Error when annotation file is gzipped

[hoelzer]

I run into an error when providing --annotation gtf.csv with content

hsa.gtf.gz

I think we should check also for annotations if they are zipped and if so unzip them

[hoelzer]

Could it be that there is also still a problem when the input FASTA is gzipped?

├─(/data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow)
└─> cat fastas.csv
/data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow/genomes/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
/data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow/genomes/eco.fna.gz
/data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow/genomes/A_fumigatus_Af293_current_chromosomes.fasta.gz
/data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow/genomes/C_albicans_SC5314_A22_current_chromosomes.fasta.gz

[cc/7d866e] process > preprocess:hisat2index                                 [  0%] 0 of 1

hoelzer@prost:/data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow$ head /data/fass2/2020-06-24_martin_home_save/2020-12-23_tilman/rnaflow/work/16/f3bf761ff767c0d723e5784f0b3305/reference.fa 
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