#!/bin/bash

set -eo pipefail

mkdir -p $par_output

echo $par_fail_trimming_multiqc > $par_output/fail_trimming_mqc.tsv
echo $par_fail_mapping_multiqc > $par_output/fail_mapping_mqc.tsv
echo $par_fail_strand_multiqc > $par_output/fail_strand_mqc.tsv

IFS="," read -ra fastqc_raw_multiqc <<< $par_fastqc_raw_multiqc && for file in "${fastqc_raw_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra fastqc_trim_multiqc <<< $par_fastqc_trim_multiqc && for file in "${fastqc_trim_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra trim_log_multiqc <<< $par_trim_log_multiqc && for file in "${trim_log_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra sortmerna_multiqc <<< $par_sortmerna_multiqc && for file in "${sortmerna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra star_multiqc <<< $par_star_multiqc && for file in "${star_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

# IFS="," read -ra hisat2_multiqc <<< $par_hisat2_multiqc && for file in "${hisat2_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra rsem_multiqc <<< $par_rsem_multiqc && for file in "${rsem_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra samtools_stats <<< $par_samtools_stats && for file in "${samtools_stats[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done

IFS="," read -ra samtools_flagstat <<< $par_samtools_flagstat && for file in "${samtools_flagstat[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done

IFS="," read -ra samtools_idxstats <<< $par_samtools_idxstats && for file in "${samtools_idxstats[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra markduplicates_multiqc <<< $par_markduplicates_multiqc && for file in "${markduplicates_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra featurecounts_multiqc <<< $par_featurecounts_multiqc && for file in "${featurecounts_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc && for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

[ -e "$par_aligner_pca_multiqc" ] && cp -r "$par_aligner_pca_multiqc" "$par_output/"

[ -e "$par_aligner_clustering_multiqc" ] && cp -r $par_aligner_clustering_multiqc "$par_output/"

[ -e "$par_pseudo_aligner_pca_multiqc" ] && cp -r $par_pseudo_aligner_pca_multiqc "$par_output/"

[ -e "$par_pseudo_aligner_clustering_multiqc" ] && cp -r $par_pseudo_aligner_clustering_multiqc "$par_output/"

IFS="," read -ra preseq_multiqc <<< $par_preseq_multiqc && for file in "${preseq_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra qualimap_multiqc <<< $par_qualimap_multiqc && for file in "${qualimap_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra dupradar_output_dup_intercept_mqc <<< $par_dupradar_output_dup_intercept_mqc && for file in "${dupradar_output_dup_intercept_mqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra dupradar_output_duprate_exp_denscurve_mqc <<< $par_dupradar_output_duprate_exp_denscurve_mqc && for file in "${dupradar_output_duprate_exp_denscurve_mqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra bamstat_multiqc <<< $par_bamstat_multiqc && for file in "${bamstat_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra inferexperiment_multiqc <<< $par_inferexperiment_multiqc && for file in "${inferexperiment_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra innerdistance_multiqc <<< $par_innerdistance_multiqc && for file in "${innerdistance_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra junctionannotation_multiqc <<< $par_junctionannotation_multiqc && for file in "${junctionannotation_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra junctionsaturation_multiqc <<< $par_junctionsaturation_multiqc && for file in "${junctionsaturation_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra readdistribution_multiqc <<< $par_readdistribution_multiqc && for file in "${readdistribution_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra readduplication_multiqc <<< $par_readduplication_multiqc && for file in "${readduplication_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

IFS="," read -ra tin_multiqc <<< $par_tin_multiqc && for file in "${tin_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

echo "Checking for custom multiqc_config"
# If the variable is empty, we use the default one (registered as a resource)
if [ -z $par_multiqc_config ]; then
  echo "No multiqc_config provided, using the default"
  cp $meta_resources_dir/multiqc_config.yml "$par_output"
else
  echo "Optional file provided"
  if [ -f $par_multiqc_config ]; then
    cp $par_multiqc_config "$par_output"/multiqc_config.yml
  else
    # Unreachable: the Viash-generated module checks this
    echo "Optional file does not exist"
    exit 1
  fi
fi

echo "Done"
