diff --git a/modules.json b/modules.json
index f5561b1..44bf8bf 100644
--- a/modules.json
+++ b/modules.json
@@ -88,9 +88,8 @@
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/samtools/view/samtools-view.diff"
+                        "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
index 141e7bd..150c377 100644
--- a/modules/nf-core/samtools/view/environment.yml
+++ b/modules/nf-core/samtools/view/environment.yml
@@ -4,4 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.17
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 613c6e7..dc61144 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_VIEW {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(index)
@@ -13,14 +13,15 @@ process SAMTOOLS_VIEW {
     path qname
 
     output:
-    tuple val(meta), path("*.bam"),  emit: bam,     optional: true
-    tuple val(meta), path("*.cram"), emit: cram,    optional: true
-    tuple val(meta), path("*.sam"),  emit: sam,     optional: true
-    tuple val(meta), path("*.bai"),  emit: bai,     optional: true
-    tuple val(meta), path("*.csi"),  emit: csi,     optional: true
-    tuple val(meta), path("*.crai"), emit: crai,    optional: true
-    tuple val(meta), path("*.unoutput"), emit: unoutput, optional: true
-    path  "versions.yml",            emit: versions
+    tuple val(meta), path("${prefix}.bam"),                                    emit: bam,              optional: true
+    tuple val(meta), path("${prefix}.cram"),                                   emit: cram,             optional: true
+    tuple val(meta), path("${prefix}.sam"),                                    emit: sam,              optional: true
+    tuple val(meta), path("${prefix}.${file_type}.bai"),                       emit: bai,              optional: true
+    tuple val(meta), path("${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
+    path  "versions.yml",                                                      emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,13 +29,13 @@ process SAMTOOLS_VIEW {
     script:
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def reference = fasta ? "--reference ${fasta}" : ""
-    def readnames = qname ? "--qname-file ${qname} --unoutput ${prefix}.unoutput": ""
-    def file_type = args.contains("--output-fmt sam") ? "sam" :
-                    args.contains("--output-fmt bam") ? "bam" :
-                    args.contains("--output-fmt cram") ? "cram" :
-                    input.getExtension()
+    file_type = args.contains("--output-fmt sam") ? "sam" :
+                args.contains("--output-fmt bam") ? "bam" :
+                args.contains("--output-fmt cram") ? "cram" :
+                input.getExtension()
+    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!"
     """
     samtools \\
@@ -54,10 +55,19 @@ process SAMTOOLS_VIEW {
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    file_type = args.contains("--output-fmt sam") ? "sam" :
+                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!"
+
+    def index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : ""
+
     """
-    touch ${prefix}.bam
-    touch ${prefix}.cram
+    touch ${prefix}.${file_type}
+    ${index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml
index 3dadafa..27be60d 100644
--- a/modules/nf-core/samtools/view/meta.yml
+++ b/modules/nf-core/samtools/view/meta.yml
@@ -73,6 +73,15 @@ output:
       type: file
       description: optional CRAM file index
       pattern: "*.{crai}"
+  # unselected and unselected_index are created when passing a qname
+  - unselected:
+      type: file
+      description: optional file with unselected alignments
+      pattern: "*.unselected.{bam,cram,sam}"
+  - unselected_index:
+      type: file
+      description: index for the "unselected" file
+      pattern: "*.unselected.{bai,csi,crai}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/samtools/view/samtools-view.diff b/modules/nf-core/samtools/view/samtools-view.diff
deleted file mode 100644
index 1fa860a..0000000
--- a/modules/nf-core/samtools/view/samtools-view.diff
+++ /dev/null
@@ -1,22 +0,0 @@
-Changes in module 'nf-core/samtools/view'
---- modules/nf-core/samtools/view/main.nf
-+++ modules/nf-core/samtools/view/main.nf
-@@ -19,6 +19,7 @@
-     tuple val(meta), path("*.bai"),  emit: bai,     optional: true
-     tuple val(meta), path("*.csi"),  emit: csi,     optional: true
-     tuple val(meta), path("*.crai"), emit: crai,    optional: true
-+    tuple val(meta), path("*.unoutput"), emit: unoutput, optional: true
-     path  "versions.yml",            emit: versions
- 
-     when:
-@@ -29,7 +30,7 @@
-     def args2 = task.ext.args2 ?: ''
-     def prefix = task.ext.prefix ?: "${meta.id}"
-     def reference = fasta ? "--reference ${fasta}" : ""
--    def readnames = qname ? "--qname-file ${qname}": ""
-+    def readnames = qname ? "--qname-file ${qname} --unoutput ${prefix}.unoutput": ""
-     def file_type = args.contains("--output-fmt sam") ? "sam" :
-                     args.contains("--output-fmt bam") ? "bam" :
-                     args.contains("--output-fmt cram") ? "cram" :
-
-************************************************************
diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf
index 3f6916c..99f0a1a 100644
--- a/subworkflows/local/filter_pacbio.nf
+++ b/subworkflows/local/filter_pacbio.nf
@@ -77,7 +77,7 @@ workflow FILTER_PACBIO {
 
 
     // Convert BAM to FASTQ
-    SAMTOOLS_FASTQ ( SAMTOOLS_FILTER.out.unoutput, true )
+    SAMTOOLS_FASTQ ( SAMTOOLS_FILTER.out.unselected, true )
     ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() )