Script compilation error

[slowkow]

Could I please ask if you might be able to help me with this error?

I ran:

git clone git@github.com:biocorecrg/indrop.git

cd indrop

vim params.config

Here is params.config:

params {
     pairs = "/path/to/lane1*R{1,2,3,4}_001.fastq.gz"
     config        = "$baseDir/conf/indrop_v3.xml"
     barcode_list  = "$baseDir/conf/indrop_v3_barcodes.txt"
     output        = "output_v3"
     genome = "/projects/external_data/10xgenomics.com/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa"
     annotation = "/projects/external_data/10xgenomics.com/refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf"
     mtgenes       = "$baseDir/anno/mitoc_genes.txt"
     dbdir         = "$baseDir/db"
     keepmulti     = "NO"
     library_tag   = "CTCTCTAT"
     version       = "3_4"
     email            = "my@email"
}

Then I ran:

nextflow indrop.nf --help

and got these errors:

N E X T F L O W  ~  version 19.10.0
Launching `indrop.nf` [admiring_einstein] - revision: fb17c3423b
Script compilation error
- file : /home/ks38/work/indrop/nextflow_dropest/indrop/indrop.nf
- cause: unable to resolve class QualityChecker
 @ line 104, column 14.
       def qc = new QualityChecker(input:read, cpus:task.cpus)
                ^

Script compilation error
- file : /home/ks38/work/indrop/nextflow_dropest/indrop/indrop.nf
- cause: unable to resolve class QualityChecker
 @ line 185, column 14.
       def qc = new QualityChecker(input:filtered_read, cpus:task.cpus)
                ^

Script compilation error
- file : /home/ks38/work/indrop/nextflow_dropest/indrop/indrop.nf
- cause: unable to resolve class QualityChecker
 @ line 204, column 14.
       def qc = new QualityChecker(input:fastq_file)
                ^

Script compilation error
- file : /home/ks38/work/indrop/nextflow_dropest/indrop/indrop.nf
- cause: unable to resolve class NGSaligner
 @ line 229, column 19.
       def aligner = new NGSaligner(reference_file:genomeFile, index:"STARgenome", annotation_file:annotationFile, read_size:read_size-1, cpus:task.cpus)
                     ^

4 errors

[lucacozzuto]

Hi @slowkow
you need an extra step :)

In the README it states:

Installing
install docker or singularity.
git clone https://github.com/biocorecrg/indrop.git; cd indrop
sh INSTALL.sh for checking Nextflow and installing bioNextflow

you miss the latest part

[slowkow]

Thanks for the tip.

Indeed, running bash INSTALL.sh fixed this issue, so now the command nextflow indrop.nf --help works as expected.