search

nf-core / smrnaseq

A small-RNA sequencing analysis pipeline
https://nf-co.re/smrnaseq
MIT License
70 stars 118 forks source link

Concatenate technical repeats #212

Open ojziff opened 1 year ago

ojziff commented 1 year ago

Description of feature

When running smrnaseq with technical repeats I get the error:

 Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT` input file name collision -- There are multiple input files for each of the following file names:

To run the pipeline I used this command:

nextflow run nf-core/smrnaseq \
        --outdir './nfcore' \
        --input './samplesheet.csv' \
        --genome GRCh38 \
        --protocol qiaseq \
         -profile crick \
        -r 2.1.0

The samplesheet.csv file has three columns, sample, fastq_1, and fastq_2. There are duplicated entries in the sample column, as some samples were sequenced over multiple runs.

Please could a concatenate step be added to merge technical repeats?

jonoave commented 1 year ago

I just experienced this error as well. As i was following the guide to creating samplesheet here: https://nf-co.re/smrnaseq/2.1.0/usage#multiple-runs-of-the-same-sample