diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8b9a3032c2..073331b0d9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#730](https://github.com/nf-core/sarek/pull/730) - Reduce number of tests
 - [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic`
 - [#733](https://github.com/nf-core/sarek/pull/733) - Add description for params.cf_chrom_len
+- [#734](https://github.com/nf-core/sarek/pull/734) - nf-core modules update -a
 
 ### Fixed
 
diff --git a/conf/modules.config b/conf/modules.config
index e21a7b1845..24e9e7e618 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -301,6 +301,8 @@ process {
 // UMI Subworkflow
 
     withName: 'FASTQTOBAM'{
+        ext.prefix       = {"${meta.id}"}
+        ext.args         = { "--read-structures $params.umi_read_structure" }
         publishDir       = [
             //specify to avoid publishing, overwritten otherwise
             enabled: false
diff --git a/modules.json b/modules.json
index 804374e532..c2064ca0b7 100644
--- a/modules.json
+++ b/modules.json
@@ -6,324 +6,324 @@
             "git_url": "https://github.com/nf-core/modules.git",
             "modules": {
                 "ascat": {
-                    "git_sha": "98ffb090029d17a9fb8de75dadcfe6bc8b6377ec",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "98ffb090029d17a9fb8de75dadcfe6bc8b6377ec"
                 },
                 "bcftools/sort": {
-                    "git_sha": "682f789f93070bd047868300dd018faf3d434e7c",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "682f789f93070bd047868300dd018faf3d434e7c"
                 },
                 "bcftools/stats": {
-                    "git_sha": "535975eb81c9e48eb0403c136b7f1dd7acb1afad",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "bwa/index": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "bwa/mem": {
-                    "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
                 },
                 "bwamem2/index": {
-                    "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "d0ff29fca32ba795177584ebfd51dcd6b0d5f890"
                 },
                 "bwamem2/mem": {
-                    "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "30b04859129f5f4235accdea9fdea8f1feb23809"
                 },
                 "cat/cat": {
-                    "git_sha": "eeda4136c096688d04cc40bb3c70d948213ed641",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "eeda4136c096688d04cc40bb3c70d948213ed641"
                 },
                 "cat/fastq": {
-                    "git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "b034029b59b1198075da8019074bc02051a6100e"
                 },
                 "cnvkit/antitarget": {
-                    "git_sha": "58c5ec2f4eb44eff1fb7cc9e02df07bd448c6aaf",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "58c5ec2f4eb44eff1fb7cc9e02df07bd448c6aaf"
                 },
                 "cnvkit/batch": {
-                    "git_sha": "2f3ddc90fbeda9fcf54f25b84465f5ac149d2b75",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "2f3ddc90fbeda9fcf54f25b84465f5ac149d2b75"
                 },
                 "cnvkit/reference": {
-                    "git_sha": "8208140d21f3a754fff2e177db7a0e570fa2af6e",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "8208140d21f3a754fff2e177db7a0e570fa2af6e"
                 },
                 "controlfreec/assesssignificance": {
-                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"
                 },
                 "controlfreec/freec": {
-                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"
                 },
                 "controlfreec/freec2bed": {
-                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"
                 },
                 "controlfreec/freec2circos": {
-                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"
                 },
                 "controlfreec/makegraph": {
-                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "9ae34a01d1747019fd37753ff4cafb05aec35a2b"
                 },
                 "custom/dumpsoftwareversions": {
-                    "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "deepvariant": {
-                    "git_sha": "fd5f6f5f4ffef4ab5a4e809bd3211bbc71c38d30",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "fd5f6f5f4ffef4ab5a4e809bd3211bbc71c38d30"
                 },
                 "dragmap/align": {
-                    "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "4f5274c3de0c9521f5033893ff61057a74c45ba9"
                 },
                 "dragmap/hashtable": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "ensemblvep": {
-                    "git_sha": "973151e9eab9bac400aa99f099075a10cdd8e84c",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "973151e9eab9bac400aa99f099075a10cdd8e84c"
                 },
                 "fastp": {
-                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "7e8ad566883449e7939062b5e2bcf53fc1e0002f"
                 },
                 "fastqc": {
-                    "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"
                 },
                 "fgbio/callmolecularconsensusreads": {
-                    "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84"
                 },
                 "fgbio/fastqtobam": {
-                    "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "36049bf544c2f3fad7508778b76f56c5e0fe1ee7"
                 },
                 "fgbio/groupreadsbyumi": {
-                    "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "6720d88f4e46e67b9a225f06bfb10c8e8ae04a84"
                 },
                 "freebayes": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
                 },
                 "gatk4/applybqsr": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/applybqsrspark": {
-                    "git_sha": "6a4732ef3b76b54d75533e6be9ba57e3008d4853",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "6a4732ef3b76b54d75533e6be9ba57e3008d4853"
                 },
                 "gatk4/applyvqsr": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/baserecalibrator": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/baserecalibratorspark": {
-                    "git_sha": "6a4732ef3b76b54d75533e6be9ba57e3008d4853",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "6a4732ef3b76b54d75533e6be9ba57e3008d4853"
                 },
                 "gatk4/calculatecontamination": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/cnnscorevariants": {
-                    "git_sha": "5d72500d601432f5396e9022c3a709854197db1a",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5d72500d601432f5396e9022c3a709854197db1a"
                 },
                 "gatk4/createsequencedictionary": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/estimatelibrarycomplexity": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/filtermutectcalls": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/filtervarianttranches": {
-                    "git_sha": "175ea9b7f95a0e2fd3679f7a052c6dcb60b61a6e",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "175ea9b7f95a0e2fd3679f7a052c6dcb60b61a6e"
                 },
                 "gatk4/gatherbqsrreports": {
-                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "848ee9a215d02d80be033bfa60881700f2bd914c"
                 },
                 "gatk4/gatherpileupsummaries": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/genomicsdbimport": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/genotypegvcfs": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/getpileupsummaries": {
-                    "git_sha": "1ac223ad436c1410e9c16a5966274b7ca1f8d855",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "1ac223ad436c1410e9c16a5966274b7ca1f8d855"
                 },
                 "gatk4/haplotypecaller": {
-                    "git_sha": "e53d091a6de1ae9fd681351c085d8abe076ba1ec",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "e53d091a6de1ae9fd681351c085d8abe076ba1ec"
                 },
                 "gatk4/intervallisttobed": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/learnreadorientationmodel": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/markduplicates": {
-                    "git_sha": "df2620cfc7e4c21b14ed03c1c928f09fbabf83c4",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "df2620cfc7e4c21b14ed03c1c928f09fbabf83c4"
                 },
                 "gatk4/markduplicatesspark": {
-                    "git_sha": "8e8f4c9c51a7b229dd45e9b287d48115c238baf3",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "8e8f4c9c51a7b229dd45e9b287d48115c238baf3"
                 },
                 "gatk4/mergemutectstats": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/mergevcfs": {
-                    "git_sha": "4199a05aeb0ec277d40cb112949bb85893310873",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "4199a05aeb0ec277d40cb112949bb85893310873"
                 },
                 "gatk4/mutect2": {
-                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
                 },
                 "gatk4/variantrecalibrator": {
-                    "git_sha": "edfe28a5e0088b66ee92e7c58186059f9b5e62d5",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "edfe28a5e0088b66ee92e7c58186059f9b5e62d5"
                 },
                 "manta/germline": {
-                    "git_sha": "ffedf09b6e84b479c9c901274f74bb33f3777243",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "manta/somatic": {
-                    "git_sha": "979e57b7ac6a405a395dd7a6dbe1a275c5bc226b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "manta/tumoronly": {
-                    "git_sha": "979e57b7ac6a405a395dd7a6dbe1a275c5bc226b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "mosdepth": {
-                    "git_sha": "72a31b76eb1b58879e0d91fb1d992e0118693098",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "72a31b76eb1b58879e0d91fb1d992e0118693098"
                 },
                 "msisensorpro/msi_somatic": {
-                    "git_sha": "f0800157544a82ae222931764483331a81812012",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "f0800157544a82ae222931764483331a81812012"
                 },
                 "msisensorpro/scan": {
-                    "git_sha": "f0800157544a82ae222931764483331a81812012",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "f0800157544a82ae222931764483331a81812012"
                 },
                 "multiqc": {
-                    "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5138acca0985ca01c38a1c4fba917d83772b1106"
                 },
                 "samblaster": {
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
                 },
                 "samtools/bam2fq": {
-                    "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
                 },
                 "samtools/collatefastq": {
-                    "git_sha": "705f8c9ac4dfdf07666e71abde28f267e2dfd5eb",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "705f8c9ac4dfdf07666e71abde28f267e2dfd5eb"
                 },
                 "samtools/convert": {
-                    "git_sha": "da79396f066a96450d9cc9f115c17c9d738595fd",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "samtools/faidx": {
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "samtools/index": {
-                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
                 },
                 "samtools/merge": {
-                    "git_sha": "720027275ccdc1363bb2a19c6412da148e31d94b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "720027275ccdc1363bb2a19c6412da148e31d94b"
                 },
                 "samtools/mpileup": {
-                    "git_sha": "454e0acc09de7cdcc90007420bfe8afa251286fb",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "samtools/stats": {
-                    "git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "f4eab7945952dc4934224309701a49913ea05ae6"
                 },
                 "samtools/view": {
-                    "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "snpeff": {
-                    "git_sha": "ffe037504897df081a7497fa5f495d8e23e93e24",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "ffe037504897df081a7497fa5f495d8e23e93e24"
                 },
                 "strelka/germline": {
-                    "git_sha": "e5b44499efcf6f7fb24874886bac60591c5d94dd",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "strelka/somatic": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "svdb/merge": {
-                    "git_sha": "6b011dd14821385c282e030c6d993d2116aed23f",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "6b011dd14821385c282e030c6d993d2116aed23f"
                 },
                 "tabix/bgziptabix": {
-                    "git_sha": "9dbaffff88013bc21460a989cde7a5aa172c2e0b",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "tabix/tabix": {
-                    "git_sha": "b3e9b88e80880f450ad79a95b2b7aa05e1de5484",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "tiddit/sv": {
-                    "git_sha": "b689b8ed88a9f89eb2f7c75d3eb0bace77ade109",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "b689b8ed88a9f89eb2f7c75d3eb0bace77ade109"
                 },
                 "untar": {
-                    "git_sha": "51be617b1ca9bff973655eb899d591ed6ab253b5",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "unzip": {
-                    "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 },
                 "vcftools": {
-                    "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d",
-                    "branch": "master"
+                    "branch": "master",
+                    "git_sha": "5e7b1ef9a5a2d9258635bcbf70fcf37dacd1b247"
                 }
             }
         }
diff --git a/modules/nf-core/modules/bcftools/stats/main.nf b/modules/nf-core/modules/bcftools/stats/main.nf
index c42ed29a8e..95251d13a9 100644
--- a/modules/nf-core/modules/bcftools/stats/main.nf
+++ b/modules/nf-core/modules/bcftools/stats/main.nf
@@ -1,6 +1,6 @@
 process BCFTOOLS_STATS {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/bwamem2/index/main.nf b/modules/nf-core/modules/bwamem2/index/main.nf
index 900f27d472..6b63ea59a8 100644
--- a/modules/nf-core/modules/bwamem2/index/main.nf
+++ b/modules/nf-core/modules/bwamem2/index/main.nf
@@ -8,11 +8,11 @@ process BWAMEM2_INDEX {
         'quay.io/biocontainers/bwa-mem2:2.2.1--he513fc3_0' }"
 
     input:
-    path fasta
+    tuple val(meta), path(fasta)
 
     output:
-    path "bwamem2"      , emit: index
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("bwamem2"), emit: index
+    path "versions.yml"             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/modules/bwamem2/index/meta.yml b/modules/nf-core/modules/bwamem2/index/meta.yml
index 1b52448d0e..a6b11ae5fd 100644
--- a/modules/nf-core/modules/bwamem2/index/meta.yml
+++ b/modules/nf-core/modules/bwamem2/index/meta.yml
@@ -14,14 +14,24 @@ tools:
       documentation: https://github.com/bwa-mem2/bwa-mem2#usage
       licence: ["MIT"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
       description: Input genome fasta file
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - index:
       type: file
       description: BWA genome index files
-      pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}"
+      pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/modules/bwamem2/mem/main.nf b/modules/nf-core/modules/bwamem2/mem/main.nf
index 978c4019b6..08dc5dfb8c 100644
--- a/modules/nf-core/modules/bwamem2/mem/main.nf
+++ b/modules/nf-core/modules/bwamem2/mem/main.nf
@@ -9,7 +9,7 @@ process BWAMEM2_MEM {
 
     input:
     tuple val(meta), path(reads)
-    path  index
+    tuple val(meta2), path(index)
     val   sort_bam
 
     output:
diff --git a/modules/nf-core/modules/bwamem2/mem/meta.yml b/modules/nf-core/modules/bwamem2/mem/meta.yml
index 25c97f91fe..a465551048 100644
--- a/modules/nf-core/modules/bwamem2/mem/meta.yml
+++ b/modules/nf-core/modules/bwamem2/mem/meta.yml
@@ -37,6 +37,11 @@ input:
       description: use samtools sort (true) or samtools view (false)
       pattern: "true or false"
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
       description: Output BAM file containing read alignments
diff --git a/modules/nf-core/modules/cat/fastq/main.nf b/modules/nf-core/modules/cat/fastq/main.nf
index b685489596..d275f19c1e 100644
--- a/modules/nf-core/modules/cat/fastq/main.nf
+++ b/modules/nf-core/modules/cat/fastq/main.nf
@@ -48,4 +48,33 @@ process CAT_FASTQ {
             """
         }
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def readList = reads.collect{ it.toString() }
+    if (meta.single_end) {
+        if (readList.size > 1) {
+            """
+            touch ${prefix}.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    } else {
+        if (readList.size > 2) {
+            """
+            touch ${prefix}_1.merged.fastq.gz
+            touch ${prefix}_2.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    }
+
 }
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
index 203e485aec..34b50b9f84 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
@@ -1,5 +1,5 @@
 process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_low'
+    label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
     conda (params.enable_conda ? 'bioconda::multiqc=1.13a' : null)
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index 787bdb7b1b..d139039254 100644
--- a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -1,10 +1,9 @@
 #!/usr/bin/env python
 
+import yaml
 import platform
 from textwrap import dedent
 
-import yaml
-
 
 def _make_versions_html(versions):
     html = [
@@ -59,12 +58,11 @@ def _make_versions_html(versions):
 for process, process_versions in versions_by_process.items():
     module = process.split(":")[-1]
     try:
-        if versions_by_module[module] != process_versions:
-            raise AssertionError(
-                "We assume that software versions are the same between all modules. "
-                "If you see this error-message it means you discovered an edge-case "
-                "and should open an issue in nf-core/tools. "
-            )
+        assert versions_by_module[module] == process_versions, (
+            "We assume that software versions are the same between all modules. "
+            "If you see this error-message it means you discovered an edge-case "
+            "and should open an issue in nf-core/tools. "
+        )
     except KeyError:
         versions_by_module[module] = process_versions
 
diff --git a/modules/nf-core/modules/fgbio/fastqtobam/main.nf b/modules/nf-core/modules/fgbio/fastqtobam/main.nf
index 76cfc0752d..a3279491cf 100644
--- a/modules/nf-core/modules/fgbio/fastqtobam/main.nf
+++ b/modules/nf-core/modules/fgbio/fastqtobam/main.nf
@@ -9,11 +9,11 @@ process FGBIO_FASTQTOBAM {
 
     input:
     tuple val(meta), path(reads)
-    val read_structure
 
     output:
-    tuple val(meta), path("*_umi_converted.bam"), emit: umibam
-    path "versions.yml"                         , emit: versions
+    tuple val(meta), path("*.bam") , emit: bam , optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,17 +21,19 @@ process FGBIO_FASTQTOBAM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def sample_name = args.contains("--sample") ? "" : "--sample ${prefix}"
+    def library_name = args.contains("--library") ? "" : "--library ${prefix}"
+    def output = prefix =~ /\.(bam|cram)$/ ? prefix : "${prefix}.bam"
     """
 
     fgbio \\
         --tmp-dir=. \\
         FastqToBam \\
-        -i $reads \\
-        -o "${prefix}_umi_converted.bam" \\
-        --read-structures $read_structure \\
-        --sample $meta.id \\
-        --library $meta.id \\
-        $args
+        ${args} \\
+        --input ${reads} \\
+        --output ${output} \\
+        ${sample_name} \\
+        ${library_name}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/modules/fgbio/fastqtobam/meta.yml b/modules/nf-core/modules/fgbio/fastqtobam/meta.yml
index 3081cafc83..6769fc1521 100644
--- a/modules/nf-core/modules/fgbio/fastqtobam/meta.yml
+++ b/modules/nf-core/modules/fgbio/fastqtobam/meta.yml
@@ -1,6 +1,6 @@
 name: fgbio_fastqtobam
 description: |
-  Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file
+  Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
 keywords:
   - fastqtobam
   - fgbio
@@ -19,15 +19,6 @@ input:
       description: pair of reads to be converted into BAM file
       pattern: "*.{fastq.gz}"
 
-  - read_structure:
-      type: string
-      description: |
-        A read structure should always be provided for each of the fastq files.
-        If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string
-        will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T").
-        If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
-        https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
-
 output:
   - meta:
       type: map
@@ -38,10 +29,15 @@ output:
       type: file
       description: File containing software version
       pattern: "*.{version.yml}"
-  - umibam:
+  - bam:
       type: file
-      description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any)
+      description: Unaligned, unsorted BAM file
       pattern: "*.{bam}"
+  - cram:
+      type: file
+      description: Unaligned, unsorted CRAM file
+      pattern: "*.{cram}"
 
 authors:
   - "@lescai"
+  - "@matthdsm"
diff --git a/modules/nf-core/modules/manta/germline/main.nf b/modules/nf-core/modules/manta/germline/main.nf
index c680dc9d3d..5f2964fbd0 100644
--- a/modules/nf-core/modules/manta/germline/main.nf
+++ b/modules/nf-core/modules/manta/germline/main.nf
@@ -1,6 +1,6 @@
 process MANTA_GERMLINE {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/manta/somatic/main.nf b/modules/nf-core/modules/manta/somatic/main.nf
index 6313c38bdd..0b40965b7c 100644
--- a/modules/nf-core/modules/manta/somatic/main.nf
+++ b/modules/nf-core/modules/manta/somatic/main.nf
@@ -1,6 +1,6 @@
 process MANTA_SOMATIC {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/manta/tumoronly/main.nf b/modules/nf-core/modules/manta/tumoronly/main.nf
index 3361cf82be..759f9cb9ec 100644
--- a/modules/nf-core/modules/manta/tumoronly/main.nf
+++ b/modules/nf-core/modules/manta/tumoronly/main.nf
@@ -1,6 +1,6 @@
 process MANTA_TUMORONLY {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::manta=1.6.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/samtools/convert/main.nf b/modules/nf-core/modules/samtools/convert/main.nf
index e0e7d725d7..eea00179c6 100644
--- a/modules/nf-core/modules/samtools/convert/main.nf
+++ b/modules/nf-core/modules/samtools/convert/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_CONVERT {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/samtools/faidx/main.nf b/modules/nf-core/modules/samtools/faidx/main.nf
index fdce7d9b8b..36b3538e55 100644
--- a/modules/nf-core/modules/samtools/faidx/main.nf
+++ b/modules/nf-core/modules/samtools/faidx/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_FAIDX {
     tag "$fasta"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -22,6 +22,7 @@ process SAMTOOLS_FAIDX {
     """
     samtools \\
         faidx \\
+        $args \\
         $fasta
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/modules/samtools/mpileup/main.nf b/modules/nf-core/modules/samtools/mpileup/main.nf
index 34a1b508e3..fe8e32b4ce 100644
--- a/modules/nf-core/modules/samtools/mpileup/main.nf
+++ b/modules/nf-core/modules/samtools/mpileup/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_MPILEUP {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/samtools/stats/main.nf b/modules/nf-core/modules/samtools/stats/main.nf
index 89b92d79eb..9b0c386789 100644
--- a/modules/nf-core/modules/samtools/stats/main.nf
+++ b/modules/nf-core/modules/samtools/stats/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_STATS {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -25,7 +25,7 @@ process SAMTOOLS_STATS {
     """
     samtools \\
         stats \\
-        --threads ${task.cpus-1} \\
+        --threads ${task.cpus} \\
         ${reference} \\
         ${input} \\
         > ${prefix}.stats
diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf
index 55194e887f..59ded5c3b8 100644
--- a/modules/nf-core/modules/samtools/view/main.nf
+++ b/modules/nf-core/modules/samtools/view/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_VIEW {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/strelka/germline/main.nf b/modules/nf-core/modules/strelka/germline/main.nf
index 02364273d6..1f59bee157 100644
--- a/modules/nf-core/modules/strelka/germline/main.nf
+++ b/modules/nf-core/modules/strelka/germline/main.nf
@@ -1,6 +1,6 @@
 process STRELKA_GERMLINE {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/strelka/somatic/main.nf b/modules/nf-core/modules/strelka/somatic/main.nf
index b61c09bd8c..08b298a463 100644
--- a/modules/nf-core/modules/strelka/somatic/main.nf
+++ b/modules/nf-core/modules/strelka/somatic/main.nf
@@ -1,6 +1,6 @@
 process STRELKA_SOMATIC {
     tag "$meta.id"
-    label 'process_high'
+    label 'process_medium'
 
     conda (params.enable_conda ? "bioconda::strelka=2.9.10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/tabix/bgziptabix/main.nf b/modules/nf-core/modules/tabix/bgziptabix/main.nf
index 03e3b0c320..0d05984add 100644
--- a/modules/nf-core/modules/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/modules/tabix/bgziptabix/main.nf
@@ -1,6 +1,6 @@
 process TABIX_BGZIPTABIX {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/tabix/tabix/main.nf b/modules/nf-core/modules/tabix/tabix/main.nf
index e155e4685a..21b2e79f48 100644
--- a/modules/nf-core/modules/tabix/tabix/main.nf
+++ b/modules/nf-core/modules/tabix/tabix/main.nf
@@ -1,6 +1,6 @@
 process TABIX_TABIX {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf
index 29ab10a505..4128652008 100644
--- a/modules/nf-core/modules/untar/main.nf
+++ b/modules/nf-core/modules/untar/main.nf
@@ -1,6 +1,6 @@
 process UNTAR {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/unzip/main.nf b/modules/nf-core/modules/unzip/main.nf
index 8476a2eba4..bb645ca63f 100644
--- a/modules/nf-core/modules/unzip/main.nf
+++ b/modules/nf-core/modules/unzip/main.nf
@@ -1,6 +1,6 @@
 process UNZIP {
     tag "$archive"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::p7zip=15.09" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/modules/nf-core/modules/vcftools/main.nf b/modules/nf-core/modules/vcftools/main.nf
index 78b95fae3f..feefb0e3f8 100644
--- a/modules/nf-core/modules/vcftools/main.nf
+++ b/modules/nf-core/modules/vcftools/main.nf
@@ -1,6 +1,6 @@
 process VCFTOOLS {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::vcftools=0.1.16" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index 58d140aff1..f2652b6f5c 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -45,17 +45,17 @@ workflow PREPARE_GENOME {
 
     ch_versions = Channel.empty()
 
-    BWAMEM1_INDEX(fasta)     // If aligner is bwa-mem
-    BWAMEM2_INDEX(fasta)     // If aligner is bwa-mem2
-    DRAGMAP_HASHTABLE(fasta) // If aligner is dragmap
+    BWAMEM1_INDEX(fasta)                                        // If aligner is bwa-mem
+    BWAMEM2_INDEX(fasta.map{ it -> [[id:it[0].baseName], it] }) // If aligner is bwa-mem2
+    DRAGMAP_HASHTABLE(fasta)                                    // If aligner is dragmap
 
     GATK4_CREATESEQUENCEDICTIONARY(fasta)
     MSISENSORPRO_SCAN(fasta.map{ it -> [[id:it[0].baseName], it] })
-    SAMTOOLS_FAIDX(fasta.map{ it -> [[id:it[0].getName()], it] })
+    SAMTOOLS_FAIDX(fasta.map{ it -> [[id:it[0].baseName], it] })
 
     // the following are flattened and mapped in case the user supplies more than one value for the param
     // written for KNOWN_INDELS, but preemptively applied to the rest
-    // [file1,file2] becomes [[meta1,file1],[meta2,file2]]
+    // [file1, file2] becomes [[meta1, file1],[meta2, file2]]
     // outputs are collected to maintain a single channel for relevant TBI files
     TABIX_DBSNP(dbsnp.flatten().map{ it -> [[id:it.baseName], it] })
     TABIX_GERMLINE_RESOURCE(germline_resource.flatten().map{ it -> [[id:it.baseName], it] })
@@ -112,13 +112,13 @@ workflow PREPARE_GENOME {
 
     emit:
         bwa                              = BWAMEM1_INDEX.out.index                                             // path: bwa/*
-        bwamem2                          = BWAMEM2_INDEX.out.index                                             // path: bwamem2/*
+        bwamem2                          = BWAMEM2_INDEX.out.index.map{ meta, index -> [index] }.collect()     // path: bwamem2/*
         hashtable                        = DRAGMAP_HASHTABLE.out.hashmap                                       // path: dragmap/*
         dbsnp_tbi                        = TABIX_DBSNP.out.tbi.map{ meta, tbi -> [tbi] }.collect()             // path: dbsnb.vcf.gz.tbi
         dict                             = GATK4_CREATESEQUENCEDICTIONARY.out.dict                             // path: genome.fasta.dict
         fasta_fai                        = SAMTOOLS_FAIDX.out.fai.map{ meta, fai -> [fai] }                    // path: genome.fasta.fai
         germline_resource_tbi            = TABIX_GERMLINE_RESOURCE.out.tbi.map{ meta, tbi -> [tbi] }.collect() // path: germline_resource.vcf.gz.tbi
-        known_snps_tbi                   = TABIX_KNOWN_SNPS.out.tbi.map{ meta, tbi -> [tbi] }.collect()      // path: {known_indels*}.vcf.gz.tbi
+        known_snps_tbi                   = TABIX_KNOWN_SNPS.out.tbi.map{ meta, tbi -> [tbi] }.collect()        // path: {known_indels*}.vcf.gz.tbi
         known_indels_tbi                 = TABIX_KNOWN_INDELS.out.tbi.map{ meta, tbi -> [tbi] }.collect()      // path: {known_indels*}.vcf.gz.tbi
         msisensorpro_scan                = MSISENSORPRO_SCAN.out.list.map{ meta, list -> [list] }              // path: genome_msi.list
         pon_tbi                          = TABIX_PON.out.tbi.map{ meta, tbi -> [tbi] }.collect()               // path: pon.vcf.gz.tbi
diff --git a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
index 030397a966..df5302619e 100644
--- a/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
+++ b/subworkflows/nf-core/fgbio_create_umi_consensus/main.nf
@@ -18,22 +18,21 @@ workflow CREATE_UMI_CONSENSUS {
     reads                     // channel: [mandatory] [ val(meta), [ reads ] ]
     fasta                     // channel: [mandatory] /path/to/reference/fasta
     map_index                 // channel: [mandatory] Pre-computed mapping index
-    read_structure            // string:  [mandatory] "read_structure"
     groupreadsbyumi_strategy  // string:  [mandatory] grouping strategy - default: "Adjacency"
 
     main:
     ch_versions = Channel.empty()
 
-    // using information in val(read_structure) FASTQ reads are converted into
-    // a tagged unmapped BAM file (uBAM)
-    FASTQTOBAM(reads, read_structure)
+    // params.umi_read_structure is passed out as ext.args
+    // FASTQ reads are converted into a tagged unmapped BAM file (uBAM)
+    FASTQTOBAM(reads)
 
     // in order to map uBAM using BWA MEM, we need to convert uBAM to FASTQ
     // TODO check if DRAGMAP works well with BAM inputs
     // but keep the appropriate UMI tags in the FASTQ comment field and produce
     // an interleaved FASQT file (hence, split = false)
     split = false
-    BAM2FASTQ(FASTQTOBAM.out.umibam, split)
+    BAM2FASTQ(FASTQTOBAM.out.bam, split)
 
     // appropriately tagged interleaved FASTQ reads are mapped to the reference
     // bams will not be sorted (hence, sort = false)
@@ -60,7 +59,7 @@ workflow CREATE_UMI_CONSENSUS {
     ch_versions = ch_versions.mix(SAMBLASTER.out.versions)
 
     emit:
-    umibam         = FASTQTOBAM.out.umibam          // channel: [ val(meta), [ bam ] ]
+    umibam         = FASTQTOBAM.out.bam             // channel: [ val(meta), [ bam ] ]
     groupbam       = GROUPREADSBYUMI.out.bam        // channel: [ val(meta), [ bam ] ]
     consensusbam   = CALLUMICONSENSUS.out.bam       // channel: [ val(meta), [ bam ] ]
     versions       = ch_versions                    // channel: [ versions.yml ]
diff --git a/subworkflows/nf-core/gatk4/mapping/main.nf b/subworkflows/nf-core/gatk4/mapping/main.nf
index 8c820677ff..bc89fdb394 100644
--- a/subworkflows/nf-core/gatk4/mapping/main.nf
+++ b/subworkflows/nf-core/gatk4/mapping/main.nf
@@ -20,9 +20,9 @@ workflow GATK4_MAPPING {
     ch_reports  = Channel.empty()
 
     // Only one of the following should be run
-    BWAMEM1_MEM(ch_reads,   ch_map_index, sort) // If aligner is bwa-mem
-    BWAMEM2_MEM(ch_reads,   ch_map_index, sort) // If aligner is bwa-mem2
-    DRAGMAP_ALIGN(ch_reads, ch_map_index, sort) // If aligner is dragmap
+    BWAMEM1_MEM(ch_reads,   ch_map_index, sort)                                        // If aligner is bwa-mem
+    BWAMEM2_MEM(ch_reads,   ch_map_index.map{ it -> [[id:it[0].baseName], it] }, sort) // If aligner is bwa-mem2
+    DRAGMAP_ALIGN(ch_reads, ch_map_index, sort)                                        // If aligner is dragmap
 
     // Get the bam files from the aligner
     // Only one aligner is run
diff --git a/tests/test_aligner.yml b/tests/test_aligner.yml
index 4d913cbb4f..ff73b59197 100644
--- a/tests/test_aligner.yml
+++ b/tests/test_aligner.yml
@@ -70,9 +70,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
 - name: Run dragmap
   command: nextflow run main.nf -profile test,docker --aligner dragmap --save_reference
   tags:
@@ -160,6 +160,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: d5f1c9389ecf52ba839e834780a94549
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: f2ae8b531aa1fb2fbffe9a92e4c81493
+      md5sum: 9f64e86202f2291b33c0e8c3e7981193
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: f7bab59db4fb8ab49eea71b668d351d5
+      md5sum: a63f247fb403d8679c8f96f3a128aba0
diff --git a/tests/test_bam_remap.yml b/tests/test_bam_remap.yml
index c30613f946..630c6cefad 100644
--- a/tests/test_bam_remap.yml
+++ b/tests/test_bam_remap.yml
@@ -44,6 +44,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: d0713716f63ac573f4a3385733e9a537
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 5201890d36c1dd127b930373b6e823e5
+      md5sum: d6634d51a009e3da43b2349e424b2d9f
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: bb2fc6118a1404c45f9e828600df8fb1
+      md5sum: 91915547ff9e654c106a42e5edfd9405
diff --git a/tests/test_default.yml b/tests/test_default.yml
index e2cef4b222..80794a291b 100644
--- a/tests/test_default.yml
+++ b/tests/test_default.yml
@@ -49,9 +49,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
     - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
       md5sum: dd87f507da7de20d5318841af312493b
     - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
@@ -121,6 +121,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: f7005dd4646700e107bfc00e36c432fe
+      md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml
index cd35041ddc..f54aaa3aea 100644
--- a/tests/test_gatk_spark.yml
+++ b/tests/test_gatk_spark.yml
@@ -45,6 +45,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
       md5sum: c259a9fd73f576626c3a29841c2dc019
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 2e4edbad7d0fb88d7834114a2d5ab534
+      md5sum: b573b2e930c5f68e7e4910faf9e51e44
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 996b6f18a9ad4aa4ebc8a38f559471a0
+      md5sum: a75731dca9b42d87d9997ea44aaf82fc
diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates.yml
index 7c8fef9ffb..563a3b35bf 100644
--- a/tests/test_markduplicates.yml
+++ b/tests/test_markduplicates.yml
@@ -45,9 +45,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
     # binary changes md5sums on reruns.
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 06fdce012030eeb6d1c1c529b382c564
+      md5sum: a0ecedb6be28639e276d38e4ac18935b
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: c37a9db008f05a0aaf591f0bb41ef387
+      md5sum: 69d2bab6fdbe21ec5c598dc404a3df00
 - name: Run markduplicates starting from CRAM
   command: nextflow run main.nf -profile test,markduplicates_cram
   tags:
@@ -95,9 +95,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
     # binary changes md5sums on reruns.
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 06fdce012030eeb6d1c1c529b382c564
+      md5sum: a0ecedb6be28639e276d38e4ac18935b
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: c37a9db008f05a0aaf591f0bb41ef387
+      md5sum: 69d2bab6fdbe21ec5c598dc404a3df00
     - path: results/samtools/test.bam
     # binary changes md5sums on reruns.
     - path: results/samtools/test.bam.bai
diff --git a/tests/test_pair.yml b/tests/test_pair.yml
index ce3063881f..409f585baf 100644
--- a/tests/test_pair.yml
+++ b/tests/test_pair.yml
@@ -78,10 +78,10 @@
     - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
       md5sum: d5f1c9389ecf52ba839e834780a94549
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
     - path: results/reports/samtools/test2/test2.md.cram.stats
-      md5sum: ad42bfa581dddc911ebd36d386a330a3
+      md5sum: 60152dbf1e109d4c407c151204388109
     - path: results/reports/samtools/test2/test2.recal.cram.stats
-      md5sum: 9cc426e4cf249288b61816f806f74bfd
+      md5sum: 2907543ab51cabd97318b15cf035c867
diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml
index 283ccdb350..0becfe55cb 100644
--- a/tests/test_prepare_recalibration.yml
+++ b/tests/test_prepare_recalibration.yml
@@ -31,7 +31,7 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b3716e5cd1744610e69c29bd4ffad259
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 61fd75f684ee1b98fd29d7005199762e
+      md5sum: 71af990f7acad8bf24d37e88c4adcded
 - name: Run prepare_recalibration starting from cram
   command: nextflow run main.nf -profile test,prepare_recalibration_cram
   tags:
@@ -59,7 +59,7 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b3716e5cd1744610e69c29bd4ffad259
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 61fd75f684ee1b98fd29d7005199762e
+      md5sum: 71af990f7acad8bf24d37e88c4adcded
 - name: Run prepare_recalibration starting from bam and skip baserecalibration
   command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka
   tags:
diff --git a/tests/test_recalibrate.yml b/tests/test_recalibrate.yml
index 2a7d47a4c6..91341c9119 100644
--- a/tests/test_recalibrate.yml
+++ b/tests/test_recalibrate.yml
@@ -27,7 +27,7 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b3716e5cd1744610e69c29bd4ffad259
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 1787b3a12b134fe35ab166431f107fc4
+      md5sum: a0841c41460d0d4bdc2a1a777ee7e7c2
 - name: Run Recalibration starting from cram
   command: nextflow run main.nf -profile test,recalibrate_cram
   tags:
@@ -53,7 +53,7 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b3716e5cd1744610e69c29bd4ffad259
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 1787b3a12b134fe35ab166431f107fc4
+      md5sum: a0841c41460d0d4bdc2a1a777ee7e7c2
 - name: Run Recalibration starting from bam and skip baserecalibration
   command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr --tools strelka
   tags:
diff --git a/tests/test_save_bam_mapped.yml b/tests/test_save_bam_mapped.yml
index abf388b8ee..71629918cc 100644
--- a/tests/test_save_bam_mapped.yml
+++ b/tests/test_save_bam_mapped.yml
@@ -51,6 +51,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
diff --git a/tests/test_save_output_bam.yml b/tests/test_save_output_bam.yml
index 5051d723b3..2f29413999 100644
--- a/tests/test_save_output_bam.yml
+++ b/tests/test_save_output_bam.yml
@@ -45,9 +45,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
 - name: Run save_output_as_bam with gatk4 spark
   command: nextflow run main.nf -profile test,use_gatk_spark --save_output_as_bam
   tags:
@@ -96,6 +96,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: cf85ba4692f016af70db2a594d9effdf
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 2e4edbad7d0fb88d7834114a2d5ab534
+      md5sum: b573b2e930c5f68e7e4910faf9e51e44
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 996b6f18a9ad4aa4ebc8a38f559471a0
+      md5sum: a75731dca9b42d87d9997ea44aaf82fc
diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml
index dd9bdceaa2..2974bebd09 100644
--- a/tests/test_skip_markduplicates.yml
+++ b/tests/test_skip_markduplicates.yml
@@ -47,9 +47,9 @@
     - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
       md5sum: e3235323f455414ee3acc7144e659caf
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 58deb5e1d74a991f863136a218c8f56c
+      md5sum: 55ddd2d98552a1483bf2a965f19d8da4
     - path: results/reports/samtools/test/test.sorted.cram.stats
-      md5sum: 494976d0d5b3ca029c986cf9e79bb7b3
+      md5sum: 59d921ed3970e19145fbae75966de3e3
     - path: results/csv/markduplicates.csv
       should_exist: false
     - path: results/csv/markduplicates_no_table.csv
@@ -97,9 +97,9 @@
     - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
       md5sum: b3716e5cd1744610e69c29bd4ffad259
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 61fd75f684ee1b98fd29d7005199762e
+      md5sum: 71af990f7acad8bf24d37e88c4adcded
     - path: results/reports/samtools/test/test.sorted.cram.stats
-      md5sum: 9fc99b31174fc1ea50cd7644c50f42aa
+      md5sum: ac78da9dde7bae6849c0e2488bf7506a
     - path: results/csv/markduplicates.csv
       should_exist: false
     - path: results/csv/markduplicates_no_table.csv
@@ -141,9 +141,9 @@
     - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
       md5sum: b3716e5cd1744610e69c29bd4ffad259
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 61fd75f684ee1b98fd29d7005199762e
+      md5sum: 71af990f7acad8bf24d37e88c4adcded
     - path: results/reports/samtools/test/test.sorted.cram.stats
-      md5sum: a0105eedd6ff6c840f0853434addb0c1
+      md5sum: 42b536ada66f772bb4dfd741098b2783
     - path: results/csv/markduplicates.csv
       should_exist: false
     - path: results/csv/markduplicates_no_table.csv
diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml
index 72c76a743c..d067e67166 100644
--- a/tests/test_split_fastq.yml
+++ b/tests/test_split_fastq.yml
@@ -52,6 +52,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: 1b65ac38cd96783394e0cf9b7bdd5bc2
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 013094be804395f1168077076accd078
+      md5sum: 44c873922c844b85c0920d22c98b08cf
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: c0bf46dc246b21320f77ef4f395eca0c
+      md5sum: 5ad46c4c701943dfc67604ed34c1c69e
diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml
index e4aba5ab9e..ce1e3b36eb 100644
--- a/tests/test_targeted.yml
+++ b/tests/test_targeted.yml
@@ -53,9 +53,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: c6d1ac97ef4dfe43731c8368d8391cab
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: ecad3c41de5b82f6bc0c429e7b24958e
+      md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98
 
 - name: Run intervals false pipeline
   command: nextflow run main.nf -profile test --intervals false
@@ -100,6 +100,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
       md5sum: 38fe39894abe62e38f8ac214cba64f2b
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 5528d952f5dc74a39f28e27165bf96be
+      md5sum: 811d834ff8849e69e7c5925dc2a34257
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
index a3f54dc1e5..9d3c289be1 100644
--- a/tests/test_tools.yml
+++ b/tests/test_tools.yml
@@ -406,9 +406,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: c6d1ac97ef4dfe43731c8368d8391cab
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: ecad3c41de5b82f6bc0c429e7b24958e
+      md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98
     - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
       md5sum: 43d53e36cbb1091f915b2499e545b41e
     - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
@@ -480,9 +480,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: b1c2a861f64e20a94108a6de3b76c582
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: f7005dd4646700e107bfc00e36c432fe
+      md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
     - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
       md5sum: 76c5919541536c12b5c8a6094d6d78d5
     - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
@@ -597,13 +597,13 @@
     - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
       md5sum: c6d1ac97ef4dfe43731c8368d8391cab
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: ecad3c41de5b82f6bc0c429e7b24958e
+      md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98
     - path: results/reports/samtools/test2/test2.md.cram.stats
-      md5sum: ad42bfa581dddc911ebd36d386a330a3
+      md5sum: 60152dbf1e109d4c407c151204388109
     - path: results/reports/samtools/test2/test2.recal.cram.stats
-      md5sum: d5ecf9b3e13d5de98fcbc2e8f2cb02be
+      md5sum: 53a0b34b67fdf90ea68fac8ea744b576
     - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
       md5sum: 43d53e36cbb1091f915b2499e545b41e
     - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
@@ -712,13 +712,13 @@
     - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi
       md5sum: 4205a09ede17cdbdaad45e3553f73105
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: dcf70bbcfb92e01027978f28d2035d78
+      md5sum: 52411f93d9b5382342b40a351c2e313c
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: f7005dd4646700e107bfc00e36c432fe
+      md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38
     - path: results/reports/samtools/test2/test2.md.cram.stats
-      md5sum: ad42bfa581dddc911ebd36d386a330a3
+      md5sum: 60152dbf1e109d4c407c151204388109
     - path: results/reports/samtools/test2/test2.recal.cram.stats
-      md5sum: 5dd3570db59cce7f7addd0257e858289
+      md5sum: 029b903797dc228e56d6ab74e677fa21
     - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary
       md5sum: 76c5919541536c12b5c8a6094d6d78d5
     - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count
diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml
index 8111c398c0..ccbdb831f6 100644
--- a/tests/test_trimming.yml
+++ b/tests/test_trimming.yml
@@ -50,6 +50,6 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: a5ad8f917979f62eacfff1461529dbaa
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: bba23d14aa20be36bf87bedf91c8832c
+      md5sum: 7382e028335a2b057cb54ea160c4be7b
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: deb6f58a0d339e821e98c25b456f7eb7
+      md5sum: 5adeae7e9ce068009e88bacba549096e
diff --git a/tests/test_umi.yml b/tests/test_umi.yml
index 4446586014..673d6cdd54 100644
--- a/tests/test_umi.yml
+++ b/tests/test_umi.yml
@@ -46,9 +46,9 @@
     - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
       md5sum: d0713716f63ac573f4a3385733e9a537
     - path: results/reports/samtools/test/test.md.cram.stats
-      md5sum: 072daded4cd3bd08f2c94ef1f1478052
+      md5sum: 9c424aaae1d200f67a1ecc3e55ad5a6a
     - path: results/reports/samtools/test/test.recal.cram.stats
-      md5sum: 1537c827260f24e3fa0f0dc257580b41
+      md5sum: e64175125c512651b2819ced400bc846
 # - name: Run UMI TSO test
 #   command: nextflow run main.nf -profile test,umi_tso
 #   tags:
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 057fee0a1a..19dd7165db 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -189,9 +189,6 @@ if (params.spliceai_snv && params.spliceai_snv_tbi && params.spliceai_indel && p
     vep_extra_files.add(file(params.spliceai_snv_tbi, checkIfExists: true))
 }
 
-// Initialize value channels based on params, not defined within the params.genomes[params.genome] scope
-umi_read_structure = params.umi_read_structure ? "${params.umi_read_structure}" : Channel.empty()
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT LOCAL/NF-CORE MODULES/SUBWORKFLOWS
@@ -414,7 +411,6 @@ workflow SAREK {
                 ch_input_fastq,
                 fasta,
                 ch_map_index,
-                umi_read_structure,
                 params.group_by_umi_strategy
             )