diff --git a/main.nf b/main.nf
index 5a35471..02062b0 100644
--- a/main.nf
+++ b/main.nf
@@ -33,649 +33,639 @@ params.help            = false
 params.resume          = false
 
 
-// log.info """
-//
-// ╔╦╗┬ ┬┌─┐  ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
-//  ║ ├─┤├┤   ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
-//  ╩ ┴ ┴└─┘  ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
-//
-// ==============================================================================
-// annotations (GTF files)          : ${params.annotations}
-// genomes (fasta files)            : ${params.genomes}
-// cluster file (txt files)         : ${params.cluster}
-// pairwise evo distances           : ${params.evodists}
-// long distance parameters         : ${params.long_dist}
-// medium distance parameters       : ${params.medium_dist}
-// short distance parameters        : ${params.short_dist}
-// pre-computed alignments		 : ${params.prevaln}
-// alignment number		 : ${params.alignmentnum}
-// orthogroup number		 : ${params.orthogroupnum}
-// extraexons (e.g. from VastDB)    : ${params.extraexons}
-// bona fide orthologous exon pairs  : ${params.bonafide_pairs}
-// orthopairs                       : ${params.orthopairs}
-// output (output folder)           : ${params.output}
-// email for notification           : ${params.email}
-//
-// INFORMATION ABOUT OPTIONS:
-// The long, medium, short distance cut-offs are in the format: "int_num;ex_seq;ex_len;prot_sim".
-// Only exon matches respecting all cut-offs are considered homologous.
-// - int_num (0,1,2): Number of surrounding intron positions required to be conserved.
-// - ex_seq (from 0 to 1): Minimum sequence similarity % between a
-//      pair of homologous exons and their corresponding upstream and
-//      downstream exons.
-// - ex_len (from 0 to 1): Maximum size difference between two homologous exons
-//      (as a fraction of either exon).
-// - prot_sim (from 0 to 1): Minimum sequence similarity over the entire pairwise alignment
-//      for a pair of protein isoforms to be considered for comparison.
-//
-// See online README at https://github.com/biocorecrg/ExOrthist for further information about the options.
-// """
-//
-// if (params.help) {
-//     log.info """ExOrthist v2.0.0"""
-//     log.info """ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales.\n"""
-//     exit 1
-// }
-
-// Load the schema
-params = new nextflow.script.ScriptBinding().getParams()
-def schema = new File("$projectDir/nextflow_schema.json")
-if (schema.exists()) {
-    params = new groovy.json.JsonSlurper().parse(schema).properties.params
+log.info """
+
+╔╦╗┬ ┬┌─┐  ╔═╗─┐ ┬╔═╗┬─┐┌┬┐┬ ┬┬┌─┐┌┬┐
+ ║ ├─┤├┤   ║╣ ┌┴┬┘║ ║├┬┘ │ ├─┤│└─┐ │
+ ╩ ┴ ┴└─┘  ╚═╝┴ └─╚═╝┴└─ ┴ ┴ ┴┴└─┘ ┴
+
+==============================================================================
+annotations (GTF files)          : ${params.annotations}
+genomes (fasta files)            : ${params.genomes}
+cluster file (txt files)         : ${params.cluster}
+pairwise evo distances           : ${params.evodists}
+long distance parameters         : ${params.long_dist}
+medium distance parameters       : ${params.medium_dist}
+short distance parameters        : ${params.short_dist}
+pre-computed alignments		 : ${params.prevaln}
+alignment number		 : ${params.alignmentnum}
+orthogroup number		 : ${params.orthogroupnum}
+extraexons (e.g. from VastDB)    : ${params.extraexons}
+bona fide orthologous exon pairs  : ${params.bonafide_pairs}
+orthopairs                       : ${params.orthopairs}
+output (output folder)           : ${params.output}
+email for notification           : ${params.email}
+
+INFORMATION ABOUT OPTIONS:
+The long, medium, short distance cut-offs are in the format: "int_num;ex_seq;ex_len;prot_sim".
+Only exon matches respecting all cut-offs are considered homologous.
+- int_num (0,1,2): Number of surrounding intron positions required to be conserved.
+- ex_seq (from 0 to 1): Minimum sequence similarity % between a
+     pair of homologous exons and their corresponding upstream and
+     downstream exons.
+- ex_len (from 0 to 1): Maximum size difference between two homologous exons
+     (as a fraction of either exon).
+- prot_sim (from 0 to 1): Minimum sequence similarity over the entire pairwise alignment
+     for a pair of protein isoforms to be considered for comparison.
+
+See online README at https://github.com/biocorecrg/ExOrthist for further information about the options.
+"""
+
+if (params.help) {
+    log.info """ExOrthist v2.0.0"""
+    log.info """ExOrthist is a Nextflow-based pipeline to obtain groups of exon orthologous at all evolutionary timescales.\n"""
+    exit 1
 }
-
-
 if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)"
 
-
-
 if( !workflow.resume ) {
     println "Removing the output folder"
-	new File("${params.output}").delete()
+	  new File("${params.output}").delete()
 }
 
-clusterfile       = file(params.cluster)
+// clusterfile       = file(params.cluster)
 outputQC          = "${params.output}/QC"
 blosumfile        = file("${baseDir}/files/blosum62.txt")
-evodisfile	  = file(params.evodists)
+// evodisfile	  = file(params.evodists)
 
 if ( !blosumfile.exists() ) exit 1, "Missing blosum file: ${blosumfile}!"
-if ( !clusterfile.exists() ) exit 1, "Missing clusterfile file: ${clusterfile}!"
-if ( !evodisfile.exists() ) exit 1, "Missing evodists file: ${evodisfile}!"
+// if ( !clusterfile.exists() ) exit 1, "Missing clusterfile file: ${clusterfile}!"
+// if ( !evodisfile.exists() ) exit 1, "Missing evodists file: ${evodisfile}!"
+//
+
+LOCAL_MODULES='./modules/local/exorthist'
 
+include { CHECK_INPUT } from "${LOCAL_MODULES}/check_input.nf"
 
 /*
  * Validate input and print log file
  */
 //Prepare input channels
-Channel.fromPath(params.annotations).collect().set{gtfs}
-Channel.fromPath(params.genomes).collect().set{fastas}
-Channel.fromFilePairs(params.annotations, size: 1).flatten().collate(2).map{[it[1].getName().toString().split(it[0].toString())[1]]}.unique().flatten().set{gtfs_suffix}
-Channel.fromFilePairs(params.genomes, size: 1).flatten().collate(2).map{[it[1].getName().toString().split(it[0].toString())[1]]}.unique().flatten().set{fastas_suffix}
-long_dist = params.long_dist
-medium_dist = params.medium_dist
-short_dist = params.short_dist
-
-process check_input {
-	publishDir "${params.output}", mode: 'copy'
-	input:
-	file(evodisfile)
-	file(clusterfile)
-	file("GTF/*") from gtfs
-        file("FASTAS/*") from fastas
-        val(gtfs_suffix)
-        val(fastas_suffix)
-	long_dist
-	medium_dist
-	short_dist
-	output:
-	file("run_info.log")
-	script:
-	"""
-	echo "Evolutionary distance parameters:" > run_info.log
-	echo "long distance: ${long_dist}" >> run_info.log
-	echo "medium distance: ${medium_dist}" >> run_info.log
-	echo -e "short distance: ${short_dist}\n" >> run_info.log
-	echo "Pairwise evolutionary distances:" >> run_info.log
-	cat ${evodisfile} >> run_info.log
-	echo -e "\nInput files parsing:" >> run_info.log
-	A0_check_input.pl -e ${evodisfile} -g GTF -gs ${gtfs_suffix} -f FASTAS -fs ${fastas_suffix} -c ${clusterfile} >> run_info.log
-	"""
-}
-
-
-/*
- * Create channels for sequences data
- */
-Channel
-    .fromFilePairs( params.genomes, size: 1)
-    .ifEmpty { error "Cannot find any genome matching: ${params.genomes}" }
-    .set {genomes}
-
-Channel
-    .fromFilePairs( params.annotations, size: 1)
-    .ifEmpty { error "Cannot find any annotation matching: ${params.annotations}" }
-    .set {annotations}
-
-
-/*
- * Create channels for optional extra exons
- */
-if (params.extraexons) {
-	Channel
-   	 .fromFilePairs( params.extraexons, size: 1)
-   	 .ifEmpty { print "Extra exons not found!" }
-   	 .set {extraexons}
-	genomes.join(annotations).into{data_to_annotation_raw; pipe_data}
-	data_to_annotation_raw.join(extraexons, remainder: true).set{data_to_annotation}
-} else {
-    genomes.join(annotations).into{pipe_data; data_to_annotation}
-}
-
-
-/*
- * Generate annotations
- */
-if (params.extraexons) {
-	process generate_annotations_with_extra_exons {
-		tag { genomeid }
-		label 'big_cpus'
-		publishDir "${params.output}/", mode: 'copy'
-
-		input:
-		set genomeid, file(genome), file(annotation), file(extraexons) from data_to_annotation
-
-		output:
-		set val(genomeid), file (genomeid) into idfolders
-
-		script:
-		def extrapars = ""
-		if (extraexons.size()>0) { extrapars = " -add_exons ${extraexons}" }
-		"""
-		A1_generate_annotations.pl -GTF ${annotation} -G ${genome} -sp ${genomeid} ${extrapars}
-		"""
-	}
-} else {
-	process generate_annotations {
-		tag { genomeid }
-		publishDir "${params.output}/", mode: 'copy'
-
-		input:
-		set genomeid, file(genome), file(annotation) from data_to_annotation
-
-		output:
-		set val(genomeid), file (genomeid) into idfolders
-
-		script:
-		"""
-		A1_generate_annotations.pl -GTF ${annotation} -G ${genome} -sp ${genomeid}
-		"""
-	}
-}
-
-
-
-
-/*
- * split cluster file
- */
-//Copy the gene cluster file to output to use for the exint_plotter and compare_exon_sets modules
-process split_clusters_by_species_pairs {
-    tag { clusterfile }
-    publishDir "${params.output}/", mode: 'copy', pattern: "gene_cluster_file.gz"
-
-    input:
-    file(clusterfile)
-
-    output:
-    file "*.cls.tab"  into cls_tab_files, cls_tab_file_4_clustering
-    file("gene_cluster_file.gz")
-
-	script:
-	"""
-   if [ `echo ${clusterfile} | grep ".gz"` ]; then
-       zcat ${clusterfile} > gene_cluster_file
-       A2_split_clusters_by_species_pairs.pl -f gene_cluster_file
-       gzip gene_cluster_file
-       #rm cluster_file
-    else
-       cat ${clusterfile} > gene_cluster_file
-       #A2_split_clusters_by_species_pairs.pl -f ${clusterfile}
-       A2_split_clusters_by_species_pairs.pl -f gene_cluster_file
-       gzip gene_cluster_file
-    fi
-	"""
-}
-
-idfolders
-  .toList().map{ [it, it] .combinations().findAll{ a, b -> a[0] < b[0]} }
-  .flatMap()
-  .map { ["${it[0][0]}-${it[1][0]}".toString(), it[0][1], it[1][1]] }
-  .into{cluster_2_split; anno_2_score_ex_int; species_to_recluster_genes; pairs_4_evodists; pairs_4_EXs_to_realign}
-
-
-
-/*
- * split clusters
-*/
-
-process split_clusters_in_chunks {
-    tag { id_comb }
-
-    input:
-    file(cls_tab_files).collect()
-    set id_comb, file(idfolder_A), file(idfolder_B) from cluster_2_split
-
-    output:
-    set file(idfolder_A), file(idfolder_B), file("${idfolder_A}_${idfolder_B}/*.cls.tab-part_*") into cls_files_2_align
-
-	script:
-	"""
-		A3_split_clusters_in_chunks.pl --sp1 ${idfolder_A} --sp2 ${idfolder_B} --expath ./ --project_dir ./ --N_split ${params.alignmentnum} --gene_cluster ${id_comb}.cls.tab
-	"""
-}
-
-cls_files_2_align.transpose().map{[it[0].getFileName().toString()+"-"+it[1].getFileName().toString(), it[0], it[1], it[2]]}.set{cls_files_2_align_t}
-
-//Create a channel for the evo distances
-Channel
-    .fromPath("${params.evodists}")
-    .splitText()
-    .map{"${it}".trim().split("\t")}.map{[it[0]+"-"+it[1], it[2]]}.set{sp1_sp2_dist}
-
-Channel
-    .fromPath("${params.evodists}")
-    .splitText()
-    .map{"${it}".trim().split("\t")}.map{[it[1]+"-"+it[0], it[2]]}.set{sp2_sp1_dist}
-
-sp1_sp2_dist.concat(sp2_sp1_dist).set{species_pairs_dist}
-//Only the species pairs with a common index will be kept
-pairs_4_evodists.join(species_pairs_dist).map{[it[0], it[3]]}.into{dist_ranges_ch; dist_ranges_ch1; dist_ranges_ch2}
-
-
-/*
- * Align pairs
- */
-//the last argument is the protein similarity alignment.
-//if a prevaln folder is provided, the protein alignments present in each species pair subfolder will not be repeated.
-
-cls_files_2_align_t.groupTuple().join(dist_ranges_ch1).transpose().set{alignment_input}
-
-process parse_IPA_prot_aln {
-    tag { "${cls_part_file}" }
-    label 'big_cpus'
-
-    input:
-    file(blosumfile)
-    set combid, file(sp1), file(sp2), file(cls_part_file), val(dist_range) from alignment_input
-
-    output:
-	set val("${sp1}-${sp2}"), path("${sp1}-${sp2}-*") into aligned_subclusters_4_splitting //05/03/21
-	file("${sp1}-${sp2}_EXs_to_split_part_*.txt") into EXs_to_split //05/03/21
-
-	script:
-    def prev_alignments = ""
-    if (params.prevaln) {prev_alignments = "${params.prevaln}"}
-
-    def cls_parts = "${cls_part_file}".split("_")
-    if (dist_range == "long")
-	dist_range_par = "${params.long_dist}".split(",")
-    if (dist_range == "medium")
-	dist_range_par = "${params.medium_dist}".split(",")
-    if (dist_range == "short")
-	dist_range_par = "${params.short_dist}".split(",")
-
-	"""
-		B1_parse_IPA_prot_aln.pl ${sp1} ${sp2} ${cls_part_file} \
-${sp1}/${sp1}_annot_exons_prot_ids.txt ${sp2}/${sp2}_annot_exons_prot_ids.txt \
-${sp1}/${sp1}_protein_ids_exons_pos.txt ${sp2}/${sp2}_protein_ids_exons_pos.txt \
-${sp1}/${sp1}_protein_ids_intron_pos_CDS.txt ${sp2}/${sp2}_protein_ids_intron_pos_CDS.txt \
-${sp1}/${sp1}.exint ${sp2}/${sp2}.exint ${cls_parts[1]} ${blosumfile} ${sp1}-${sp2}-${cls_parts[1]} ${dist_range_par[3]} ${task.cpus} ${prev_alignments}
-	"""
-}
-
-//Collapse EXs_to_split in batches of 500 files
-EXs_to_split.toSortedList().flatten().buffer(size : 500, remainder: true).set{EXs_to_split_batches}
-
-
-/*
- * Split exons pairs to realign
- */
-
-process split_EX_pairs_to_realign {
-
-    input:
-    file("*") from EXs_to_split_batches
-
-    output:
-    file("*EXs_to_realign_part_*") into EXs_to_realign_batches
-
-    script:
-    """
-	for file in \$(ls *); do B2_split_EX_pairs_to_realign.py -i \${file} -n ${params.alignmentnum}; done
-    """
-}
-
-//Flatten the results from the previous batch run and combine with sp1 and sp2 information, using sp1-sp2 as key.
-EXs_to_realign_batches.flatten().map{[it.getName().toString().split("_")[0],it]}.groupTuple()
-.join(pairs_4_EXs_to_realign).transpose().set{EXs_to_realign}
-
-/*
- * Realign exons pairs (with multiple hits)
- */
-
-process realign_EX_pairs {
-    label 'incr_time_cpus'
-
-    input:
-    file(blosumfile)
-    set val(comp_id), file(EXs_to_realign), file(sp1), file(sp2) from EXs_to_realign //05/03/21
-
-    output:
-    set val(comp_id), file("realigned_*") into realigned_exons_4_merge //05/03/21
-
-    script:
-    """
-	B3_realign_EX_pairs.pl ${sp1} ${sp2} ${EXs_to_realign} \
-	${sp1}/${sp1}.exint ${sp2}/${sp2}.exint 1 realigned_${EXs_to_realign} \
-	${sp1}_${sp2} ${blosumfile} ${task.cpus}
-    """
-}
-
-//Combine all the aln_info with the realigned_exon_info for each species pair
-aligned_subclusters_4_splitting.groupTuple().join(realigned_exons_4_merge.groupTuple()).set{data_4_merge}
-
-
-/*
- * Merge alignments information
- */
-
-process merge_PROT_EX_INT_aln_info {
-    tag { "${comp_id}" }
-    label 'incr_time_cpus'
-
-    stageInMode = 'copy'
-    //this matches all_PROT_aln_features.txt, all_EX_aln_features.txt, all_INT_aln_features.txt, Exint_Alignments.aln.gz
-    publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/all_*_aln_features.txt"
-    publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/EXINT_aln.gz"
-
-    input:
-    set comp_id, file("FOLDERS_*"), file("*") from data_4_merge //05/03/21
-
-    output:
-    set val(comp_id), file("${comp_id}/") into folder_jscores
-    file("${comp_id}/all_*_aln_features.txt")
-    file("${comp_id}/EXINT_aln.gz")
-	script:
-	"""
-	    mkdir ${comp_id}
-	    mv FOLDERS_*/* ${comp_id}/
-	    mv realigned_* ${comp_id}/
-
-    	B4_merge_PROT_EX_INT_aln_info.pl ${comp_id}
-	"""
-}
-
-folder_jscores.join(anno_2_score_ex_int).map{
-   [it[0], it[1..-1] ]
-}.set{data_to_score}
-
-
-/*
- * Score EX matches from aln info
- */
-
-process score_EX_matches {
-    tag { "${comp_id}" }
-    label('big_mem_retry')
-    //I need to modify the name so that it has the species pair in the output.
-    storeDir "${params.output}/${comp_id}"
-
-    input:
-    set val(comp_id), file("*") from data_to_score
-
-    output:
-    file("all_PROT_EX_INT_aln_features_*")
-    set val(comp_id), file("all_scored_EX_matches.txt") into all_scores_to_filt
-
-	script:
-    def species = comp_id.split("-")
-	"""
-    B5_format_aln_info_by_best_isoform_match.pl ${species[0]} ${species[1]} \
-    ${comp_id}/all_PROT_aln_features.txt ${comp_id}/all_EX_aln_features.txt ${comp_id}/all_INT_aln_features.txt \
-    ${species[0]}/${species[0]}.exint ${species[1]}/${species[1]}.exint \
-    ${species[0]}/${species[0]}_protein_ids_intron_pos_CDS.txt ${species[1]}/${species[1]}_protein_ids_intron_pos_CDS.txt \
-    all_PROT_EX_INT_aln_features_${comp_id}.txt;
-    C1_score_EX_matches.pl all_PROT_EX_INT_aln_features_${comp_id}.txt .
-    """
-}
-
-
-/*
- * Filter the best matches above score cutoffs by target gene.
- */
-
-process filter_and_select_best_EX_matches_by_targetgene {
-    tag { "${comp_id}" }
-    publishDir "${params.output}", mode: "copy", pattern: "best_scored_EX_matches_by_targetgene.txt", saveAs: { filename -> "${comp_id}/foo_$filename" }
-
-    input:
-    set val(comp_id), file(all_scores), val(dist_range) from all_scores_to_filt.join(dist_ranges_ch)
-
-    output:
-    file("*.tab") into filterscore_per_joining
-    file("best_scored_EX_matches_by_targetgene.txt")
-
-    script:
-    def species = comp_id.split("-")
-    if (dist_range == "long")
-	dist_range_par = "${params.long_dist}".split(",")
-    if (dist_range == "medium")
-	dist_range_par = "${params.medium_dist}".split(",")
-    if (dist_range == "short")
-	dist_range_par = "${params.short_dist}".split(",")
-    """
-    C2_filter_and_select_best_EX_matches_by_targetgene.pl -b ${all_scores} -sps ${species[0]},${species[1]} -int ${dist_range_par[0]} -id ${dist_range_par[1]} -max_size ${dist_range_par[2]}
-    """
-}
-
-/*
- * join filtered scored EX matches
- */
-process join_filtered_EX_matches {
-    publishDir "${params.output}/", mode: 'copy'
-
-    input:
-    file ("filtered_best_scored-*") from filterscore_per_joining.collect()
-
-    output:
-    file("filtered_best_scored_EX_matches_by_targetgene.tab") into filtered_all_scores
-
-	script:
-	"""
-    echo "GeneID_sp1\tExon_coords_sp1\tGeneID_sp2\tExon_coords_sp2\tSp1\tSp2" > filtered_best_scored_EX_matches_by_targetgene.tab;
-    for file in \$(ls filtered_best_scored-*); do cat \$file | tail -n+2 >> filtered_best_scored_EX_matches_by_targetgene.tab; done
-    """
-}
-
-/*
- * Removing matches from overlapping exons
- */
-process collapse_overlapping_matches {
-    publishDir "${params.output}/", mode: "copy"
-    input:
-    file(scores) from filtered_all_scores
-
-    output:
-    file("filtered_best_scored_EX_matches_by_targetgene-NoOverlap.tab") into (score_exon_hits_pairs, exon_pairs_for_reclustering)
-    file("overlapping_EXs_by_species.tab")
-
-	script:
-	bonafide = ""
-	if (params.bonafide_pairs != "") {
-		bonafide = file(params.bonafide_pairs)
-		if ( !bonafide.exists() ) exit 1, "Missing file with bonafide pairs: ${bonafide}!"
-
-	}
-	"""
-    C3_count_matches_by_EX.pl ${scores} EX_matches_count_by_species.tab ${bonafide}
-    C4_get_overlapping_EXs.pl -i EX_matches_count_by_species.tab -o overlapping_EXs_by_species.tab
-    C5_collapse_overlapping_matches.pl overlapping_EXs_by_species.tab ${scores} filtered_best_scored_EX_matches_by_targetgene-NoOverlap.tab ${bonafide}
-    """
-}
-
-/*
-* Split the file of exon pairs
-*/
-clusterfile = file(params.cluster)
-process format_EX_clusters_input {
-    input:
-    file(score_exon_hits_pairs)
-    file(clusterfile)
-
-    output:
-    file("PART_*-cluster_input.tab") into cluster_parts
-
-	script:
-	"""
-   if [ `echo ${clusterfile} | grep ".gz"` ]; then
-       zcat ${clusterfile} > cluster_file
-       D1_format_EX_clusters_input.pl cluster_file ${score_exon_hits_pairs} ${params.orthogroupnum}
-       rm cluster_file
-    else
-       D1_format_EX_clusters_input.pl ${clusterfile} ${score_exon_hits_pairs} ${params.orthogroupnum}
-    fi
-	"""
-}
-
-/*
-* Split the file of exon pairs
-*/
-//Unclustered are the exons ending up in single-exon clusters
-process cluster_EXs {
-
-    input:
-    file(cluster_part) from cluster_parts.flatten()
-
-    output:
-    file("EXs_${cluster_part}") into ex_clusters
-    file("unclustered_EXs_${cluster_part}") into unclustered_exs
-
-	script:
-	"""
-    D2_cluster_EXs.R ${cluster_part} EXs_${cluster_part} unclustered_EXs_${cluster_part}
-    """
-}
-
-/*
-* Final exon clusters
-*/
-process format_EX_clusters_output {
-    publishDir "${params.output}/", mode: 'copy'
-
-    input:
-    file("*") from ex_clusters.collect()
-    file("*") from unclustered_exs.collect()
-
-    output:
-    file("EX_clusters.tab") into exon_cluster_for_reclustering
-    file("EX_clusters_info.tab.gz")
-    file("unclustered_EXs.txt")
-
-	script:
-	"""
-	D3_format_EX_clusters_output.pl
-	"""
-}
-
-/*
-* Re-clustering of genes
-*/
-
-process recluster_genes_by_species_pair {
-    publishDir "${params.output}/reclustering", mode: 'copy'
-    tag { "${combid}" }
-
-    when:
-    params.orthopairs != ""
-
-    input:
-    set combid, file(folderA), file(folderB) from species_to_recluster_genes
-    file(clusterfile)
-    //file(orthopairs) from orthopairs_file
-
-    output:
-    set combid, file("reclustered_genes_*.tab") into recl_genes_for_rec_exons
-
-	script:
-	def species = "${combid}".split("-")
-	def orthopairs = file("${params.orthopairs}")
-	"""
- 	D3.1_recluster_genes_by_species_pair.py -og ${clusterfile} -op ${orthopairs} --species1 ${species[0]} --species2 ${species[1]} -out reclustered_genes_${combid}.tab
-    	"""
-}
-
-
-/*
-* Re-clustering of exons
-*/
-
-process recluster_EXs_by_species_pair {
-    publishDir "${params.output}/reclustering", mode: 'copy'
-    tag { "${combid}" }
-
-	when:
-	params.orthopairs != ""
-
-    input:
-    set combid, file(recl_genes) from recl_genes_for_rec_exons
-    file(exon_clusters) from exon_cluster_for_reclustering
-    file(exon_pairs) from exon_pairs_for_reclustering
-
-    output:
-    file("reclustered_EXs_*.tab")
-
-	script:
-	def combid1 = combid.replace("-", "_")
-	def species = "${combid1}".split("-")
-	"""
-	D3.2_recluster_EXs_by_species_pair.py -ep ${exon_pairs} -rg ${recl_genes} -ec ${exon_clusters} -sp1 ${species[0]} -sp2 ${species[1]} -out reclustered_EXs_${combid1}.tab
-    	"""
-}
-
-/*
- * Mail notification
- */
-
-if (params.email == "yourmail@yourdomain" || params.email == "") {
-    log.info 'Skipping the email\n'
-}
-else {
-    log.info "Sending the email to ${params.email}\n"
-
-    workflow.onComplete {
-
-    def msg = """\
-        Pipeline execution summary
-        ---------------------------
-        Completed at: ${workflow.complete}
-        Duration    : ${workflow.duration}
-        Success     : ${workflow.success}
-        workDir     : ${workflow.workDir}
-        exit status : ${workflow.exitStatus}
-        Error report: ${workflow.errorReport ?: '-'}
-        """
-        .stripIndent()
-
-        sendMail(to: params.email, subject: "VectorQC execution", body: msg,  attach: "${outputMultiQC}/multiqc_report.html")
-    }
-}
-
-workflow.onComplete {
-    println "--- Pipeline BIOCORE@CRG ExOrthist ---"
-    println "Started at  $workflow.start"
-    println "Finished at $workflow.complete"
-    println "Time elapsed: $workflow.duration"
-    println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+workflow {
+    gtfs = Channel.fromPath(params.annotations).collect()
+    fastas = Channel.fromPath(params.genomes).collect()
+
+    // TODO: Review this in an easier way
+    gtfs_suffix = Channel.fromFilePairs(params.annotations, size: 1).flatten().collate(2).map{[it[1].getName().toString().split(it[0].toString())[1]]}.unique().flatten()
+    fastas_suffix = Channel.fromFilePairs(params.genomes, size: 1).flatten().collate(2).map{[it[1].getName().toString().split(it[0].toString())[1]]}.unique().flatten()
+
+   // Print contents of each channel
+    gtfs.view { "GTF file: $it" }
+    fastas.view { "FASTA file: $it" }
+    gtfs_suffix.view { "GTF suffix: $it" }
+    fastas_suffix.view { "FASTA suffix: $it" }
+
+    evodists_ch = Channel.fromPath(params.evodists)
+    clusterfile_ch = Channel.fromPath(params.cluster)
+
+    CHECK_INPUT(
+        evodists_ch,
+        clusterfile_ch,
+        gtfs,
+        fastas,
+        gtfs_suffix,
+        fastas_suffix,
+        params.long_dist,
+        params.medium_dist,
+        params.short_dist
+    )
+
+    // You can now use the output in subsequent processes
+    CHECK_INPUT.out.run_info.view()
 }
 
+// /*
+//  * Create channels for sequences data
+//  */
+// Channel
+//     .fromFilePairs( params.genomes, size: 1)
+//     .ifEmpty { error "Cannot find any genome matching: ${params.genomes}" }
+//     .set {genomes}
+//
+// Channel
+//     .fromFilePairs( params.annotations, size: 1)
+//     .ifEmpty { error "Cannot find any annotation matching: ${params.annotations}" }
+//     .set {annotations}
+//
+//
+// /*
+//  * Create channels for optional extra exons
+//  */
+// if (params.extraexons) {
+// 	Channel
+//    	 .fromFilePairs( params.extraexons, size: 1)
+//    	 .ifEmpty { print "Extra exons not found!" }
+//    	 .set {extraexons}
+// 	genomes.join(annotations).into{data_to_annotation_raw; pipe_data}
+// 	data_to_annotation_raw.join(extraexons, remainder: true).set{data_to_annotation}
+// } else {
+//     genomes.join(annotations).into{pipe_data; data_to_annotation}
+// }
+//
+//
+// /*
+//  * Generate annotations
+//  */
+// if (params.extraexons) {
+// 	process generate_annotations_with_extra_exons {
+// 		tag { genomeid }
+// 		label 'big_cpus'
+// 		publishDir "${params.output}/", mode: 'copy'
+//
+// 		input:
+// 		set genomeid, file(genome), file(annotation), file(extraexons) from data_to_annotation
+//
+// 		output:
+// 		set val(genomeid), file (genomeid) into idfolders
+//
+// 		script:
+// 		def extrapars = ""
+// 		if (extraexons.size()>0) { extrapars = " -add_exons ${extraexons}" }
+// 		"""
+// 		A1_generate_annotations.pl -GTF ${annotation} -G ${genome} -sp ${genomeid} ${extrapars}
+// 		"""
+// 	}
+// } else {
+// 	process generate_annotations {
+// 		tag { genomeid }
+// 		publishDir "${params.output}/", mode: 'copy'
+//
+// 		input:
+// 		set genomeid, file(genome), file(annotation) from data_to_annotation
+//
+// 		output:
+// 		set val(genomeid), file (genomeid) into idfolders
+//
+// 		script:
+// 		"""
+// 		A1_generate_annotations.pl -GTF ${annotation} -G ${genome} -sp ${genomeid}
+// 		"""
+// 	}
+// }
+//
+//
+//
+//
+// /*
+//  * split cluster file
+//  */
+// //Copy the gene cluster file to output to use for the exint_plotter and compare_exon_sets modules
+// process split_clusters_by_species_pairs {
+//     tag { clusterfile }
+//     publishDir "${params.output}/", mode: 'copy', pattern: "gene_cluster_file.gz"
+//
+//     input:
+//     file(clusterfile)
+//
+//     output:
+//     file "*.cls.tab"  into cls_tab_files, cls_tab_file_4_clustering
+//     file("gene_cluster_file.gz")
+//
+// 	script:
+// 	"""
+//    if [ `echo ${clusterfile} | grep ".gz"` ]; then
+//        zcat ${clusterfile} > gene_cluster_file
+//        A2_split_clusters_by_species_pairs.pl -f gene_cluster_file
+//        gzip gene_cluster_file
+//        #rm cluster_file
+//     else
+//        cat ${clusterfile} > gene_cluster_file
+//        #A2_split_clusters_by_species_pairs.pl -f ${clusterfile}
+//        A2_split_clusters_by_species_pairs.pl -f gene_cluster_file
+//        gzip gene_cluster_file
+//     fi
+// 	"""
+// }
+//
+// idfolders
+//   .toList().map{ [it, it] .combinations().findAll{ a, b -> a[0] < b[0]} }
+//   .flatMap()
+//   .map { ["${it[0][0]}-${it[1][0]}".toString(), it[0][1], it[1][1]] }
+//   .into{cluster_2_split; anno_2_score_ex_int; species_to_recluster_genes; pairs_4_evodists; pairs_4_EXs_to_realign}
+//
+//
+//
+// /*
+//  * split clusters
+// */
+//
+// process split_clusters_in_chunks {
+//     tag { id_comb }
+//
+//     input:
+//     file(cls_tab_files).collect()
+//     set id_comb, file(idfolder_A), file(idfolder_B) from cluster_2_split
+//
+//     output:
+//     set file(idfolder_A), file(idfolder_B), file("${idfolder_A}_${idfolder_B}/*.cls.tab-part_*") into cls_files_2_align
+//
+// 	script:
+// 	"""
+// 		A3_split_clusters_in_chunks.pl --sp1 ${idfolder_A} --sp2 ${idfolder_B} --expath ./ --project_dir ./ --N_split ${params.alignmentnum} --gene_cluster ${id_comb}.cls.tab
+// 	"""
+// }
+//
+// cls_files_2_align.transpose().map{[it[0].getFileName().toString()+"-"+it[1].getFileName().toString(), it[0], it[1], it[2]]}.set{cls_files_2_align_t}
+//
+// //Create a channel for the evo distances
+// Channel
+//     .fromPath("${params.evodists}")
+//     .splitText()
+//     .map{"${it}".trim().split("\t")}.map{[it[0]+"-"+it[1], it[2]]}.set{sp1_sp2_dist}
+//
+// Channel
+//     .fromPath("${params.evodists}")
+//     .splitText()
+//     .map{"${it}".trim().split("\t")}.map{[it[1]+"-"+it[0], it[2]]}.set{sp2_sp1_dist}
+//
+// sp1_sp2_dist.concat(sp2_sp1_dist).set{species_pairs_dist}
+// //Only the species pairs with a common index will be kept
+// pairs_4_evodists.join(species_pairs_dist).map{[it[0], it[3]]}.into{dist_ranges_ch; dist_ranges_ch1; dist_ranges_ch2}
+//
+//
+// /*
+//  * Align pairs
+//  */
+// //the last argument is the protein similarity alignment.
+// //if a prevaln folder is provided, the protein alignments present in each species pair subfolder will not be repeated.
+//
+// cls_files_2_align_t.groupTuple().join(dist_ranges_ch1).transpose().set{alignment_input}
+//
+// process parse_IPA_prot_aln {
+//     tag { "${cls_part_file}" }
+//     label 'big_cpus'
+//
+//     input:
+//     file(blosumfile)
+//     set combid, file(sp1), file(sp2), file(cls_part_file), val(dist_range) from alignment_input
+//
+//     output:
+// 	set val("${sp1}-${sp2}"), path("${sp1}-${sp2}-*") into aligned_subclusters_4_splitting //05/03/21
+// 	file("${sp1}-${sp2}_EXs_to_split_part_*.txt") into EXs_to_split //05/03/21
+//
+// 	script:
+//     def prev_alignments = ""
+//     if (params.prevaln) {prev_alignments = "${params.prevaln}"}
+//
+//     def cls_parts = "${cls_part_file}".split("_")
+//     if (dist_range == "long")
+// 	dist_range_par = "${params.long_dist}".split(",")
+//     if (dist_range == "medium")
+// 	dist_range_par = "${params.medium_dist}".split(",")
+//     if (dist_range == "short")
+// 	dist_range_par = "${params.short_dist}".split(",")
+//
+// 	"""
+// 		B1_parse_IPA_prot_aln.pl ${sp1} ${sp2} ${cls_part_file} \
+// ${sp1}/${sp1}_annot_exons_prot_ids.txt ${sp2}/${sp2}_annot_exons_prot_ids.txt \
+// ${sp1}/${sp1}_protein_ids_exons_pos.txt ${sp2}/${sp2}_protein_ids_exons_pos.txt \
+// ${sp1}/${sp1}_protein_ids_intron_pos_CDS.txt ${sp2}/${sp2}_protein_ids_intron_pos_CDS.txt \
+// ${sp1}/${sp1}.exint ${sp2}/${sp2}.exint ${cls_parts[1]} ${blosumfile} ${sp1}-${sp2}-${cls_parts[1]} ${dist_range_par[3]} ${task.cpus} ${prev_alignments}
+// 	"""
+// }
+//
+// //Collapse EXs_to_split in batches of 500 files
+// EXs_to_split.toSortedList().flatten().buffer(size : 500, remainder: true).set{EXs_to_split_batches}
+//
+//
+// /*
+//  * Split exons pairs to realign
+//  */
+//
+// process split_EX_pairs_to_realign {
+//
+//     input:
+//     file("*") from EXs_to_split_batches
+//
+//     output:
+//     file("*EXs_to_realign_part_*") into EXs_to_realign_batches
+//
+//     script:
+//     """
+// 	for file in \$(ls *); do B2_split_EX_pairs_to_realign.py -i \${file} -n ${params.alignmentnum}; done
+//     """
+// }
+//
+// //Flatten the results from the previous batch run and combine with sp1 and sp2 information, using sp1-sp2 as key.
+// EXs_to_realign_batches.flatten().map{[it.getName().toString().split("_")[0],it]}.groupTuple()
+// .join(pairs_4_EXs_to_realign).transpose().set{EXs_to_realign}
+//
+// /*
+//  * Realign exons pairs (with multiple hits)
+//  */
+//
+// process realign_EX_pairs {
+//     label 'incr_time_cpus'
+//
+//     input:
+//     file(blosumfile)
+//     set val(comp_id), file(EXs_to_realign), file(sp1), file(sp2) from EXs_to_realign //05/03/21
+//
+//     output:
+//     set val(comp_id), file("realigned_*") into realigned_exons_4_merge //05/03/21
+//
+//     script:
+//     """
+// 	B3_realign_EX_pairs.pl ${sp1} ${sp2} ${EXs_to_realign} \
+// 	${sp1}/${sp1}.exint ${sp2}/${sp2}.exint 1 realigned_${EXs_to_realign} \
+// 	${sp1}_${sp2} ${blosumfile} ${task.cpus}
+//     """
+// }
+//
+// //Combine all the aln_info with the realigned_exon_info for each species pair
+// aligned_subclusters_4_splitting.groupTuple().join(realigned_exons_4_merge.groupTuple()).set{data_4_merge}
+//
+//
+// /*
+//  * Merge alignments information
+//  */
+//
+// process merge_PROT_EX_INT_aln_info {
+//     tag { "${comp_id}" }
+//     label 'incr_time_cpus'
+//
+//     stageInMode = 'copy'
+//     //this matches all_PROT_aln_features.txt, all_EX_aln_features.txt, all_INT_aln_features.txt, Exint_Alignments.aln.gz
+//     publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/all_*_aln_features.txt"
+//     publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/EXINT_aln.gz"
+//
+//     input:
+//     set comp_id, file("FOLDERS_*"), file("*") from data_4_merge //05/03/21
+//
+//     output:
+//     set val(comp_id), file("${comp_id}/") into folder_jscores
+//     file("${comp_id}/all_*_aln_features.txt")
+//     file("${comp_id}/EXINT_aln.gz")
+// 	script:
+// 	"""
+// 	    mkdir ${comp_id}
+// 	    mv FOLDERS_*/* ${comp_id}/
+// 	    mv realigned_* ${comp_id}/
+//
+//     	B4_merge_PROT_EX_INT_aln_info.pl ${comp_id}
+// 	"""
+// }
+//
+// folder_jscores.join(anno_2_score_ex_int).map{
+//    [it[0], it[1..-1] ]
+// }.set{data_to_score}
+//
+//
+// /*
+//  * Score EX matches from aln info
+//  */
+//
+// process score_EX_matches {
+//     tag { "${comp_id}" }
+//     label('big_mem_retry')
+//     //I need to modify the name so that it has the species pair in the output.
+//     storeDir "${params.output}/${comp_id}"
+//
+//     input:
+//     set val(comp_id), file("*") from data_to_score
+//
+//     output:
+//     file("all_PROT_EX_INT_aln_features_*")
+//     set val(comp_id), file("all_scored_EX_matches.txt") into all_scores_to_filt
+//
+// 	script:
+//     def species = comp_id.split("-")
+// 	"""
+//     B5_format_aln_info_by_best_isoform_match.pl ${species[0]} ${species[1]} \
+//     ${comp_id}/all_PROT_aln_features.txt ${comp_id}/all_EX_aln_features.txt ${comp_id}/all_INT_aln_features.txt \
+//     ${species[0]}/${species[0]}.exint ${species[1]}/${species[1]}.exint \
+//     ${species[0]}/${species[0]}_protein_ids_intron_pos_CDS.txt ${species[1]}/${species[1]}_protein_ids_intron_pos_CDS.txt \
+//     all_PROT_EX_INT_aln_features_${comp_id}.txt;
+//     C1_score_EX_matches.pl all_PROT_EX_INT_aln_features_${comp_id}.txt .
+//     """
+// }
+//
+//
+// /*
+//  * Filter the best matches above score cutoffs by target gene.
+//  */
+//
+// process filter_and_select_best_EX_matches_by_targetgene {
+//     tag { "${comp_id}" }
+//     publishDir "${params.output}", mode: "copy", pattern: "best_scored_EX_matches_by_targetgene.txt", saveAs: { filename -> "${comp_id}/foo_$filename" }
+//
+//     input:
+//     set val(comp_id), file(all_scores), val(dist_range) from all_scores_to_filt.join(dist_ranges_ch)
+//
+//     output:
+//     file("*.tab") into filterscore_per_joining
+//     file("best_scored_EX_matches_by_targetgene.txt")
+//
+//     script:
+//     def species = comp_id.split("-")
+//     if (dist_range == "long")
+// 	dist_range_par = "${params.long_dist}".split(",")
+//     if (dist_range == "medium")
+// 	dist_range_par = "${params.medium_dist}".split(",")
+//     if (dist_range == "short")
+// 	dist_range_par = "${params.short_dist}".split(",")
+//     """
+//     C2_filter_and_select_best_EX_matches_by_targetgene.pl -b ${all_scores} -sps ${species[0]},${species[1]} -int ${dist_range_par[0]} -id ${dist_range_par[1]} -max_size ${dist_range_par[2]}
+//     """
+// }
+//
+// /*
+//  * join filtered scored EX matches
+//  */
+// process join_filtered_EX_matches {
+//     publishDir "${params.output}/", mode: 'copy'
+//
+//     input:
+//     file ("filtered_best_scored-*") from filterscore_per_joining.collect()
+//
+//     output:
+//     file("filtered_best_scored_EX_matches_by_targetgene.tab") into filtered_all_scores
+//
+// 	script:
+// 	"""
+//     echo "GeneID_sp1\tExon_coords_sp1\tGeneID_sp2\tExon_coords_sp2\tSp1\tSp2" > filtered_best_scored_EX_matches_by_targetgene.tab;
+//     for file in \$(ls filtered_best_scored-*); do cat \$file | tail -n+2 >> filtered_best_scored_EX_matches_by_targetgene.tab; done
+//     """
+// }
+//
+// /*
+//  * Removing matches from overlapping exons
+//  */
+// process collapse_overlapping_matches {
+//     publishDir "${params.output}/", mode: "copy"
+//     input:
+//     file(scores) from filtered_all_scores
+//
+//     output:
+//     file("filtered_best_scored_EX_matches_by_targetgene-NoOverlap.tab") into (score_exon_hits_pairs, exon_pairs_for_reclustering)
+//     file("overlapping_EXs_by_species.tab")
+//
+// 	script:
+// 	bonafide = ""
+// 	if (params.bonafide_pairs != "") {
+// 		bonafide = file(params.bonafide_pairs)
+// 		if ( !bonafide.exists() ) exit 1, "Missing file with bonafide pairs: ${bonafide}!"
+//
+// 	}
+// 	"""
+//     C3_count_matches_by_EX.pl ${scores} EX_matches_count_by_species.tab ${bonafide}
+//     C4_get_overlapping_EXs.pl -i EX_matches_count_by_species.tab -o overlapping_EXs_by_species.tab
+//     C5_collapse_overlapping_matches.pl overlapping_EXs_by_species.tab ${scores} filtered_best_scored_EX_matches_by_targetgene-NoOverlap.tab ${bonafide}
+//     """
+// }
+//
+// /*
+// * Split the file of exon pairs
+// */
+// clusterfile = file(params.cluster)
+// process format_EX_clusters_input {
+//     input:
+//     file(score_exon_hits_pairs)
+//     file(clusterfile)
+//
+//     output:
+//     file("PART_*-cluster_input.tab") into cluster_parts
+//
+// 	script:
+// 	"""
+//    if [ `echo ${clusterfile} | grep ".gz"` ]; then
+//        zcat ${clusterfile} > cluster_file
+//        D1_format_EX_clusters_input.pl cluster_file ${score_exon_hits_pairs} ${params.orthogroupnum}
+//        rm cluster_file
+//     else
+//        D1_format_EX_clusters_input.pl ${clusterfile} ${score_exon_hits_pairs} ${params.orthogroupnum}
+//     fi
+// 	"""
+// }
+//
+// /*
+// * Split the file of exon pairs
+// */
+// //Unclustered are the exons ending up in single-exon clusters
+// process cluster_EXs {
+//
+//     input:
+//     file(cluster_part) from cluster_parts.flatten()
+//
+//     output:
+//     file("EXs_${cluster_part}") into ex_clusters
+//     file("unclustered_EXs_${cluster_part}") into unclustered_exs
+//
+// 	script:
+// 	"""
+//     D2_cluster_EXs.R ${cluster_part} EXs_${cluster_part} unclustered_EXs_${cluster_part}
+//     """
+// }
+//
+// /*
+// * Final exon clusters
+// */
+// process format_EX_clusters_output {
+//     publishDir "${params.output}/", mode: 'copy'
+//
+//     input:
+//     file("*") from ex_clusters.collect()
+//     file("*") from unclustered_exs.collect()
+//
+//     output:
+//     file("EX_clusters.tab") into exon_cluster_for_reclustering
+//     file("EX_clusters_info.tab.gz")
+//     file("unclustered_EXs.txt")
+//
+// 	script:
+// 	"""
+// 	D3_format_EX_clusters_output.pl
+// 	"""
+// }
+//
+// /*
+// * Re-clustering of genes
+// */
+//
+// process recluster_genes_by_species_pair {
+//     publishDir "${params.output}/reclustering", mode: 'copy'
+//     tag { "${combid}" }
+//
+//     when:
+//     params.orthopairs != ""
+//
+//     input:
+//     set combid, file(folderA), file(folderB) from species_to_recluster_genes
+//     file(clusterfile)
+//     //file(orthopairs) from orthopairs_file
+//
+//     output:
+//     set combid, file("reclustered_genes_*.tab") into recl_genes_for_rec_exons
+//
+// 	script:
+// 	def species = "${combid}".split("-")
+// 	def orthopairs = file("${params.orthopairs}")
+// 	"""
+//  	D3.1_recluster_genes_by_species_pair.py -og ${clusterfile} -op ${orthopairs} --species1 ${species[0]} --species2 ${species[1]} -out reclustered_genes_${combid}.tab
+//     	"""
+// }
+//
+//
+// /*
+// * Re-clustering of exons
+// */
+//
+// process recluster_EXs_by_species_pair {
+//     publishDir "${params.output}/reclustering", mode: 'copy'
+//     tag { "${combid}" }
+//
+// 	when:
+// 	params.orthopairs != ""
+//
+//     input:
+//     set combid, file(recl_genes) from recl_genes_for_rec_exons
+//     file(exon_clusters) from exon_cluster_for_reclustering
+//     file(exon_pairs) from exon_pairs_for_reclustering
+//
+//     output:
+//     file("reclustered_EXs_*.tab")
+//
+// 	script:
+// 	def combid1 = combid.replace("-", "_")
+// 	def species = "${combid1}".split("-")
+// 	"""
+// 	D3.2_recluster_EXs_by_species_pair.py -ep ${exon_pairs} -rg ${recl_genes} -ec ${exon_clusters} -sp1 ${species[0]} -sp2 ${species[1]} -out reclustered_EXs_${combid1}.tab
+//     	"""
+// }
+//
+// /*
+//  * Mail notification
+//  */
+//
+// if (params.email == "yourmail@yourdomain" || params.email == "") {
+//     log.info 'Skipping the email\n'
+// }
+// else {
+//     log.info "Sending the email to ${params.email}\n"
+//
+//     workflow.onComplete {
+//
+//     def msg = """\
+//         Pipeline execution summary
+//         ---------------------------
+//         Completed at: ${workflow.complete}
+//         Duration    : ${workflow.duration}
+//         Success     : ${workflow.success}
+//         workDir     : ${workflow.workDir}
+//         exit status : ${workflow.exitStatus}
+//         Error report: ${workflow.errorReport ?: '-'}
+//         """
+//         .stripIndent()
+//
+//         sendMail(to: params.email, subject: "VectorQC execution", body: msg,  attach: "${outputMultiQC}/multiqc_report.html")
+//     }
+// }
+//
+// workflow.onComplete {
+//     println "--- Pipeline BIOCORE@CRG ExOrthist ---"
+//     println "Started at  $workflow.start"
+//     println "Finished at $workflow.complete"
+//     println "Time elapsed: $workflow.duration"
+//     println "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
+// }
+//
diff --git a/modules/local/exorthist/check_input.nf b/modules/local/exorthist/check_input.nf
new file mode 100644
index 0000000..59db1ed
--- /dev/null
+++ b/modules/local/exorthist/check_input.nf
@@ -0,0 +1,30 @@
+process CHECK_INPUT {
+    tag "Checking input files"
+    publishDir "${params.output}", mode: 'copy'
+
+    input:
+    path evodisfile
+    path clusterfile
+    path "GTF/*"
+    path "FASTAS/*"
+    val gtfs_suffix
+    val fastas_suffix
+    val long_dist
+    val medium_dist
+    val short_dist
+
+    output:
+    path "run_info.log", emit: run_info
+
+    script:
+    """
+    echo "Evolutionary distance parameters:" > run_info.log
+    echo "long distance: ${long_dist}" >> run_info.log
+    echo "medium distance: ${medium_dist}" >> run_info.log
+    echo -e "short distance: ${short_dist}\n" >> run_info.log
+    echo "Pairwise evolutionary distances:" >> run_info.log
+    cat ${evodisfile} >> run_info.log
+    echo -e "\nInput files parsing:" >> run_info.log
+    A0_check_input.pl -e ${evodisfile} -g GTF -gs ${gtfs_suffix} -f FASTAS -fs ${fastas_suffix} -c ${clusterfile} >> run_info.log
+    """
+}