Error with gzipped annotation file

[grst]

When I try to run the pipeline with a gzipped annotation file (ensembl/Homo_sapiens.GRCh38.98.gtf.gz), it fails with the following error:

No such variable: gtf_star

 -- Check script 'rnaseq/main.nf' at line: 1037 or see '.nextflow.log' file for more details

From what I understood from the script, it should, in principle, accept gzipped files and unzip them automatically. Running the same command with an unzipped file works flawlessly.

Further information

command

nextflow run nf-core/rnaseq -profile conda -c nf-core-rnaseq.config

nf-core-rnaseq.config

params {
  genome = "GRCh38"
  reads = "/home/sturm/mydata/XXXX/fastq/**/*_{1,2}.fq.gz"
  genomes {
    "GRCh38" {
      star = '/data/genomes/hg38/index/STAR/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly/200'
      fasta = '/data/genomes/hg38/fasta/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly.fa'
// does not work 
      gtf = '/data/genomes/hg38/annotation/ensembl/Homo_sapiens.GRCh38.98.gtf.gz'
// works
//      gtf = '/data/scratch/sturm/data/XXXX/Homo_sapiens.GRCh38.98.gtf'
    }
  }
}

process {
  executor = 'sge'
  penv = 'smp'
  clusterOptions = { "-V -S /bin/bash -R y -q all.q" }
}

full pipeline log

N E X T F L O W  ~  version 19.10.0                                                                                                                                                                                                                                               
Launching `./rnaseq/main.nf` [happy_mirzakhani] - revision: efd50c97fd                                                                                                                                                                                                            
----------------------------------------------------                                                                                                                                                                                                                              
                                        ,--./,-.                                                                                                                                                                                                                                  
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq v1.4.2                                             
----------------------------------------------------
Run Name          : happy_mirzakhani
Reads             : /home/sturm/mydata/XXX/fastq/**/*_{1,2}.fq.gz                                                              
Data Type         : Paired-End                                      
Genome            : GRCh38                                          
Strandedness      : None                                            
Trimming          : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0 / NextSeq Trim: 0                                                              
Aligner           : STAR                                            
STAR Index        : /data/genomes/hg38/index/STAR/ensembl/Homo_sapiens.GRCh38.dna.primary_assembly/200                            
GTF Annotation    : /data/genomes/hg38/annotation/ensembl/Homo_sapiens.GRCh38.98.gtf.gz                                                  
BED Annotation    : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed                                      
Remove Ribosomal RNA: false                                         
Biotype GTF field : gene_biotype                                    
Save prefs        : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No                                                     
Max Resources     : 128 GB memory, 16 cpus, 10d time per job
Output dir        : ./results                                       
Launch dir        : /home/sturm/projects/2019/XXX
Working dir       : /home/sturm/scratch/projects/2019/XXX/work_rnaseq                                                           
Script dir        : /home/sturm/projects/2019/XXX/rnaseqUser              : sturm                                           
Config Profile    : conda                                           
----------------------------------------------------
[-        ] process > get_software_versions -                       
[-        ] process > fastqc                -                       
[-        ] process > trim_galore           -                       
No such variable: gtf_star                                          

 -- Check script 'rnaseq/main.nf' at line: 1037 or see '.nextflow.log' file for more details                                

[drpatelh]

This should be fixed now in the DSL2 version of the pipeline I am currently implementing @grst As you can see in this commit I have added a sub-workflow to specifically check if a given file is zipped and if so, to unzip.