0485.wf_sv.vcf.gz
   A0485.wf_sv.vcf.gz.tbi
   A0485.wf_sv_clinvar.vcf
   OPTIONAL_FILE
   execution/report.html
   execution/timeline.html
   execution/trace.txt
   input.1
   jbrowse.json
   qdna_seq/A0485_bins.bed
   qdna_seq/A0485_calls.bed
   qdna_seq/A0485_calls.vcf
   qdna_seq/A0485_combined.bed
   qdna_seq/A0485_cov.png
   qdna_seq/A0485_isobar_plot.png
   qdna_seq/A0485_noise_plot.png
   qdna_seq/A0485_plots.pdf
   qdna_seq/A0485_raw_bins.bed
   qdna_seq/A0485_segs.bed
   qdna_seq/A0485_segs.seg
   qdna_seq/A0485_segs.vcf
   wf-human-variation-alignment-report.html

I'm suspecting that perhaps the version of wf-human-variation I was running was just super out of date...

I did some updating and ran just cnv, and got the desired cnv output files, via spectre now though.

I haven't tested --mod yet though.

[RenzoTale88]

@fidibidi yes, the documentation is updated at each release to reflect the changes introduced to the workflow. The modkit output is being renamed to .wf_mods.bedmethyl.gz as of version 1.9.0. I'd suggest to update to the latest release and come back to us if you still find discrepancies in the outputs.