More modules added to align

main.nf

@@ -98,6 +98,7 @@ LOCAL_MODULES='./modules/local/exorthist'
 include { CHECK_INPUT } from "${LOCAL_MODULES}/check_input.nf"
 include { GENERATE_ANNOTATIONS } from "${LOCAL_MODULES}/generate_annotations.nf"
 include { PARSE_IPA_PROT_ALN } from "${LOCAL_MODULES}/align_pairs.nf"
+include { REALIGN_EX_PAIRS } from "${LOCAL_MODULES}/realign_pairs.nf"
 include { SPLIT_CLUSTERS_IN_CHUNKS } from "${LOCAL_MODULES}/split_clusters_chunks.nf"
 include { SPLIT_CLUSTERS_BY_SPECIES_PAIRS } from "${LOCAL_MODULES}/split_clusters_species.nf"
 include { SPLIT_EX_PAIRS_TO_REALIGN } from "${LOCAL_MODULES}/split_pairs.nf"
@@ -210,6 +211,8 @@ workflow {
     EXs_to_realign_batches = SPLIT_EX_PAIRS_TO_REALIGN.out.EXs_to_realign_batches
     // Flatten the results from the previous batch run and combine with sp1 and sp2 information, using sp1-sp2 as key.
     EXs_to_realign = EXs_to_realign_batches.flatten().map{[it.getName().toString().split("_")[0],it]}.groupTuple().join(clusters_split_ch).transpose()
+    //  Realign exons pairs (with multiple hits)
+    REALIGN_EX_PAIRS(blosumfile, EXs_to_realign)
 
     // Review outputs below
     CHECK_INPUT.out.run_info.view()
@@ -222,31 +225,10 @@ workflow {
     PARSE_IPA_PROT_ALN.out.aligned_subclusters_4_splitting.view { "SC: $it" }
     PARSE_IPA_PROT_ALN.out.EXs_to_split.view { "EX: $it" }
     EXs_to_realign.view { "EXR: $it" }
-
+    REALIGN_EX_PAIRS.out.realigned_exons_4_merge.view{ "RER: $it" }
 }
 
 
-// /*
-//  * 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}

modules/local/exorthist/align_pairs.nf

@@ -0,0 +1,37 @@
+process PARSE_IPA_PROT_ALN {
+    tag { cls_part_file.name }
+    label 'big_cpus'
+
+    input:
+    path blosumfile
+    tuple val(combid), path(sp1), path(sp2), path(cls_part_file), val(dist_range)
+
+    output:
+    tuple val("${sp1.name}-${sp2.name}"), path("${sp1.name}-${sp2.name}-*"), emit: aligned_subclusters_4_splitting
+    path "${sp1.name}-${sp2.name}_EXs_to_split_part_*.txt", emit: EXs_to_split
+
+    script:
+    def prev_alignments = params.prevaln ? params.prevaln : ""
+    def cls_parts = cls_part_file.name.split("_")
+    def dist_range_par
+
+    switch(dist_range) {
+        case "long":
+            dist_range_par = params.long_dist.split(",")
+            break
+        case "medium":
+            dist_range_par = params.medium_dist.split(",")
+            break
+        case "short":
+            dist_range_par = params.short_dist.split(",")
+            break
+    }
+
+    """
+    B1_parse_IPA_prot_aln.pl ${sp1.name} ${sp2.name} ${cls_part_file} \
+    ${sp1}/${sp1.name}_annot_exons_prot_ids.txt ${sp2}/${sp2.name}_annot_exons_prot_ids.txt \
+    ${sp1}/${sp1.name}_protein_ids_exons_pos.txt ${sp2}/${sp2.name}_protein_ids_exons_pos.txt \
+    ${sp1}/${sp1.name}_protein_ids_intron_pos_CDS.txt ${sp2}/${sp2.name}_protein_ids_intron_pos_CDS.txt \
+    ${sp1}/${sp1.name}.exint ${sp2}/${sp2.name}.exint ${cls_parts[1]} ${blosumfile} ${sp1.name}-${sp2.name}-${cls_parts[1]} ${dist_range_par[3]} ${task.cpus} ${prev_alignments}
+    """
+}

modules/local/exorthist/realign_pairs.nf

@@ -0,0 +1,17 @@
+process REALIGN_EX_PAIRS {
+    label 'incr_time_cpus'
+
+    input:
+    path blosumfile
+    tuple val(comp_id), path(EXs_to_realign), path(sp1), path(sp2)
+
+    output:
+    tuple val(comp_id), path("realigned_*"), emit: realigned_exons_4_merge
+
+    script:
+    """
+    B3_realign_EX_pairs.pl ${sp1.name} ${sp2.name} ${EXs_to_realign} \
+    ${sp1}/${sp1.name}.exint ${sp2}/${sp2.name}.exint 1 realigned_${EXs_to_realign.name} \
+    ${sp1.name}_${sp2.name} ${blosumfile} ${task.cpus}
+    """
+}

modules/local/exorthist/split_pairs.nf

@@ -0,0 +1,15 @@
+process SPLIT_EX_PAIRS_TO_REALIGN {
+    label 'pandas'
+    input:
+    path '*'
+
+    output:
+    path '*EXs_to_realign_part_*', emit: EXs_to_realign_batches
+
+    script:
+    """
+    for file in \$(ls *); do
+        B2_split_EX_pairs_to_realign.py -i \${file} -n ${params.alignmentnum}
+    done
+    """
+}