Single-end analysis not working

[ahwanpandey]

Hello,

I am using v4.0.0

This is my samplesheet:

sample,fastq_1,fastq_2,strandedness
66130_Ascites,/researchers/ahwan.pandey/Projects/RNAseq/Project_LC/AZ_ADC/raw_07_11_2025/Sample_2-66130-Ascites/2-66130-Ascites_S201_R1_001.fastq.gz,,reverse

This is my params file:

{
"input": "/researchers/ahwan.pandey/Projects/RNAseq/Project_LC/AZ_ADC/analysis_07_11_2025_1/Sample_66130_Ascites/nfcore_samplesheet.csv",
"outdir": "/researchers/ahwan.pandey/Projects/RNAseq/Project_LC/AZ_ADC/analysis_07_11_2025_1/Sample_66130_Ascites",
"genome": "GRCh38",
"genome_gencode_version": 46,
"genomes_base": "/researchers/ahwan.pandey/references/nf-core/rnafusion/Homo_sapiens",
"adapter_fasta": "/researchers/ahwan.pandey/Projects/RNAseq/Project_LC/AZ_ADC/resources/adapters.fa",
"read_length": 100,
"tools_cutoff": 1,
"seq_center": "PM",
"seq_platform": "ILLUMINA",
"tools": "fastp,arriba",
"multiqc_title": "66130_Ascites"
}

This is the error I am getting:

Dec-30 14:50:43.852 [main] DEBUG nextflow.Session - Session aborted -- Cause: The following invalid input values have been detected:

* --input (/researchers/ahwan.pandey/Projects/RNAseq/Project_LC/AZ_ADC/analysis_07_11_2025_1/Sample_66130_Ascites/nfcore_samplesheet.csv): Validation of file failed:
        -> Entry 1: Missing required field(s): fastq_2
        -> Entry 1: Missing required field(s): bam
        -> Entry 1: Missing required field(s): cram
        -> Entry 1: Missing required field(s): junctions
        -> Entry 1: Missing required field(s): splice_junctions
        -> Entry 1: Value does not match against any of the schemas

I have tried various combination of "tools" in the params file, still the same error.

I have attached the .netflow.log in case that helps. The pipeline works perfectly file when I run it on my paired-end data.

Thanks!
Ahwan

.nextflow.log

[ahwanpandey]

Hello,

Just checking if you were able to look into this?

Thanks!