ERROR ~ Unable to read script: '/home/nanoneuro/.nextflow/assets/nf-core/smrnaseq/./workflows/smrnaseq.nf'

[alexmascension]

Description of the bug

I'm running a basic run with the following configuration and the output of the error is

ERROR ~ Unable to read script: '/home/nanoneuro/.nextflow/assets/nf-core/smrnaseq/./workflows/smrnaseq.nf' -- cause: https://mirbase.org/ftp/CURRENT/mature.fa.gz

I guess this error occurs because the new ftp access is https://mirbase.org/download/CURRENT/and not https://mirbase.org/ftp/CURRENT/

Command used and terminal output

nextflow run nf-core/smrnaseq \
   -profile docker \
   --input samplesheet.csv \
    --genome 'GRCm38' \
    --mirtrace_species 'mmu' \
    --protocol 'illumina' \
    --outdir $OUTDIR

Relevant files

No response

System information

No response

[alexmascension]

So far I'm solving it with custom parameters --mature https://www.mirbase.org/download_file/mature.fa/ and --hairpin https://www.mirbase.org/download_file/hairpin.fa/, which seem to be the new file locations. The default argument should be changed.

[alexmascension]

The same happens with the process NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT, with the following error:

Can't stage file https://mirbase.org/ftp/CURRENT/genomes/mmu.gff3 -- reason: No subject alternative DNS name matching mirbase.org found.

I used the --mirna_gtf https://www.mirbase.org/download_file/mmu.gff3/ argument as a workaround.

[anmeert]

I'm encountering the same issue.
I needed to adapt the links again slightly:

--mature https://mirbase.org/download/CURRENT/mature.fa
--hairpin https://mirbase.org/download/CURRENT/hairpin.fa
--mirna_gtf https://mirbase.org/download/hsa.gff3

However, i get following error when trying to run:

Error executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT_PARSE_MATURE'

Caused by:
   Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_MATURE` terminated with an error exit status (255)

Command error:
   [ERRO] fastx: invalid FASTA/Q format

So i think there is some issue when parsing the fasta file.

[apeltzer]

Fixed in #269