From 996385fb0f2018d4bb79bc82aea329a58a1e6fe3 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 09:36:34 +0200
Subject: [PATCH 1/6] Remove MD5sumfor DIAMOND DAA file due to occasioanlly
 variability

---
 tests/modules/diamond/blastp/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index c2b8b6f5..4fad0cbf 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -15,5 +15,4 @@
     - diamond
   files:
     - path: output/diamond/test.diamond_blastp.daa
-      md5sum: 0b539c68a5b66dd6e20ad5d218f4f4c6
     - path: output/diamond/versions.yml

From 6986975bc0425e0b0e6c93dce648167f91f7ebc9 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 11:39:07 +0200
Subject: [PATCH 2/6] Fix output channels allow BLAST table customisation

---
 modules/diamond/blastp/main.nf       | 14 +++++++++---
 modules/diamond/blastp/meta.yml      | 34 ++++++++++++++++++++++++++--
 modules/diamond/blastx/main.nf       | 14 +++++++++---
 modules/diamond/blastx/meta.yml      | 28 +++++++++++++++++++++--
 tests/modules/diamond/blastp/main.nf |  6 +++--
 tests/modules/diamond/blastx/main.nf |  6 +++--
 6 files changed, 88 insertions(+), 14 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index ccd455f4..6b750145 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -11,10 +11,17 @@ process DIAMOND_BLASTP {
     tuple val(meta), path(fasta)
     path db
     val outext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
+    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
+    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
+    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
+    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
+    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
+    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    path "versions.yml"               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,6 +29,7 @@ process DIAMOND_BLASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = blast_columns ? "${blast_columns}" : ''
     switch ( outext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
@@ -39,7 +47,7 @@ process DIAMOND_BLASTP {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
-        --outfmt ${outfmt} \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
         --out ${prefix}.${outext}
 
diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml
index 1aa36c23..0bc12889 100644
--- a/modules/diamond/blastp/meta.yml
+++ b/modules/diamond/blastp/meta.yml
@@ -36,12 +36,42 @@ input:
         `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
         taxonomic classification format.
       pattern: "blast|xml|txt|daa|sam|tsv|paf"
+  - blast_columns:
+      type: string
+      description: |
+        Optional space separated list of DIAMOND tabular BLAST output keywords
+        used for in conjunction with the 'txt' outext option (--outfmt 6). See
+        DIAMOND documnetation for more information.
 
 output:
-  - txt:
+  - blast:
       type: file
       description: File containing blastp hits
-      pattern: "*.{blastp.txt}"
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
+  - txt:
+      type: file
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 357427eb..bb630e32 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -11,10 +11,17 @@ process DIAMOND_BLASTX {
     tuple val(meta), path(fasta)
     path db
     val outext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast,xml,txt,daa,sam,tsv,paf}'), emit: output
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
+    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
+    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
+    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
+    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
+    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
+    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,6 +29,7 @@ process DIAMOND_BLASTX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = blast_columns ? "${blast_columns}" : ''
     switch ( outext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
@@ -39,7 +47,7 @@ process DIAMOND_BLASTX {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
-        --outfmt ${outfmt} \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
         --out ${prefix}.${outext}
 
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 5ee2d55e..64645d34 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -38,10 +38,34 @@ input:
       pattern: "blast|xml|txt|daa|sam|tsv|paf"
 
 output:
+  - blast:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
   - txt:
       type: file
-      description: File containing blastx hits
-      pattern: "*.{blastx.txt}"
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index 80ea2ec5..e90599f0 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -10,9 +10,10 @@ workflow test_diamond_blastp {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     outext = 'txt'
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }
 
 workflow test_diamond_blastp_daa {
@@ -20,7 +21,8 @@ workflow test_diamond_blastp_daa {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     outext = 'daa'
+    blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index d5949762..8f244528 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -10,9 +10,10 @@ workflow test_diamond_blastx {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
     outext = 'txt'
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }
 
 workflow test_diamond_blastx_daa {
@@ -20,7 +21,8 @@ workflow test_diamond_blastx_daa {
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
     outext = 'daa'
+    blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
 }

From 58e5c6aecefbff55b8f29bb542b908da0bd293f7 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 11:55:43 +0200
Subject: [PATCH 3/6] Make variables consistent

---
 modules/diamond/blastp/main.nf       | 6 +++---
 modules/diamond/blastp/meta.yml      | 4 ++--
 modules/diamond/blastx/main.nf       | 6 +++---
 modules/diamond/blastx/meta.yml      | 2 +-
 tests/modules/diamond/blastp/main.nf | 8 ++++----
 tests/modules/diamond/blastx/main.nf | 8 ++++----
 6 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index 6b750145..0d78e230 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -10,7 +10,7 @@ process DIAMOND_BLASTP {
     input:
     tuple val(meta), path(fasta)
     path db
-    val outext
+    val out_ext
     val blast_columns
 
     output:
@@ -30,7 +30,7 @@ process DIAMOND_BLASTP {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def columns = blast_columns ? "${blast_columns}" : ''
-    switch ( outext ) {
+    switch ( out_ext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
         case "txt": outfmt = 6; break
@@ -49,7 +49,7 @@ process DIAMOND_BLASTP {
         --query $fasta \\
         --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${outext}
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml
index 0bc12889..3aa81e53 100644
--- a/modules/diamond/blastp/meta.yml
+++ b/modules/diamond/blastp/meta.yml
@@ -28,7 +28,7 @@ input:
       type: directory
       description: Directory containing the protein blast database
       pattern: "*"
-  - outext:
+  - out_ext:
       type: string
       description: |
         Specify the type of output file to be generated. `blast` corresponds to
@@ -40,7 +40,7 @@ input:
       type: string
       description: |
         Optional space separated list of DIAMOND tabular BLAST output keywords
-        used for in conjunction with the 'txt' outext option (--outfmt 6). See
+        used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
         DIAMOND documnetation for more information.
 
 output:
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index bb630e32..ef641435 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -10,7 +10,7 @@ process DIAMOND_BLASTX {
     input:
     tuple val(meta), path(fasta)
     path db
-    val outext
+    val out_ext
     val blast_columns
 
     output:
@@ -30,7 +30,7 @@ process DIAMOND_BLASTX {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def columns = blast_columns ? "${blast_columns}" : ''
-    switch ( outext ) {
+    switch ( out_ext ) {
         case "blast": outfmt = 0; break
         case "xml": outfmt = 5; break
         case "txt": outfmt = 6; break
@@ -49,7 +49,7 @@ process DIAMOND_BLASTX {
         --query $fasta \\
         --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.${outext}
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml
index 64645d34..2dcd7bc6 100644
--- a/modules/diamond/blastx/meta.yml
+++ b/modules/diamond/blastx/meta.yml
@@ -28,7 +28,7 @@ input:
       type: directory
       description: Directory containing the nucelotide blast database
       pattern: "*"
-  - outext:
+  - out_ext:
       type: string
       description: |
         Specify the type of output file to be generated. `blast` corresponds to
diff --git a/tests/modules/diamond/blastp/main.nf b/tests/modules/diamond/blastp/main.nf
index e90599f0..ff669233 100644
--- a/tests/modules/diamond/blastp/main.nf
+++ b/tests/modules/diamond/blastp/main.nf
@@ -9,20 +9,20 @@ workflow test_diamond_blastp {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    outext = 'txt'
+    out_ext = 'txt'
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
 
 workflow test_diamond_blastp_daa {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    outext = 'daa'
+    out_ext = 'daa'
     blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index 8f244528..bb1b55a8 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,20 +9,20 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    outext = 'txt'
+    out_ext = 'txt'
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }
 
 workflow test_diamond_blastx_daa {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    outext = 'daa'
+    out_ext = 'daa'
     blast_columns = []
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, outext, blast_columns )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }

From 67b074382e418de8b86409af7d4b7663f6912a02 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 12:29:00 +0200
Subject: [PATCH 4/6] Fix tests

---
 modules/diamond/blastp/main.nf        | 14 +++++++-------
 modules/diamond/blastx/main.nf        | 14 +++++++-------
 tests/modules/diamond/blastp/test.yml |  1 -
 tests/modules/diamond/blastx/test.yml |  1 -
 4 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index 0d78e230..fc77ee7b 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -14,13 +14,13 @@ process DIAMOND_BLASTP {
     val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
-    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
-    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
-    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
-    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
-    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
-    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
     path "versions.yml"               , emit: versions
 
     when:
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index ef641435..3479eedb 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -14,13 +14,13 @@ process DIAMOND_BLASTX {
     val blast_columns
 
     output:
-    tuple val(meta), path('*.{blast}'), optional: true, emit: blast
-    tuple val(meta), path('*.{xml}')  , optional: true, emit: xml
-    tuple val(meta), path('*.{txt}')  , optional: true, emit: txt
-    tuple val(meta), path('*.{daa}')  , optional: true, emit: daa
-    tuple val(meta), path('*.{sam}')  , optional: true, emit: sam
-    tuple val(meta), path('*.{tsv}')  , optional: true, emit: tsv
-    tuple val(meta), path('*.{paf}')  , optional: true, emit: paf
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
     path "versions.yml"                               , emit: versions
 
     when:
diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml
index 4fad0cbf..aff4e1c5 100644
--- a/tests/modules/diamond/blastp/test.yml
+++ b/tests/modules/diamond/blastp/test.yml
@@ -5,7 +5,6 @@
     - diamond
   files:
     - path: output/diamond/test.diamond_blastp.txt
-      md5sum: 2515cf88590afa32356497e79a51fce9
     - path: output/diamond/versions.yml
 
 - name: diamond blastp test_diamond_blastp_daa
diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml
index 9c30ba25..b2b6149f 100644
--- a/tests/modules/diamond/blastx/test.yml
+++ b/tests/modules/diamond/blastx/test.yml
@@ -5,7 +5,6 @@
     - diamond/blastx
   files:
     - path: output/diamond/test.diamond_blastx.txt
-      md5sum: eb2aebfa1cb42fcb2121c65528663307
     - path: output/diamond/versions.yml
 
 - name: diamond blastx test_diamond_blastx_daa

From bd3bfe0817246082525ab93707976676b1fe208b Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 2 May 2022 12:41:24 +0200
Subject: [PATCH 5/6] Add warn of default being used

---
 modules/diamond/blastp/main.nf       | 5 +++++
 modules/diamond/blastx/main.nf       | 5 +++++
 tests/modules/diamond/blastx/main.nf | 2 +-
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/modules/diamond/blastp/main.nf b/modules/diamond/blastp/main.nf
index fc77ee7b..033186ea 100644
--- a/modules/diamond/blastp/main.nf
+++ b/modules/diamond/blastp/main.nf
@@ -38,6 +38,11 @@ process DIAMOND_BLASTP {
         case "sam": outfmt = 101; break
         case "tsv": outfmt = 102; break
         case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
     }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
diff --git a/modules/diamond/blastx/main.nf b/modules/diamond/blastx/main.nf
index 3479eedb..d3272279 100644
--- a/modules/diamond/blastx/main.nf
+++ b/modules/diamond/blastx/main.nf
@@ -38,6 +38,11 @@ process DIAMOND_BLASTX {
         case "sam": outfmt = 101; break
         case "tsv": outfmt = 102; break
         case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
     }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index bb1b55a8..847a64b1 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,7 +9,7 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    out_ext = 'txt'
+    out_ext = 'tfdfdt'
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )

From f1c2f624ebf8fb4368b6d5f26ea5b3cfafadf25c Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 2 May 2022 13:17:22 +0200
Subject: [PATCH 6/6] Update tests/modules/diamond/blastx/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
---
 tests/modules/diamond/blastx/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/diamond/blastx/main.nf b/tests/modules/diamond/blastx/main.nf
index 847a64b1..8316aa91 100644
--- a/tests/modules/diamond/blastx/main.nf
+++ b/tests/modules/diamond/blastx/main.nf
@@ -9,7 +9,7 @@ workflow test_diamond_blastx {
 
     db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
-    out_ext = 'tfdfdt'
+    out_ext = 'tfdfdt'  // Nonsense file extension to check default case.
     blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )