move out and carry on

biocorecrg · Nov 4, 2024 · 12e3750 · 12e3750
1 parent bdf20d5
commit 12e3750
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/modules/local/exorthist/score_matches.nf b/modules/local/exorthist/score_matches.nf
@@ -2,10 +2,11 @@ process SCORE_EX_MATCHES {
     tag { comp_id }
     label 'big_mem'
 
-    storeDir "${params.output}/${comp_id}"
+    storeDir "${outdir}/${comp_id}"
 
     input:
     tuple val(comp_id), path("*")
+    path outdir
 
     output:
     path "all_PROT_EX_INT_aln_features_*", emit: all_features

diff --git a/subworkflows/local/exorthist/score.nf b/subworkflows/local/exorthist/score.nf
@@ -15,12 +15,13 @@ workflow SCORE {
     long_dist
     medium_dist
     short_dist
+    outdir
 
     main:
 
     data_to_score = folder_jscores.join(clusters_split_ch).map{ [it[0], it[1..-1] ]}
     // Score EX matches from aln info
-    SCORE_EX_MATCHES(data_to_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)

diff --git a/workflows/main.nf b/workflows/main.nf
@@ -40,7 +40,8 @@ workflow MAIN {
         params.bonafide_pairs,
         params.long_dist,
         params.medium_dist,
-        params.short_dist
+        params.short_dist,
+        params.output
     )
 
     CLUSTER(