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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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Decompress transcript fasta error #798

Closed rrdavis77 closed 2 years ago

rrdavis77 commented 2 years ago

Description of the bug

When providing a gz compressed transcript file with --transcript_fasta the pipeline errors with 

[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -
Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_TRANSCRIPT_FASTA` declares 1 input channel but 2 were specified

 -- Check script '/home/ryan/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome.nf' at line: 109 or see '.nextflow.log' file for more details

The error does not happen with providing a decompressed transcript fasta.

Command used and terminal output

nextflow run nf-core/rnaseq --input /home/ryan/NGS_Data/Wang_Hongbin_RNA-3-14-22/RNA_sample_list.csv --aligner star_salmon --pseudo_aligner salmon --gencode --outdir /home/ryan/NGS_Data/Carr-Ascher/RNAseq_analysis --fasta /home/ryan/Reference/Homo_sapiens/Ensembl/gencode_GRCH38/GRCh38.primary_assembly.genome.fa --gtf /home/ryan/Reference/Homo_sapiens/transcriptome/gencode.v39.annotation.gtf.gz --transcript_fasta /home/ryan/Reference/Homo_sapiens/transcriptome/gencode.v39.transcripts.fa.gz --save_reference --skip_stringtie --max_cpus 8 --max_memory 40GB -profile docker -c /home/ryan/NGS_Data/Wang_Hongbin_RNA-3-14-22/nextflow_rnaseq.config

WARN: =============================================================================
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
===================================================================================
[-        ] process > NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_GTF -
Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GUNZIP_TRANSCRIPT_FASTA` declares 1 input channel but 2 were specified

 -- Check script '/home/ryan/.nextflow/assets/nf-core/rnaseq/./workflows/../subworkflows/local/prepare_genome.nf' at line: 109 or see '.nextflow.log' file for more details

Relevant files

No response

System information

N E X T F L O W ~ version 21.10.3 Desktop local executor Docker container Ubuntu 16.04 nfcore/rnaseq version 3.6

drpatelh commented 2 years ago

FIxed in https://github.com/nf-core/rnaseq/pull/811