From 38ffbfdb63454d20c56cd16e9b8b489165fea0c9 Mon Sep 17 00:00:00 2001
From: Mei Wu <25568561+projectoriented@users.noreply.github.com>
Date: Mon, 28 Feb 2022 16:16:29 +0100
Subject: [PATCH] bcftools/annotate follow up corrections (#1359)

* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

* using match instead of find

* bcftools/annotate refactored with complete test

* rm trailing white space

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
---
 modules/bcftools/annotate/main.nf        |  4 ++--
 tests/config/test_data.config            |  2 ++
 tests/modules/bcftools/annotate/main.nf  | 15 ++++++++++++---
 tests/modules/bcftools/annotate/test.yml | 18 ++++++++++++++----
 4 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/modules/bcftools/annotate/main.nf b/modules/bcftools/annotate/main.nf
index 437baaf3..40e32047 100644
--- a/modules/bcftools/annotate/main.nf
+++ b/modules/bcftools/annotate/main.nf
@@ -22,7 +22,7 @@ process BCFTOOLS_ANNOTATE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def matcher = input =~ /vcf/
+    def matcher = input ==~ /\S+\.*vcf\.\S*/
     def output_suffix = matcher ? "vcf.gz" : "bcf"
     def output_type_compressed = matcher ? "z" : "b"
     """
@@ -36,7 +36,7 @@ process BCFTOOLS_ANNOTATE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
     END_VERSIONS
     """
 }
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index e28b0cb0..7c3e183c 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -67,6 +67,8 @@ params {
 
                 test_computematrix_mat_gz                      = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
 
+                test_bcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf"
+                
                 test_vcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
                 test_vcf_gz                                    = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
                 test_vcf_gz_tbi                                = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
diff --git a/tests/modules/bcftools/annotate/main.nf b/tests/modules/bcftools/annotate/main.nf
index 2f2b66c9..0d096ca9 100644
--- a/tests/modules/bcftools/annotate/main.nf
+++ b/tests/modules/bcftools/annotate/main.nf
@@ -4,11 +4,20 @@ nextflow.enable.dsl = 2
 
 include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf'
 
-workflow test_bcftools_annotate {
-    
+workflow test_bcftools_annotate_out_vcf {
+
     input = [ 
-    [ id:'test_compressed', single_end:false ], // meta map
+    [ id:'test_compressed_vcf', single_end:false ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
 
     BCFTOOLS_ANNOTATE ( input )
 }
+
+workflow test_bcftools_annotate_out_bcf {
+
+    input = [ 
+    [ id:'test_compressed_bcf', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true) ]
+
+    BCFTOOLS_ANNOTATE ( input )
+}
diff --git a/tests/modules/bcftools/annotate/test.yml b/tests/modules/bcftools/annotate/test.yml
index 43537180..e8cdcc4b 100644
--- a/tests/modules/bcftools/annotate/test.yml
+++ b/tests/modules/bcftools/annotate/test.yml
@@ -1,9 +1,19 @@
-- name: bcftools annotate test_bcftools_annotate
-  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate -c tests/config/nextflow.config
+- name: bcftools annotate test_bcftools_annotate_out_vcf
+  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_vcf -c tests/config/nextflow.config
   tags:
     - bcftools/annotate
     - bcftools
   files:
-    - path: output/bcftools/test_compressed_annotated.vcf.gz
+    - path: output/bcftools/test_compressed_vcf_annotated.vcf.gz
     - path: output/bcftools/versions.yml
-      md5sum: b647b465acc221f6fe6fbcc319724eed
+      md5sum: de86d4d411baef1aaee0e72f519dbe1f
+
+- name: bcftools annotate test_bcftools_annotate_out_bcf
+  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate_out_bcf -c tests/config/nextflow.config
+  tags:
+    - bcftools/annotate
+    - bcftools
+  files:
+    - path: output/bcftools/test_compressed_bcf_annotated.bcf
+    - path: output/bcftools/versions.yml
+      md5sum: a57e62a5a189fe85aabd52c010d88ca6