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moving out params
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toniher committed Oct 21, 2024
1 parent 3c86c70 commit 166ea27
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Showing 3 changed files with 19 additions and 5 deletions.
10 changes: 9 additions & 1 deletion main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,15 @@ workflow {
params.extraexons
)

ALIGN(blosumfile, PREPARE.out.alignment_input, PREPARE.out.clusters_split_ch)
ALIGN(
blosumfile,
PREPARE.out.alignment_input,
PREPARE.out.clusters_split_ch,
params.long_dist,
params.medium_dist,
params.short_dist,
)

SCORE(ALIGN.out.folder_jscores, PREPARE.out.clusters_split_ch, PREPARE.out.dist_ranges_ch, params.bonafide_pairs)
CLUSTER(SCORE.out.score_exon_hits_pairs, PREPARE.out.clusters_split_ch, clusterfile_ch, orthopairs_ch)
}
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9 changes: 6 additions & 3 deletions modules/local/exorthist/align_pairs.nf
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,9 @@ process PARSE_IPA_PROT_ALN {
input:
path blosumfile
tuple val(combid), path(sp1), path(sp2), path(cls_part_file), val(dist_range)
val long_dist
val medium_dist
val short_dist

output:
tuple val("${sp1.name}-${sp2.name}"), path("${sp1.name}-${sp2.name}-*"), emit: aligned_subclusters_4_splitting
Expand All @@ -17,13 +20,13 @@ process PARSE_IPA_PROT_ALN {

switch(dist_range) {
case "long":
dist_range_par = params.long_dist.split(",")
dist_range_par = long_dist.split(",")
break
case "medium":
dist_range_par = params.medium_dist.split(",")
dist_range_par = medium_dist.split(",")
break
case "short":
dist_range_par = params.short_dist.split(",")
dist_range_par = short_dist.split(",")
break
}

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5 changes: 4 additions & 1 deletion subworkflows/local/exorthist/align.nf
Original file line number Diff line number Diff line change
Expand Up @@ -11,11 +11,14 @@ workflow ALIGN {
blosumfile
alignment_input
clusters_split_ch
long_dist
medium_dist
short_dist

main:
// 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.
PARSE_IPA_PROT_ALN(blosumfile, alignment_input)
PARSE_IPA_PROT_ALN(blosumfile, alignment_input, long_dist, medium_dist, short_dist)

// Collapse EXs_to_split in batches of 500 files
EXs_to_split = PARSE_IPA_PROT_ALN.out.EXs_to_split
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