Help with rnaseq pipeline - looks like it is not recognizing the --input path

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Hello Seqera team!

I ran rnaseq/nf-core pipeline many times already in a different server and never saw this type of error before. I am still a beginner in the bioinformatics life and might be doing something wrong, but I need your help to figure this out.
This is interesting (and kind of funny!). I am running some rnaseq analysis from elks blood and I did set up my pipeline (please find it below) and added the genome and gtf, both from cervus canadensis.
Which is interesting is that instead of the elks/cervus, at the end I am getting some chicken gut results :sweat_smile: (I have no idea where this data is from).

If you see the out.txt file, it looks like is getting the data from a different place and not from my dir, even setting up the pipeline for that in the --input part. I added the entire path, already checked all the files to make sure everyone is in the same folder, or have the correct information and I am still getting results from chicken gut at the end. :frowning:

Have you seen this error before? Do you have any idea about how I can fix it?
Please find below some information about the code I am using and the out.txt.

Thank you in advance for your help.

Code:

GENOME=GCF_019320065.1_ASM1932006v1_genomic.fna

GTF=GCF_019320065.1_ASM1932006v1_genomic.gtf

 
module load nextflow apptainer

nextflow run nextflow-io/rnaseq-nf \

        --input /project/elk_project/sample_sheet.csv \

        --outdir star_rsem_output \

        --fasta ${GENOME}  \

        --gtf ${GTF} \

        -with-singularity \

        -resume \

        --aligner star_rsem

Output files/folders:
fastqc_ggal_gut_logs
multiqc_report.html

Out.txt

 N E X T F L O W   ~  version 24.04.2

 

Launching `https://github.com/nextflow-io/rnaseq-nf` [serene_bartik] DSL2 - revision: 1c3027e306 [master]

 

 R N A S E Q - N F   P I P E L I N E

 ===================================

 transcriptome: /home/bruna.petry/.nextflow/assets/nextflow-io/rnaseq-nf/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa

 reads        : /home/bruna.petry/.nextflow/assets/nextflow-io/rnaseq-nf/data/ggal/ggal_gut_{1,2}.fq

 outdir       : star_rsem_output

 

[-        ] RNASEQ:INDEX  -

[-        ] RNASEQ:FASTQC -

[-        ] RNASEQ:QUANT  -

 

[-        ] RNASEQ:INDEX  -

[-        ] RNASEQ:FASTQC -

[-        ] RNASEQ:QUANT  -

[-        ] MULTIQC       -

 
[fe/e4bf99] RNA…(ggal_1_48850000_49020000) | 1 of 1, cached: 1 ✔

[55/b56f37] RNA…ASTQC (FASTQC on ggal_gut) | 1 of 1, cached: 1 ✔

[92/2005cf] RNASEQ:QUANT (ggal_gut)        | 1 of 1, cached: 1 ✔

[90/35bdca] MULTIQC                        | 1 of 1, cached: 1 ✔

[fe/e4bf99] RNA…(ggal_1_48850000_49020000) | 1 of 1, cached: 1 ✔

[55/b56f37] RNA…ASTQC (FASTQC on ggal_gut) | 1 of 1, cached: 1 ✔

[92/2005cf] RNASEQ:QUANT (ggal_gut)        | 1 of 1, cached: 1 ✔

[90/35bdca] MULTIQC                        | 1 of 1, cached: 1 ✔
2

Hi Bruna! Welcome to the community forum :slight_smile:

You’re not running the nf-core/rnaseq pipeline. You’re running a toy pipeline called rnaseq-nf that we use for teaching Nextflow. It’s rather simple (as you can see by the number of processes) and it uses different parameters. That’s why your parameters are being ignored and it’s using the training data that we use :wink:

You should be running nextflow run nf-core/rnaseq at the beginning of your command line, not nextflow-io/rnaseq-nf :sweat_smile:

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Hey Marcel,
Well, I guess I should be happy because it was something very easy to fix but… my goodness! :sweat_smile: :rofl: :rofl:

Thank you! :smiley:

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