Check script 'main.nf' at line: 267

[yangchuhua]

To Whom It May Concern:

your pipeline is awesome. Thanks for all your effort in this job.

When I ran pipeline by the following commands I got the error report that "No such variable: readPaths--- Check script 'main.nf' at line: 267 or see '.nextflow.log' file for more details " $ /raid3/homedirs/yang/software/nextflow run /raid3/homedirs/yang/software/rnaseq/main.nf \

--readPathFile ../test.fastq.filePath \ -profile docker \ --genomes GRCh38 \ --singleEnd true \ --aligner 'star' \ --star_index ../hg38_genocode_v26_primary_star_index_sjdbOverhang149 \ --fastq ../GRCh38.p10.genome.fa \ --gff ../gencode.v26.chr_patch_hapl_scaff.annotation.gff3 \ --run_salmon false \ --run_txrevise false \ --run_exon_quant fasle \ --run_tx_exp_quant false \ --run_leafcutter true \ --skip_qc true \ --skip_multiqc true \ --skip_edger true \ --skip_alignment false

N E X T F L O W ~ version 21.04.3 Launching ../rnaseq/main.nf [prickly_hamilton] - revision: 4e88dccf0e No such variable: readPaths -- Check script 'main.nf' at line: 267 or see '.nextflow.log' file for more details

I wonder if the "readPaths" is the parameter "--reads" in your main.nf.

Best, Chuhua

[kauralasoo]

Hi Chuhua,

I think you have a small typo in your command. The name of the parameter should be --readPathsFile, not --readPathFile.

We have some more instructions here: https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/blob/master/tutorials/workflow_execution.md

Best, Kaur

[yangchuhua]

Hi Chuhua,

I think you have a small typo in your command. The name of the parameter should be --readPathsFile, not --readPathFile.

We have some more instructions here: https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/blob/master/tutorials/workflow_execution.md

Best, Kaur

Hi Kaur,

Thank you very, very much! It really was a typo.

Thank you for sharing the link. It was very helpful!

Best, Chuhua