From 589ce2d73a0b9a3109f5291587eff425ca7fbfa5 Mon Sep 17 00:00:00 2001
From: jtangrot <jeanette.tangrot@umu.se>
Date: Mon, 23 May 2022 14:02:10 +0200
Subject: [PATCH] Add options for output file type

---
 modules/vsearch/usearchglobal/main.nf         | 38 +++++++++++++++----
 tests/modules/vsearch/usearchglobal/main.nf   | 14 ++++++-
 .../vsearch/usearchglobal/nextflow.config     |  4 +-
 tests/modules/vsearch/usearchglobal/test.yml  | 14 ++++++-
 4 files changed, 58 insertions(+), 12 deletions(-)

diff --git a/modules/vsearch/usearchglobal/main.nf b/modules/vsearch/usearchglobal/main.nf
index 65ee62cc..0b31842f 100644
--- a/modules/vsearch/usearchglobal/main.nf
+++ b/modules/vsearch/usearchglobal/main.nf
@@ -10,7 +10,7 @@
 //                 bwa mem | samtools view -B -T ref.fasta
 
 process VSEARCH_USEARCHGLOBAL {
-    tag '$queryfasta'
+    tag "$meta.id"
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::vsearch=2.21.1" : null)
@@ -19,29 +19,53 @@ process VSEARCH_USEARCHGLOBAL {
         'quay.io/biocontainers/vsearch:2.21.1--h95f258a_0' }"
 
     input:
-    path queryfasta
+    tuple val(meta), path(queryfasta)
     path db
-    val  outprefix
+    val outoption
+    val user_columns
 
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
 
     output:
-    path ("*.tsv")        , emit: tsv
-    path "versions.yml"   , emit: versions
-
+    tuple val(meta), path('*.aln')  , optional: true, emit: aln
+    tuple val(meta), path('*.biom') , optional: true, emit: biom
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.uc')   , optional: true, emit: uc
+    path "versions.yml"                             , emit: versions
+    
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = user_columns ? "--userfields ${user_columns}" : ''
+    switch ( outoption ) {
+        case "alnout": outfmt = "--alnout"; out_ext = 'aln'; break
+        case "biomout": outfmt = "--biomout"; out_ext = 'biom'; break
+	case "blast6out": outfmt = "--blast6out"; out_ext = 'blast6out.tsv'; break
+        case "mothur_shared_out": outfmt = "--mothur_shared_out"; out_ext = 'mothur.tsv'; break
+	case "otutabout": outfmt = "--otutabout"; out_ext = 'otu.tsv'; break
+	case "samout": outfmt = "--samout"; out_ext = 'sam'; break
+	case "uc": outfmt = "--uc"; out_ext = 'uc'; break
+	case "userout": outfmt = "--userout"; out_ext = 'user.tsv'; break
+	case "lcaout": outfmt = "--lcaout"; out_ext = 'lca.tsv'; break
+        default:
+            outfmt = "--alnout";
+            out_ext = 'aln';
+            log.warn("Unknown output file format provided (${outoption}): selectingpairwise alignments (alnout)");
+            break
+    }
     """
     vsearch \\
         --usearch_global $queryfasta \\
         --db $db \\
         --threads $task.cpus \\
         $args \\
-        --blast6out ${outprefix}.tsv
+        ${columns} \\
+        ${outfmt} ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/vsearch/usearchglobal/main.nf b/tests/modules/vsearch/usearchglobal/main.nf
index 02becd21..cdf0fb2f 100644
--- a/tests/modules/vsearch/usearchglobal/main.nf
+++ b/tests/modules/vsearch/usearchglobal/main.nf
@@ -8,5 +8,17 @@ workflow test_vsearch_usearchglobal {
     
     query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
     db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    VSEARCH_USEARCHGLOBAL ( query, db, "blast6out_results" )
+    
+    outoption = "xcfert"  // Nonsense text to check default case.
+    columns = "" 
+    VSEARCH_USEARCHGLOBAL ( [ [id:'test'], query ], db, outoption, columns )
+}
+
+workflow test_vsearch_usearchglobal_userout {
+    
+    query = file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)
+    db = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    outoption = "userout"
+    columns = "query+target+id" 
+    VSEARCH_USEARCHGLOBAL ( [ [id:'test'], query ], db, outoption, columns )
 }
diff --git a/tests/modules/vsearch/usearchglobal/nextflow.config b/tests/modules/vsearch/usearchglobal/nextflow.config
index aab29979..3148a59e 100644
--- a/tests/modules/vsearch/usearchglobal/nextflow.config
+++ b/tests/modules/vsearch/usearchglobal/nextflow.config
@@ -1,5 +1,5 @@
 process {
     ext.args = '--id 0.985'
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
+} 
+
diff --git a/tests/modules/vsearch/usearchglobal/test.yml b/tests/modules/vsearch/usearchglobal/test.yml
index b013519d..b7ebec4a 100644
--- a/tests/modules/vsearch/usearchglobal/test.yml
+++ b/tests/modules/vsearch/usearchglobal/test.yml
@@ -1,7 +1,17 @@
 - name: vsearch usearchglobal test_vsearch_usearchglobal
   command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal -c ./tests/config/nextflow.config  -c ./tests/modules/vsearch/usearchglobal/nextflow.config
   tags:
+    - vsearch
     - vsearch/usearchglobal
   files:
-    - path: output/vsearch/blast6out_results.tsv
-      md5sum: 09733131643f1d951321a6e17a35eb8c
+    - path: output/vsearch/test.aln
+      md5sum: 7b7479c16e0ecb503913da8bde48d6c5
+
+- name: vsearch usearchglobal test_vsearch_usearchglobal_userout
+  command: nextflow run ./tests/modules/vsearch/usearchglobal -entry test_vsearch_usearchglobal_userout -c ./tests/config/nextflow.config  -c ./tests/modules/vsearch/usearchglobal/nextflow.config
+  tags:
+    - vsearch
+    - vsearch/usearchglobal
+  files:
+    - path: output/vsearch/test.user.tsv
+      md5sum: b6cc50f7c8d18cb82e74dab70ed4baab