process fungal_reads_extraction {
     publishDir("${params.extraction_output}" , mode: 'copy') 
     
     input:
     path namesspecies
     
     output:
     path "*" , emit: reads_extracted_out
     
     script:
     """
   while read -r species_name; do
//Extract lines from the Kraken file where the third word matches the species name
     awk -F'\t' -v "$species_name" 'BEGIN {OFS="\t"} \$3 ~ "$species_name" {print}' output.kraken > "${species_name}_lines.txt"
//Extract accessions from species lines
     awk -F'\t' '{print \$2}' "${species_name}_lines.txt" > "${species_name}_accessions.txt"
//Add "@" symbol to the beginning of each line in the accession file
     awk '{print "@" \$0}' "${species_name}_accessions.txt" > "${species_name}_full_accessions.txt"
//Extract reads assigned to the species
     cat $sequences | awk 'NR==FNR {accessions[\$1]=1; next} \$1 in accessions {print; getline; print; getline; print; getline; print}' "${species_name}_full_accessions.txt" - > "${species_name}_reads.fastq"
//Cleanup intermediate files
     rm "${species_name}_lines.txt" "${species_name}_accessions.txt" "${species_name}_full_accessions.txt"
   done < fungal_species.txt
     """
}

ERROR ~ Error executing process > 'fungal_reads_extraction (1)'
Caused by:
  No such variable: species_name -- Check script 'pipeline.nf' at line: 193

species_ch = Channel.fromPath(params.path_to_fungal_species).splitText().map{it.trim()}
(...)
process fungal_reads_extraction {
     input:
     val(one_name)
     (...)