samplesheet.csv merge error

[ojziff]

Description of the bug

Attempting to download all 24 SRA experiments (RNAseq) from this regional astrocyte paper https://dev.biologists.org/content/146/13/dev170910.abstract

Accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133489
SRA Run Selector
Download Accession list for all 24 items (SRR_Acc_List.txt)

Error with nf-core/rnaseq --public_data_ids run with input file name collision in samplesheet.

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/rnaseq \ --outdir '/camp/lab/luscomben/home/shared/projects/patani-collab/public-data/regional-astrocytes-ipsc-bradley-2019/nfcore' \ --public_data_ids '/camp/lab/luscomben/home/shared/projects/patani-collab/public-data/regional-astrocytes-ipsc-bradley-2019/sample-details/SRR_Acc_List.txt' \ --email oliver.ziff@crick.ac.uk -profile crick -r 3.0 -resume
2. See error: Error executing process > 'SRA_DOWNLOAD:SRA_MERGE_SAMPLESHEET'
   Caused by:
   Process SRA_DOWNLOAD:SRA_MERGE_SAMPLESHEET input file name collision -- There are multiple input files for each of the following file names: samplesheets/SRX6374119_T1.samplesheet.csv, samplesheets/SRX6374116_T2.samplesheet.csv, samplesheets/SRX6374120_T1.samplesheet.csv, samplesheets/SRX6374121_T1.samplesheet.csv, samplesheets/SRX6374117_T1.samplesheet.csv, samplesheets/SRX6374118_T1.samplesheet.csv, samplesheets/SRX6374119_T2.samplesheet.csv, samplesheets/SRX6374113_T2.samplesheet.csv, samplesheets/SRX6374118_T2.samplesheet.csv, samplesheets/SRX6374112_T2.samplesheet.csv, samplesheets/SRX6374117_T2.samplesheet.csv, samplesheets/SRX6374114_T2.samplesheet.csv, samplesheets/SRX6374115_T2.samplesheet.csv, samplesheets/SRX6374113_T1.samplesheet.csv, samplesheets/SRX6374114_T1.samplesheet.csv, samplesheets/SRX6374115_T1.samplesheet.csv, samplesheets/SRX6374121_T2.samplesheet.csv, samplesheets/SRX6374122_T2.samplesheet.csv, samplesheets/SRX6374123_T2.samplesheet.csv, sampleshe
   ets/SRX6
   374116_T1.samplesheet.csv, samplesheets/SRX6374120_T2.samplesheet.csv, samplesheets/SRX6374123_T1.samplesheet.csv, samplesheets/SRX6374112_T1.samplesheet.csv, samplesheets/SRX6374122_T1.samplesheet.csv

All the SRX files do downloaded - but it is only the samplesheet that fails to merge.

Expected behaviour

Create samplesheet.csv with group, replicate, fastq_1... headings etc

Log files

Have you provided the following extra information/files:

• [y ] The command used to run the pipeline
• [ n] The .nextflow.log file - too large

System

• Hardware: Crick HPC
• Executor: slurm
• OS: linux
• Version 3

Nextflow Installation

• Version: 20.12.0

Container engine

• Engine: singularity
• version: 3.4.2
• Image tag: nfcore/rnaseq:3.0.0

Additional context

File: SRR_Acc_List.txt

SRR9610957
SRR9610958
SRR9610959
SRR9610960
SRR9610961
SRR9610962
SRR9610963
SRR9610964
SRR9610965
SRR9610966
SRR9610967
SRR9610968
SRR9610969
SRR9610970
SRR9610971
SRR9610972
SRR9610973
SRR9610974
SRR9610975
SRR9610976
SRR9610977
SRR9610978
SRR9610979
SRR9610980

[drpatelh]

Thanks @ojziff ! Will test this out and try and fix when I get around to sorting out the next release.

[drpatelh]

Ok. Reproduced this locally and all it took was this to fix 😁 ad3b8ae Thanks @ojziff !