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Description
Description of the bug
Hi friends,
I encountered a error(Workflow RNASEQ declares 18 input channels but 0 were given) when I was using nf-core/rnaseq on hpc. The code, other relevant file was presented. I didn't find any similar errors reorted before. Thank you for your help!!
By the way ,as for the reasons why I added somany skip_, because if I don't ,it will produce error with "parameter_skip_"
Command used and terminal output
/public/slst/home/chusy2024/nextflow/nextflow-24.04.4-all run \
/public/slst/home/chusy2024/nextflow/nf-core-rnaseq_3.18.0/3_18_0/workflows/rnaseq/main.nf \
--input /public/slst/home/chusy2024/RNA/LXX/0620/nextflow/samplesheet.csv \
--skip_alignment false \
--skip_qc false \
--skip_biotype_qc false \
--skip_bbsplit true \
--featurecounts_group_type gene_name \
--publish_dir_mode copy \
--skip_dupradar false \
--skip_multiqc false \
--skip_preseq false \
--remove_ribo_rna false \
--skip_stringtie false \
--contaminant_screening false \
--skip_pseudo_alignment true \
--skip_markduplicates false \
--with_umi false \
--rseqc_modules '["bam_stat","inner_distance", "junction_saturation", "infer_experiment", "junction_annotation", "read_distribution","read_duplication"]' \
--skip_rseqc false \
--skip_fastqc false \
--skip_trimming false \
--skip_bigwig false \
--skip_deseq2_qc false \
--fasta "/public/slst/home/chusy2024/nextflow/GRCh38.primary_assembly.genome.fa" \
--transcript_fasta "/public/slst/home/chusy2024/nextflow/gencode.v48.transcripts.fa" \
--gtf "/public/slst/home/chusy2024/nextflow/gencode.v48.annotation.gtf" \
--gencode \
--trimmer fastp \
--aligner star_rsem \
--skip_qualimap true \
--save_reference \
--outdir results \
-c "/public/slst/home/chusy2024/RNA/LXX/0620/nextflow/teset/singularity.config" \
-entry RNASEQ \
-profile singularity
singularity.config：
// /public/slst/home/chusy2024/RNA/LXX/0620/nextflow/teset/singularity.config
profiles {
singularity {
singularity {
enabled = true
cacheDir = '/public/slst/home/chusy2024/nextflow/nf-core-rnaseq_3.13.2/singularity-images/'
autoMounts = true
pullStrategy = 'LOCAL_ONLY' //
}
}
}
sample.txt:
sample fastq_1 fastq_2 strandedness
L1HJE2800737-pr1 /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800737-pr1_R1.fastq.gz /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800737-pr1_R2.fastq.gz auto
L1HJE2800738-pr2 /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800738-pr2_R1.fastq.gz /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800738-pr2_R2.fastq.gz auto
L1HJE2800739-pr3 /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800739-pr3_R1.fastq.gz /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800739-pr3_R2.fastq.gz auto
L1HJE2800740-pr4 /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800740-pr4_R1.fastq.gz /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800740-pr4_R2.fastq.gz auto
L1HJE2800741-ctrl1 /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800741-ctrl1_R1.fastq.gz /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800741-ctrl1_R2.fastq.gz auto
L1HJE2800742-ctrl2 /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800742-ctrl2_R1.fastq.gz /public/slst/home/chusy2024/RNA/LXX/0620/nextflow_rawdata/L1HJE2800742-ctrl2_R2.fastq.gz autoRelevant files
No response
System information
Nextflow version 24.10.4
HPC
Singularity
nf-core-rnaseq_3.18.0