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remove params.output
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toniher committed Nov 4, 2024
1 parent 12e3750 commit 92093a5
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Showing 9 changed files with 14 additions and 8 deletions.
1 change: 0 additions & 1 deletion TODO.md
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@@ -1,3 +1,2 @@
- Review params.output from modules (optional)
- Add stub to modules (optional)
- Include colors into the terminal messages (optional)
3 changes: 2 additions & 1 deletion main.nf
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Expand Up @@ -47,7 +47,8 @@ workflow {
params.relevant_exs,
params.ordered_species,
params.isoformID,
params.sub_orthologs
params.sub_orthologs,
params.output
)

} else {
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3 changes: 2 additions & 1 deletion modules/local/exorthist/filter_matches.nf
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@@ -1,7 +1,7 @@
process FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE {
tag { comp_id }

publishDir "${params.output}", mode: "copy",
publishDir "${outdir}", mode: "copy",
pattern: "best_scored_EX_matches_by_targetgene.txt",
saveAs: { filename -> "${comp_id}/$filename" }

Expand All @@ -10,6 +10,7 @@ process FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE {
val(long_dist)
val(medium_dist)
val(short_dist)
path outdir

output:
path "*.tab", emit: filterscore_per_joining
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5 changes: 3 additions & 2 deletions modules/local/exorthist/merge_aligns.nf
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Expand Up @@ -4,11 +4,12 @@ process MERGE_PROT_EX_INT_ALN_INFO {

stageInMode 'copy'

publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/all_*_aln_features.txt"
publishDir "${params.output}", mode: "copy", pattern: "${comp_id}/EXINT_aln.gz"
publishDir "${outdir}", mode: "copy", pattern: "${comp_id}/all_*_aln_features.txt"
publishDir "${outdir}", mode: "copy", pattern: "${comp_id}/EXINT_aln.gz"

input:
tuple val(comp_id), path("FOLDERS_*"), path("*")
path outdir

output:
tuple val(comp_id), path("${comp_id}/"), emit: folder_jscores
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3 changes: 2 additions & 1 deletion modules/local/exorthist/plot/get_exons.nf
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@@ -1,12 +1,13 @@
process GET_ISOFORM_EXONS {
tag "${isoformID}"
label 'pandas'
publishDir "${params.output}/${geneID}/processed_table", mode: 'copy'
publishDir "${outdir}/${geneID}/processed_table", mode: 'copy'

input:
val(isoformID)
tuple val(species), path(exons_info), path(overlap_info)
val(geneID)
path outdir

output:
stdout emit: isoform_interesting_exs
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3 changes: 2 additions & 1 deletion subworkflows/local/exorthist/align.nf
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Expand Up @@ -16,6 +16,7 @@ workflow ALIGN {
short_dist
alignmentnum
prevaln
outdir

main:

Expand Down Expand Up @@ -46,7 +47,7 @@ workflow ALIGN {
realigned_exons_4_merge = REALIGN_EX_PAIRS.out.realigned_exons_4_merge
data_4_merge = aligned_subclusters_4_splitting.groupTuple().join(realigned_exons_4_merge.groupTuple())
// Merge alignments information
MERGE_PROT_EX_INT_ALN_INFO(data_4_merge)
MERGE_PROT_EX_INT_ALN_INFO(data_4_merge, outdir)

emit:
folder_jscores = MERGE_PROT_EX_INT_ALN_INFO.out.folder_jscores
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2 changes: 1 addition & 1 deletion subworkflows/local/exorthist/score.nf
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Expand Up @@ -24,7 +24,7 @@ workflow SCORE {
SCORE_EX_MATCHES(data_to_score, outdir)
// Filter the best matches above score cutoffs by target gene.
all_scores_to_filt_ch = SCORE_EX_MATCHES.out.all_scores_to_filt
FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE(all_scores_to_filt_ch.join(dist_ranges_ch), long_dist, medium_dist, short_dist)
FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE(all_scores_to_filt_ch.join(dist_ranges_ch), long_dist, medium_dist, short_dist, outdir)
// Join filtered scored EX matches
filterscore_per_joining_ch = FILTER_AND_SELECT_BEST_EX_MATCHES_BY_TARGETGENE.out.filterscore_per_joining
JOIN_FILTERED_EX_MATCHES(filterscore_per_joining_ch.collect())
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1 change: 1 addition & 0 deletions workflows/main.nf
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Expand Up @@ -31,6 +31,7 @@ workflow MAIN {
params.short_dist,
params.alignmentnum,
params.prevaln
params.output
)

SCORE(
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1 change: 1 addition & 0 deletions workflows/plot.nf
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Expand Up @@ -17,6 +17,7 @@ workflow PLOT {
ordered_species
isoformID
sub_orthologs
outdir

main:

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