From 6e79dbb2d50d743a0958846b32b63ec540384ec7 Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toni.hermoso@crg.eu>
Date: Tue, 3 Dec 2024 13:03:45 +0100
Subject: [PATCH] adding actual dummy nofile for avoiding errors in some setups

---
 files/NO_FILE                           |  1 +
 subworkflows/local/exorthist/align.nf   |  3 ++-
 subworkflows/local/exorthist/cluster.nf |  3 ++-
 subworkflows/local/exorthist/prepare.nf |  3 ++-
 subworkflows/local/exorthist/score.nf   |  3 ++-
 workflows/main.nf                       | 17 ++++++++++++-----
 6 files changed, 21 insertions(+), 9 deletions(-)
 create mode 100644 files/NO_FILE

diff --git a/files/NO_FILE b/files/NO_FILE
new file mode 100644
index 0000000..dc7d99a
--- /dev/null
+++ 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
index 14abb05..ffe3d1a 100644
--- 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
index e587df5..1a3e204 100644
--- a/subworkflows/local/exorthist/cluster.nf
+++ b/subworkflows/local/exorthist/cluster.nf
@@ -14,6 +14,7 @@ workflow CLUSTER {
     clusterfile
     orthopairs
     orthogroupnum
+    nofile
 
     main:
 
@@ -21,7 +22,7 @@ workflow CLUSTER {
     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
index 8a8ba03..6a417fa 100644
--- 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
index b7c43f3..4fd45d7 100644
--- 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
index 5e45fc1..9466cc1 100644
--- 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 {
 
@@ -19,11 +22,12 @@ 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,
@@ -31,7 +35,8 @@ workflow MAIN {
         params.short_dist,
         params.alignmentnum,
         params.prevaln,
-        params.output
+        params.output,
+        nofile
     )
 
     SCORE(
@@ -42,7 +47,8 @@ workflow MAIN {
         params.long_dist,
         params.medium_dist,
         params.short_dist,
-        params.output
+        params.output,
+        nofile
     )
 
     CLUSTER(
@@ -50,7 +56,8 @@ workflow MAIN {
         PREPARE.out.clusters_split_ch,
         params.cluster,
         params.orthopairs,
-        params.orthogroupnum
+        params.orthogroupnum,
+        nofile
     )
 
     emit: