anchor heatmap did not run

[chstellar]

Hi, I have encountered a problem in running SPLASH in heatmap mode. I have run SPLASH successfully and I want to visualise the results using heatmap. My input was: nextflow run kaitlinchaung/nomad -r main -latest --input sheet.csv --element_annotations_samplesheet ../samplesheet.csv --run_anchor_heatmaps true --results_dir <results_dir> --use_heatmap_anchor_list true --heatmap_anchor_list anchor.tsv but the pipeline ends in seconds and I saw no update the result folder: `[d8/537650] process > RUN_NOMAD:ANCHOR_HEATMAPS (h... [100%] 1 of 1 ✔

-[salzmanlab/nomad] Pipeline completed successfully-` I also tried to add a command that should induce an error message: ` nextflow run kaitlinchaung/nomad -r main -latest --input sheet.csv --element_annotations_samplesheet ../samplesheet.csv --run_anchor_heatmaps true --results_dir --use_heatmap_anchor_list true --heatmap_anchor_list anchor.tsv **--additional_summary test** ` but again the pipeline run without an error but gave no output. Could you please help with this?

[kaitlinchaung]

Hi @chstellar,

The anchor heatmaps should be output in "${params.results_dir}/anchor_heatmaps". It won't be located in ${params.outdir}.

Also, we recommend using the newer version of the codebase here: https://github.com/refresh-bio/SPLASH

[chstellar]

There was no directory named anchor_heatmaps generated in the designated results_dir... But I will check SPLASH2 for my analysis. Thanks!