Added the optional .gzi output of "samtools faidx" (#1935)

modules/samtools/faidx/main.nf

@@ -12,6 +12,7 @@ process SAMTOOLS_FAIDX {
 
     output:
     tuple val(meta), path ("*.fai"), emit: fai
+    tuple val(meta), path ("*.gzi"), emit: gzi, optional: true
     path "versions.yml"            , emit: versions
 
     when:

modules/samtools/faidx/meta.yml

@@ -33,6 +33,10 @@ output:
       type: file
       description: FASTA index file
       pattern: "*.{fai}"
+  - gzi:
+      type: file
+      description: Optional gzip index file for compressed inputs
+      pattern: "*.gzi"
   - versions:
       type: file
       description: File containing software versions

tests/config/test_data.config

@@ -6,6 +6,7 @@ params {
         'sarscov2' {
             'genome' {
                 genome_fasta                                   = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta"
+                genome_fasta_gz                                = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.gz"
                 genome_fasta_fai                               = "${test_data_dir}/genomics/sarscov2/genome/genome.fasta.fai"
                 genome_dict                                    = "${test_data_dir}/genomics/sarscov2/genome/genome.dict"
                 genome_gff3                                    = "${test_data_dir}/genomics/sarscov2/genome/genome.gff3"

tests/modules/samtools/faidx/main.nf

@@ -11,3 +11,11 @@ workflow test_samtools_faidx {
 
     SAMTOOLS_FAIDX ( input )
 }
+
+workflow test_samtools_faidx_bgzip {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta_gz'], checkIfExists: true) ]
+
+    SAMTOOLS_FAIDX ( input )
+}

tests/modules/samtools/faidx/test.yml

@@ -7,3 +7,14 @@
     - path: output/samtools/genome.fasta.fai
       md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
     - path: output/samtools/versions.yml
+- name: samtools faidx test_samtools_faidx_bgzip
+  command: nextflow run tests/modules/samtools/faidx -entry test_samtools_faidx_bgzip -c tests/config/nextflow.config
+  tags:
+    - samtools
+    - samtools/faidx
+  files:
+    - path: output/samtools/genome.fasta.gz.fai
+      md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
+    - path: output/samtools/genome.fasta.gz.gzi
+      md5sum: 7dea362b3fac8e00956a4952a3d4f474
+    - path: output/samtools/versions.yml