Error when try to run scflow

[Chrisdoan9]

Hi there!

I try to run scflow and got this error: Would you please have a look? When I run the command view manifest.txt, I don't have the number 1 and 2 before each row. Thank you so much! nextflow run nf-core/scflow \--manifest manifest.txt \--input sample_sheet.tsv \-c scflow_analysis.config \-profile singularity -r dev

ERROR ~ Error executing process > 'SCFLOW:SCFLOW_CHECKINPUTS (SCFLOW_CHECKINPUTS)'
Caused by:
  Process `SCFLOW:SCFLOW_CHECKINPUTS (SCFLOW_CHECKINPUTS)` terminated with an error exit status (1)
Command executed:
  check_inputs.r \
      --input sample_sheet.tsv         --manifest manifest.txt
  scflow_version=$(Rscript -e 'cat(as.character(utils::packageVersion("scFlow")))'); echo "scFlow ${scflow_version}" > "scFlow_${scflow_version}.version.txt"
Command exit status:
  1
Command output:
  The following paths were not found: -
    key                                                   filepath
  1  wt   /labs/chris/sn_mouse/wt/filtered_feature_bc_matrix
  2  mt /labs/chris/sn_mouse/ko/filtered_feature_bc_matrix
Command error:
  /apps/modules/lmod/lmod/init/bash: line 16: __lmod_vx: unbound variable
  INFO:    Converting SIF file to temporary sandbox...
  Warning message:
  In read.table(file = file, header = header, sep = sep, quote = quote,  :
    incomplete final line found by readTableHeader on 'sample_sheet.tsv' (edited)

manifest.txt

key filepath wt /labs/chris/sn_mouse/WT/filtered_feature_bc_matrix mt /labs/chris/sn_mouse/KO/filtered_feature_bc_matrix

sample_sheet.txt

individual group diagnosis manifest 1 wt wt wt 2 ko ko ko

[smoe]

Hello, I see two bits. The trivial one is that you likely miss a terminal newline in your sample_sheet.tsv file, which would make that warning disappear. When editing files in Windows this commonly happens. The not so trivial part (for me) is that

INFO:    Converting SIF file to temporary sandbox...

warning. This likely means that your singularity box cannot access anything outside of what is local to it in the file tree. I tried multiple things

• add containerOptions flag with -B /labs

• set environment variable SINGULARITY_BIND

  but in the end it only helped to copy/move the data to a local subdirectory and then adjust the paths.