Regarding of fastqc custom script

[hmkim]

https://training.nextflow.io/basic_training/rnaseq_pipeline/#custom-scripts
https://github.com/nextflow-io/training/blob/master/docs/basic_training/rnaseq_pipeline.md

#!/bin/bash
set -e
set -u

sample_id=${1}
reads=${2}

mkdir fastqc_${sample_id}_logs
fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}

to

#!/bin/bash
set -e
set -u

sample_id=${1}
reads=${2}

fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}

[hmkim]

Maybe default behavior is making directory by fastqc

[mribeirodantas]

Hi, @hmkim!

Are you running script7.nf with the default nextflow/rnaseq-nf as the Docker container image?

This error might be related to a different version of the software. It works fine from my side following the training material instructions.

[hmkim]

Hi, @mribeirodantas !

Thanks for your reply. As you mentioned, this might be related to a different version of fastqc.

I tested it on Cloud9 of AWS.

I also following the training material instructions.

I'll check the version of fastqc and docker container image between Cloud9 and gitpod.