Support CRAM in the hifitrimmer module

Author: muffato

modules/nf-core/hifitrimmer/filterbam/main.nf

@@ -24,7 +24,8 @@ process HIFITRIMMER_FILTERBAM {
    def args = task.ext.args ?: ''
    def args2 = task.ext.args2 ?: ''
    def suffix = args.contains('-f') ? "fastq.gz"  : "fasta.gz"
-   def input_convert = !input.name.endsWith('bam') ? "<(samtools import ${input} ${args2} -@ ${task.cpus})" : input
+   def input_convert = input.name.endsWith('cram') ? "<(samtools view -u ${args2} -@ ${task.cpus} ${input}" :
+        !input.name.endsWith('bam') ? "<(samtools import ${input} ${args2} -@ ${task.cpus})" : input
    """
    hifi_trimmer filter_bam \\
       -t ${task.cpus} \\

modules/nf-core/hifitrimmer/filterbam/tests/main.nf.test

@@ -93,6 +93,33 @@ nextflow_process {
         }
     }
 
+    test("hifi_trimmer filter_bam test - input cram") {
+
+        when {
+            params {
+                filter_bam_args    = ""
+            }
+            process {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id:'test_cram' ], // meta map
+                        file(params.modules_testdata_base_path + '/genomics/eukaryotes/Pipistrellus_nathusii/genome/test.cram', checkIfExists: true),
+                        file(params.modules_testdata_base_path + '/delete_me/hifitrimmer/test.bed.gz', checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("hifi_trimmer test - stub") {
 
         options "-stub"

modules/nf-core/hifitrimmer/filterbam/tests/main.nf.test.snap

@@ -164,6 +164,61 @@
         },
         "timestamp": "2026-02-24T13:47:30.864859989"
     },
+    "hifi_trimmer filter_bam test - input cram": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_cram"
+                        },
+                        "test_cram.fastq.gz:md5,0915fb7cf10a2de8b07a9e0ae81f6316"
+                    ]
+                ],
+                "1": [
+                    [
+                        "HIFITRIMMER_FILTERBAM",
+                        "hifi_trimmer",
+                        "2.2.0"
+                    ]
+                ],
+                "2": [
+                    [
+                        "HIFITRIMMER_FILTERBAM",
+                        "samtools",
+                        "1.23"
+                    ]
+                ],
+                "filtered": [
+                    [
+                        {
+                            "id": "test_bam"
+                        },
+                        "test_cram.fastq.gz:md5,0915fb7cf10a2de8b07a9e0ae81f6316"
+                    ]
+                ],
+                "versions_hifitrimmer": [
+                    [
+                        "HIFITRIMMER_FILTERBAM",
+                        "hifi_trimmer",
+                        "2.2.0"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "HIFITRIMMER_FILTERBAM",
+                        "samtools",
+                        "1.23"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2026-02-24T13:46:26.986596372"
+    },
     "hifi_trimmer filter_bam test - input bam": {
         "content": [
             {
@@ -219,4 +274,4 @@
         },
         "timestamp": "2026-02-24T13:46:26.986596372"
     }
-}
+}