Samplesheet path must have a file separator in it

[olgabot]

Hello,
I was testing out your pipeline to see if it would be compatible with how we currently run our demuxing, and ran into some issues. Here is the command:

nextflow run csawye01/nf-core-demultiplex \
        -profile docker \
        --samplesheet 190617_NB501961_0254_AHCYVWBGXB.csv \
        --runfolder /mnt/SEQS/NextSeq-01/190617_NB501961_0254_AHCYVWBGXB \
        --outdir /mnt/ibm_lg/olga/demux/190617_NB501961_0254_AHCYVWBGXB \
        -work-dir /mnt/ibm_lg/olga/nextflow-intermediates/demux \
        --awsregion us-west-2 \
        -latest --max_cpus 32 --max_memory 512.GB
N E X T F L O W  ~  version 19.04.1
Pulling csawye01/nf-core-demultiplex ...
downloaded from https://github.com/csawye01/nf-core-demultiplex.git
Launching `csawye01/nf-core-demultiplex` [marvelous_lovelace] - revision: 87ccff9190 [master]
ERROR ~ String index out of range: -1

 -- Check script 'main.nf' at line: 95 or see '.nextflow.log' file for more details

I tracked it down to here where the samplesheet folder name is used for the run name (which I think is not flexible to all possible workflows, but a separate issue), but since there's no folder name

But if one adds a ./ before the samplesheet CSV, then it runs fine!

nextflow run csawye01/nf-core-demultiplex \
        -profile docker \
        --samplesheet ./190617_NB501961_0254_AHCYVWBGXB.csv \
        --runfolder /mnt/SEQS/NextSeq-01/190617_NB501961_0254_AHCYVWBGXB \
        --outdir /mnt/ibm_lg/olga/demux/190617_NB501961_0254_AHCYVWBGXB \
        -work-dir /mnt/ibm_lg/olga/nextflow-intermediates/demux \
        --awsregion us-west-2 \
        -latest --max_cpus 32 --max_memory 512.GB
N E X T F L O W  ~  version 19.04.1
Pulling csawye01/nf-core-demultiplex ...
Launching `csawye01/nf-core-demultiplex` [special_pauling] - revision: 87ccff9190 [master]
[2m----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/demultiplex v1.0dev
----------------------------------------------------
Pipeline Release      : master
Run Name              : special_pauling
10X Genome Dir        : ./tenx
Adapter Stringency    : 0.9
Barcode Mismatch      : 0
Skip Missing BCLs     : true
Skip Missing Filter   : true
Skip Missing Positions: true
Min Trim Read Length  : 35
Mask Short Adapt Reads: 22
FastQ Compress Level  : 4
Max Resources         : 512.GB memory, 32 cpus, 10d time per job
Container             : docker - drpatelh/nf-core-demultiplex:dev
Output dir            : /mnt/ibm_lg/olga/demux/190617_NB501961_0254_AHCYVWBGXB
Launch dir            : /home/olga/code/demux-workflows/NextSeq-01
Working dir           : /mnt/ibm_lg/olga/nextflow-intermediates/demux
Script dir            : /home/olga/.nextflow/assets/csawye01/nf-core-demultiplex
User                  : olga
Config Profile        : docker
[2m----------------------------------------------------

Seems like there's likely a way around this, but I wasn't able to look into it.
Warmest,
Olga

[csawye01]

Hi Olga,

Thank you for pointing that out as I'm changing this pipeline from institute specific to be more general and there are still a few things that need tweaking. I have now changed the script to add the parameter of --runfolder so it will now parse the Run Name from that run directory. I have not tested this as of yet but will in the next week or two.