From cde237e7cec07798e5754b72aeca44efe89fc6db Mon Sep 17 00:00:00 2001
From: Jose Espinosa-Carrasco <kadomu@gmail.com>
Date: Thu, 23 Dec 2021 18:22:07 +0100
Subject: [PATCH] Fix error messages mentioning suffix (#1190)

---
 modules/last/postmask/main.nf    | 2 +-
 modules/plink/extract/main.nf    | 2 +-
 modules/pmdtools/filter/main.nf  | 2 +-
 modules/samblaster/main.nf       | 2 +-
 modules/samtools/fixmate/main.nf | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/last/postmask/main.nf b/modules/last/postmask/main.nf
index fb097a11..ca981e1c 100644
--- a/modules/last/postmask/main.nf
+++ b/modules/last/postmask/main.nf
@@ -17,7 +17,7 @@ process LAST_POSTMASK {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate"
+    if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz
 
diff --git a/modules/plink/extract/main.nf b/modules/plink/extract/main.nf
index 9b8a52f3..688ada67 100644
--- a/modules/plink/extract/main.nf
+++ b/modules/plink/extract/main.nf
@@ -19,7 +19,7 @@ process PLINK_EXTRACT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
+    if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     plink \\
         --bfile ${meta.id} \\
diff --git a/modules/pmdtools/filter/main.nf b/modules/pmdtools/filter/main.nf
index 0b3bcbc6..b647b6d3 100644
--- a/modules/pmdtools/filter/main.nf
+++ b/modules/pmdtools/filter/main.nf
@@ -22,7 +22,7 @@ process PMDTOOLS_FILTER {
     def args3 = task.ext.args3 ?: ''
     def split_cpus = Math.floor(task.cpus/2)
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use the suffix option to disambiguate!"
+    if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     //threshold and header flags activate filtering function of pmdtools
     """
     samtools \\
diff --git a/modules/samblaster/main.nf b/modules/samblaster/main.nf
index c6573283..4627b978 100644
--- a/modules/samblaster/main.nf
+++ b/modules/samblaster/main.nf
@@ -19,7 +19,7 @@ process SAMBLASTER {
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate"
+    if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     samtools view -h $args2 $bam | \\
     samblaster $args | \\
diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf
index 8f86c1c4..d108f8d6 100644
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@@ -17,7 +17,7 @@ process SAMTOOLS_FIXMATE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use the suffix option to disambiguate!"
+    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
 
     """
     samtools \\