adding actual dummy nofile for avoiding errors in some setups

biocorecrg · Dec 3, 2024 · 6e79dbb · 6e79dbb
1 parent df7e1d3
commit 6e79dbb
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Showing 6 changed files with 21 additions and 9 deletions.
diff --git a/files/NO_FILE b/files/NO_FILE
@@ -0,0 +1 @@
+https://nextflow-io.github.io/patterns/optional-input/
diff --git a/subworkflows/local/exorthist/align.nf b/subworkflows/local/exorthist/align.nf
@@ -17,6 +17,7 @@ workflow ALIGN {
     alignmentnum
     prevaln
     outdir
+    nofile
 
     main:
 
@@ -25,7 +26,7 @@ workflow ALIGN {
     if (prevaln) {
         prevaln_ch = Channel.fromPath(prevaln, type: 'dir', checkIfExists: true).collect()
     } else {
-        prevaln_ch = Channel.fromPath("/path/to/NO_FILE").collect()
+        prevaln_ch = Channel.fromPath(nofile).collect()
     }
 
     // the last argument is the protein similarity alignment.

diff --git a/subworkflows/local/exorthist/cluster.nf b/subworkflows/local/exorthist/cluster.nf
@@ -14,14 +14,15 @@ workflow CLUSTER {
     clusterfile
     orthopairs
     orthogroupnum
+    nofile
 
     main:
 
     clusterfile_ch = Channel.fromPath(clusterfile, checkIfExists: true).collect()
     if (orthopairs) {
         orthopairs_ch = Channel.fromPath(orthopairs, checkIfExists: true).collect()
     } else {
-        orthopairs_ch = Channel.fromPath("/path/to/NO_FILE").collect()
+        orthopairs_ch = Channel.fromPath(nofile).collect()
     }
 
     FORMAT_EX_CLUSTERS_INPUT(score_exon_hits_pairs, clusterfile_ch, orthogroupnum)

diff --git a/subworkflows/local/exorthist/prepare.nf b/subworkflows/local/exorthist/prepare.nf
@@ -17,6 +17,7 @@ workflow PREPARE {
     short_dist
     extraexons
     alignmentnum
+    nofile
 
     main:
 
@@ -66,7 +67,7 @@ workflow PREPARE {
     } else {
         // Sic: https://nextflow-io.github.io/patterns/optional-input/
         data_to_annotation.map { entry ->
-            entry.add(['/path/to/NO_FILE'])
+            entry.add([nofile])
         }
         // data_to_annotation.view()
         GENERATE_ANNOTATIONS(data_to_annotation)

diff --git a/subworkflows/local/exorthist/score.nf b/subworkflows/local/exorthist/score.nf
@@ -16,6 +16,7 @@ workflow SCORE {
     medium_dist
     short_dist
     outdir
+    nofile
 
     main:
 
@@ -37,7 +38,7 @@ workflow SCORE {
         bonafide_pairs_ch = Channel.fromPath(bonafide_pairs, checkIfExists: true).collect()
         COLLAPSE_OVERLAPPING_MATCHES(filtered_all_scores, bonafide_pairs_ch)
     } else {
-        COLLAPSE_OVERLAPPING_MATCHES(filtered_all_scores, Channel.fromPath("/path/to/NO_FILE").collect())
+        COLLAPSE_OVERLAPPING_MATCHES(filtered_all_scores, Channel.fromPath(nofile).collect())
     }
 
     emit:

diff --git a/workflows/main.nf b/workflows/main.nf
@@ -5,6 +5,9 @@ include { CLUSTER } from "${LOCAL_SUBWORKFLOWS}/cluster.nf"
 include { PREPARE } from "${LOCAL_SUBWORKFLOWS}/prepare.nf"
 include { SCORE } from "${LOCAL_SUBWORKFLOWS}/score.nf"
 
+def blosum = "${projectDir}/files/blosum62.txt"
+// https://nextflow-io.github.io/patterns/optional-input/
+def nofile = "${projectDir}/files/NO_FILE"
 
 workflow MAIN {
 
@@ -19,19 +22,21 @@ workflow MAIN {
         params.medium_dist,
         params.short_dist,
         params.extraexons,
-        params.alignmentnum
+        params.alignmentnum,
+        nofile
     )
 
     ALIGN(
-        "${projectDir}/files/blosum62.txt",
+        blosum,
         PREPARE.out.alignment_input,
         PREPARE.out.clusters_split_ch,
         params.long_dist,
         params.medium_dist,
         params.short_dist,
         params.alignmentnum,
         params.prevaln,
-        params.output
+        params.output,
+        nofile
     )
 
     SCORE(
@@ -42,15 +47,17 @@ workflow MAIN {
         params.long_dist,
         params.medium_dist,
         params.short_dist,
-        params.output
+        params.output,
+        nofile
     )
 
     CLUSTER(
         SCORE.out.score_exon_hits_pairs,
         PREPARE.out.clusters_split_ch,
         params.cluster,
         params.orthopairs,
-        params.orthogroupnum
+        params.orthogroupnum,
+        nofile
     )
 
     emit:
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		https://nextflow-io.github.io/patterns/optional-input/