Add index format to samtools view

modules/nf-core/samtools/view/main.nf

@@ -11,6 +11,7 @@ process SAMTOOLS_VIEW {
     tuple val(meta), path(input), path(index)
     tuple val(meta2), path(fasta)
     path qname
+    val index_format
 
     output:
     tuple val(meta), path("${prefix}.bam"),                                    emit: bam,              optional: true
@@ -20,7 +21,7 @@ process SAMTOOLS_VIEW {
     tuple val(meta), path("${prefix}.${file_type}.csi"),                       emit: csi,              optional: true
     tuple val(meta), path("${prefix}.${file_type}.crai"),                      emit: crai,             optional: true
     tuple val(meta), path("${prefix}.unselected.${file_type}"),                emit: unselected,       optional: true
-    tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true
+    tuple val(meta), path("${prefix}.unselected.${file_type}.{csi,crai}"),     emit: unselected_index, optional: true
     path  "versions.yml",                                                      emit: versions
 
     when:
@@ -35,16 +36,27 @@ process SAMTOOLS_VIEW {
                 args.contains("--output-fmt bam") ? "bam" :
                 args.contains("--output-fmt cram") ? "cram" :
                 input.getExtension()
+
+    output_file = index_format ? "${prefix}.${file_type}##idx##${prefix}.${file_type}.${index_format} --write-index" : "${prefix}.${file_type}"
+    // Can't choose index type of unselected file
     readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": ""
+
     if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if (index_format) {
+        if (!index_format.matches('bai|csi|crai')) {
+            error "Index format not one of bai, csi, crai."
+        } else if (file_type == "sam") {
+            error "Indexing not compatible with SAM output"
+        }
+    }
     """
     samtools \\
         view \\
         --threads ${task.cpus-1} \\
         ${reference} \\
         ${readnames} \\
         $args \\
-        -o ${prefix}.${file_type} \\
+        -o ${output_file} \\
         $input \\
         $args2
 
@@ -61,13 +73,27 @@ process SAMTOOLS_VIEW {
                 args.contains("--output-fmt bam") ? "bam" :
                 args.contains("--output-fmt cram") ? "cram" :
                 input.getExtension()
-    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
-
-    index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
+    default_index_format =
+        file_type == "bam" ? "csi" :
+        file_type == "cram" ? "crai" : ""
+    index =  index_format ? "touch ${prefix}.${file_type}.${index_format}" : args.contains("--write-index") ? "touch ${prefix}.${file_type}.${default_index_format}" : ""
+    unselected = qname ? "touch ${prefix}.unselected.${file_type}" : ""
+    // Can't choose index type of unselected file
+    unselected_index = qname && (args.contains("--write-index") || index_format) ? "touch ${prefix}.unselected.${file_type}.${default_index_format}" : ""
 
+    if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if (index_format) {
+        if (!index_format.matches('bai|csi|crai')) {
+            error "Index format not one of bai, csi, crai."
+        } else if (file_type == "sam") {
+            error "Indexing not compatible with SAM output."
+        }
+    }
     """
     touch ${prefix}.${file_type}
     ${index}
+    ${unselected}
+    ${unselected_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/samtools/view/meta.yml

@@ -43,6 +43,10 @@ input:
         type: file
         description: Optional file with read names to output only select alignments
         pattern: "*.{txt,list}"
+  - - index_format:
+        type: string
+        description: Index format, used together with ext.args = '--write-index'
+        pattern: "*.{bai,csi,crai}"
 output:
   - bam:
       - meta:
@@ -120,10 +124,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - ${prefix}.unselected.${file_type}.{bai,csi,crsi}:
+      - ${prefix}.unselected.${file_type}.{csi,crai}:
           type: file
           description: index for the "unselected" file
-          pattern: "*.unselected.{bai,csi,crai}"
+          pattern: "*.unselected.{csi,crai}"
   - versions:
       - versions.yml:
           type: file

modules/nf-core/samtools/view/tests/cram_index.config

@@ -0,0 +1,3 @@
+process {
+    ext.args = "--output-fmt cram --write-index"
+}