My nextflow workflow calls Rmd render (NXF version 22.11.0-edge run with sge, apptainer in scratch directory). But the Rmd file is unable to find the files, directory path is passed in as a param.
nextflow.config has param outdir = "../results"
params.rscript = "$projectDir/run_quality_report.Rmd"
process run_report {
publishDir params.outdir, mode:'copy'
input:
tuple val(pair_id), path('file.tsv'),
path rscript
output:
file('report.html')
script:
"""
Rscript -e 'rmarkdown::render(input = "$rscript", output_dir = getwd(), params = list(directory = "${params.outdir}"))'
"""
}
Error message. The file is not being found.
Command executed:
Rscript -e 'rmarkdown::render(input = "run_quality_report.Rmd", output_dir = getwd(), params = list(directory = "../results"))'
Command error:
processing file: run_quality_report.Rmd
Error: '../results/Bam_stats_pf_Final.tsv' does not exist in current working directory ('/scratch/769451.1.long.q/nxf.jI7GjjSY7c').
Execution halted
Work dir:
/wynton/scratch/finterly/new_workflow/work/91/b1888cccc40f39d394ed315b4ba432
The Rmd file looks like this:
title: ...
params:
directory:
value: x
---
```
file_df <-read_tsv(file.path(params$directory, "file.tsv"), show_col_types = FALSE)
```
use a full path for params.outdir
not:
--outdir ../results/Bam_stats_pf_Final.ts
but
--outdir ${PWD}/../results/Bam_stats_pf_Final.ts
and it looks like it was the same problem as previously: Nextflow: [E::bwa_idx_load_from_disk] fail to locate the index files ...
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tuple val(pair_id), path('file.tsv'),I'm surprised that the input contains a
pathwith a quoted string. It looks like an error.and how about all your previous questions left without comment or validation ? Nextflow Gatk DepthOfCoverage: Failure working with the tmp directory ; Nextflow workflow errors when run from Scratch dir? ; Nextflow: [E::bwa_idx_load_from_disk] fail to locate the index files ; Nextflow Singularity/Apptainer error: command not found ; Fetching UniProt ID Mapping results as TSV using Python? ; etc...
Hi. Thank you for bringing this to my attention. I will try my best to leave comments and validation (as in select an answer?).