atacseq
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ERROR: Please check design file header: group,replicate,fastq_1,fastq_2 != group,replicate,fastq_1,fastq_2
Reposting here from the nf-core Slack for posterity. Thanks for @drpatelh for figuring this out!
Problem
nextflow/atacseq pipeline does not recognize the design.csv file, even though it follows the structure indicated here.
The example bash script below follows a modified version of the command shown here.
Bash script
#!/bin/bash
source ~/.bashrc
module load nextflow
export repo_dir=$HOME/neurogenomics/GitRepos/CUT_n_TAG
export project_id=HK5M2BBXY
mkdir -p $repo_dir/processed_data/$project_id
nextflow run nf-core/atacseq \
--input $repo_dir/raw_data/$project_id/design_noindex.csv \
--genome GRCh37 \
--narrow_peak \
--outdir $repo_dir/processed_data/$project_id \
-with-singularity $HOME/atacseq_latest.sif \
-c $repo_dir/hpc_config \
-r 1.2.1
Error output
...
Error executing process > 'CHECK_DESIGN (design.csv)'
Caused by:
Process `CHECK_DESIGN (design.csv)` terminated with an error exit status (1)
Command executed:
check_design.py design.csv design_reads.csv
Command exit status:
1
Command output:
ERROR: Please check design file header: group,replicate,fastq_1,fastq_2 != group,replicate,fastq_1,fastq_2
Command wrapper:
singularity/default :: no need to load a module to use singularity
ERROR: Please check design file header: group,replicate,fastq_1,fastq_2 != group,replicate,fastq_1,fastq_2
============================================
Job resource usage summary
Memory (GB) NCPUs
Requested : 6 1
Used : 0 (peak) 0.50 (ave)
============================================
Work dir:
/rds/general/user/bms20/ephemeral/tmp/b8/e3357840d49b488c3f691f8db4592d
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Solution
The design.csv file MUST be in plain csv format, not UTF-8 encoded, which is the default in Excel.
See attached screenshot of how to save as correct format.
![Screenshot 2020-12-17 at 17 52 43](https://user-images.githubusercontent.com/34280215/102553381-a9b15d00-40ba-11eb-9c1b-29340df5458c.png)