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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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strandness error #1420

Open aheravi opened 6 days ago

aheravi commented 6 days ago

Description of the bug

Hi there, Could you comment on my error on strandness below. My sample sheet is something like this:

sample,fastq_1,fastq_2,strandedness
MaleKO_S1,/projects/S1.R1.fastq.gz,/projects/S1.R2.fastq.gz,auto
...
STQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (MaleWT_F143557); status: COMPLETED; exit: 0; error: -; workDir: /p
rojects/work/17/bfcfef3c832d1422450c1ec6be7658]
Oct.-17 12:05:01.059 [Actor Thread 113] ERROR nextflow.extension.OperatorImpl - @unknown
groovy.lang.MissingPropertyException: No such property: strandedness for class: Script_6526763402877652
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:65)

Command used and terminal output

No response

Relevant files

No response

System information

No response

tdanhorn commented 6 days ago

Can you confirm that this fails reproducibly with the newest version 3.16.1 that came out yesterday? It would probably also be helpful if you could post the .nextflow.log and any information about your configuration (where you are running it, any config files and profiles, etc.).

aheravi commented 6 days ago

Acutally it is 3.15.1. nf-core/rnaseq v3.15.1-g4053b2e How can I run the latest?

How I run it (on a linux machine):

nextflow-23.10.0-all run nf-core/rnaseq \
    --input /projects/samplesheet_male_ko_wt.csv \
    --outdir /projects/output_male_KO_WT \
    --gtf /projects/hg38_no_alt/annotations/ensembl100/Homo_sapiens.GRCh38.100.remapped.gtf \
    --fasta /projects/hg38_no_alt/genome/fasta/hg38_no_alt.fa \
    -profile singularity \
    --aligner star_rsem \