From f6afe61dbe88945c381a0788d1a6fb61cb356718 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 25 May 2023 16:35:31 +0200
Subject: [PATCH 1/8] add module and remove redundant parameters

---
 conf/modules/prepare_references.config    |   9 +
 main.nf                                   |   9 +-
 modules.json                              | 283 ++++++++++++++++------
 modules/nf-core/gatk4/shiftfasta/main.nf  |  66 +++++
 modules/nf-core/gatk4/shiftfasta/meta.yml |  81 +++++++
 modules/nf-core/samtools/faidx/main.nf    |  12 +-
 modules/nf-core/samtools/faidx/meta.yml   |  14 +-
 nextflow_schema.json                      |  58 +----
 subworkflows/local/prepare_references.nf  |  30 ++-
 workflows/raredisease.nf                  |  36 ++-
 10 files changed, 426 insertions(+), 172 deletions(-)
 create mode 100644 modules/nf-core/gatk4/shiftfasta/main.nf
 create mode 100644 modules/nf-core/gatk4/shiftfasta/meta.yml

diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
index 8504a34c..af73549a 100644
--- a/conf/modules/prepare_references.config
+++ b/conf/modules/prepare_references.config
@@ -49,6 +49,11 @@ process {
         ext.when = {!params.fai}
     }
 
+    withName: '.*PREPARE_REFERENCES:SAMTOOLS_EXTRACT_MT' {
+        ext.args = { " ${params.mito_name} -o ${meta.id}_mt.fa" }
+        ext.when = {!params.mt_fasta && !params.skip_mt_analysis}
+    }
+
     withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_SHIFT_MT' {
         ext.when = {!params.mt_fai_shift && params.mt_fasta_shift && !(params.analysis_type == "wes")}
     }
@@ -57,6 +62,10 @@ process {
         ext.when = {!params.sequence_dictionary}
     }
 
+    withName: '.*PREPARE_REFERENCES:GATK_SHIFTFASTA' {
+        ext.args = { "--interval-file-name ${meta.id}_mt" }
+    }
+
     withName: '.*PREPARE_REFERENCES:GATK_SD_SHIFT_MT' {
         ext.when = {!params.mt_sequence_dictionary_shift && params.mt_fasta_shift && !(params.analysis_type == "wes")}
     }
diff --git a/main.nf b/main.nf
index 7e0ceb8a..fe93d397 100644
--- a/main.nf
+++ b/main.nf
@@ -32,14 +32,7 @@ params.known_dbsnp_tbi                = WorkflowMain.getGenomeAttribute(params,
 params.known_indels                   = WorkflowMain.getGenomeAttribute(params, 'known_indels')
 params.known_mills                    = WorkflowMain.getGenomeAttribute(params, 'known_mills')
 params.ml_model                       = WorkflowMain.getGenomeAttribute(params, 'ml_model')
-params.mt_backchain_shift             = WorkflowMain.getGenomeAttribute(params, 'mt_backchain_shift')
-params.mt_bwa_index_shift             = WorkflowMain.getGenomeAttribute(params, 'mt_bwa_index_shift')
-params.mt_bwamem2_index_shift         = WorkflowMain.getGenomeAttribute(params, 'mt_bwamem2_index_shift')
-params.mt_fasta_shift                 = WorkflowMain.getGenomeAttribute(params, 'mt_fasta_shift')
-params.mt_fai_shift                   = WorkflowMain.getGenomeAttribute(params, 'mt_fai_shift')
-params.mt_intervals                   = WorkflowMain.getGenomeAttribute(params, 'mt_intervals')
-params.mt_intervals_shift             = WorkflowMain.getGenomeAttribute(params, 'mt_intervals_shift')
-params.mt_sequence_dictionary_shift   = WorkflowMain.getGenomeAttribute(params, 'mt_sequence_dictionary_shift')
+params.mt_fasta                       = WorkflowMain.getGenomeAttribute(params, 'mt_fasta')
 params.reduced_penetrance             = WorkflowMain.getGenomeAttribute(params, 'reduced_penetrance')
 params.sequence_dictionary            = WorkflowMain.getGenomeAttribute(params, 'sequence_dictionary')
 params.score_config_snv               = WorkflowMain.getGenomeAttribute(params, 'score_config_snv')
diff --git a/modules.json b/modules.json
index 6b0ebcbc..0622ed2e 100644
--- a/modules.json
+++ b/modules.json
@@ -8,345 +8,488 @@
                     "bcftools/annotate": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/concat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/filter": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/merge": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/norm": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/reheader": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/roh": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bcftools/view": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bwamem2/mem": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cadd": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "deepvariant": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "expansionhunter": {
                         "branch": "master",
                         "git_sha": "0260e5d22372eae434816d6970dedf3f5adc0053",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/filtermutectcalls": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/intervallisttools": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/mergebamalignment": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/mutect2": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/printreads": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/revertsam": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/samtofastq": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/selectvariants": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
+                    "gatk4/shiftfasta": {
+                        "branch": "master",
+                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/splitintervals": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gatk4/variantfiltration": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "genmod/annotate": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "genmod/compound": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "genmod/models": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "genmod/score": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "glnexus": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "haplocheck": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "haplogrep2/classify": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "manta/germline": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "mosdepth": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "peddy": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/addorreplacereadgroups": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",
                         "git_sha": "0ce3ab0ac301f160225b22254fa238478b4389f2",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/collectwgsmetrics": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/liftovervcf": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/renamesampleinvcf": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "picard/sortvcf": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "qualimap/bamqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "rhocall/annotate": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "bf8ff98531167f8245ba5c44ce7d781503ddf936",
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/stats": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "smncopynumbercaller": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "stranger": {
                         "branch": "master",
                         "git_sha": "0260e5d22372eae434816d6970dedf3f5adc0053",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "svdb/merge": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "svdb/query": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
                         "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tiddit/cov": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tiddit/sv": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "ucsc/wigtobigwig": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "vcfanno": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/gatk4/shiftfasta/main.nf b/modules/nf-core/gatk4/shiftfasta/main.nf
new file mode 100644
index 00000000..cf984e8b
--- /dev/null
+++ b/modules/nf-core/gatk4/shiftfasta/main.nf
@@ -0,0 +1,66 @@
+process GATK4_SHIFTFASTA {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "bioconda::gatk4=4.4.0.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0':
+        'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    tuple val(meta2), path(fasta_fai)
+    tuple val(meta3), path(dict)
+
+    output:
+    tuple val(meta), path("*_shift.fasta")       , emit: shift_fa
+    tuple val(meta), path("*_shift.fasta.fai")   , emit: shift_fai
+    tuple val(meta), path("*_shift.back_chain")  , emit: shift_back_chain
+    tuple val(meta), path("*_shift.dict")        , emit: dict              , optional: true
+    tuple val(meta), path("*.intervals")         , emit: intervals         , optional: true
+    tuple val(meta), path("*.shifted.intervals") , emit: shift_intervals   , optional: true
+    path "versions.yml"                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def seq_dict = dict ? "--sequence-dictionary ${dict}" : ""
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[GATK ShiftFasta] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}M" ShiftFasta \\
+        --reference $fasta \\
+        --output ${prefix}_shift.fasta \\
+        --shift-back-output ${prefix}_shift.back_chain \\
+        $args \\
+        $seq_dict \\
+        --tmp-dir .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch test.intervals
+    touch test_shift.back_chain
+    touch test_shift.dict
+    touch test.shifted.intervals
+    touch test_shift.fasta
+    touch test_shift.fasta.fai
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gatk4/shiftfasta/meta.yml b/modules/nf-core/gatk4/shiftfasta/meta.yml
new file mode 100644
index 00000000..6d563ded
--- /dev/null
+++ b/modules/nf-core/gatk4/shiftfasta/meta.yml
@@ -0,0 +1,81 @@
+name: "gatk4_shiftfasta"
+description: Create a fasta with the bases shifted by offset
+keywords:
+  - mitochondria
+  - shiftfasta
+  - shiftchain
+  - shiftintervals
+tools:
+  - gatk4:
+      description: |
+        Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
+        with a primary focus on variant discovery and genotyping. Its powerful processing engine
+        and high-performance computing features make it capable of taking on projects of any size.
+      homepage: https://gatk.broadinstitute.org/hc/en-us
+      documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
+      tool_dev_url: "https://github.com/broadinstitute/gatk"
+      doi: 10.1158/1538-7445.AM2017-3590
+      licence: ["Apache-2.0"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - fasta:
+      type: file
+      description: fasta file
+      pattern: "*.{fa,fasta}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - fasta_fai:
+      type: file
+      description: index for fasta file
+      pattern: "*.{fai}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - dict:
+      type: file
+      description: sequence dictionary file
+      pattern: "*.{dict}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing fasta information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - dict:
+      type: file
+      description: sequence dictionary file
+      pattern: "*.{dict}"
+  - intervals:
+      type: file
+      description: Intervals file for the fasta file
+      pattern: "*.{intervals}"
+  - shift_back_chain:
+      type: file
+      description: The shiftback chain file to use when lifting over
+      pattern: "*.{back_chain}"
+  - shift_fa:
+      type: file
+      description: Shifted fasta file
+      pattern: "*.{fa,fasta}"
+  - shift_intervals:
+      type: file
+      description: Intervals file for the shifted fasta file
+      pattern: "*.{shifted.intervals}"
+
+authors:
+  - "@ramprasadn"
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index 4dd0e5b0..c1e8ef3a 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -9,11 +9,13 @@ process SAMTOOLS_FAIDX {
 
     input:
     tuple val(meta), path(fasta)
+    tuple val(meta2), path(fai)
 
     output:
-    tuple val(meta), path ("*.fai"), emit: fai
-    tuple val(meta), path ("*.gzi"), emit: gzi, optional: true
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true
+    tuple val(meta), path ("*.fai")        , emit: fai, optional: true
+    tuple val(meta), path ("*.gzi")        , emit: gzi, optional: true
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,8 +25,8 @@ process SAMTOOLS_FAIDX {
     """
     samtools \\
         faidx \\
-        $args \\
-        $fasta
+        $fasta \\
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
index fe2fe9a1..957b25e5 100644
--- a/modules/nf-core/samtools/faidx/meta.yml
+++ b/modules/nf-core/samtools/faidx/meta.yml
@@ -3,6 +3,7 @@ description: Index FASTA file
 keywords:
   - index
   - fasta
+  - faidx
 tools:
   - samtools:
       description: |
@@ -17,12 +18,21 @@ input:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
   - fasta:
       type: file
       description: FASTA file
       pattern: "*.{fa,fasta}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'test' ]
+  - fai:
+      type: file
+      description: FASTA index file
+      pattern: "*.{fai}"
 output:
   - meta:
       type: map
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 842d6375..44810f84 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -156,22 +156,6 @@
                     "description": "Name of the mitochondrial contig in the reference fasta file",
                     "help_text": "Used to extract relevant information from the references to analyse mitochondria"
                 },
-                "mt_intervals": {
-                    "type": "string",
-                    "format": "path",
-                    "fa_icon": "fas fa-file",
-                    "pattern": "^\\S+\\.intervals?(_list)?$",
-                    "description": "Path to the interval list of the non control mitochondral region.",
-                    "help_text": "Path to the interval list of the non control mitochondral regions for Mutect2"
-                },
-                "mt_intervals_shift": {
-                    "type": "string",
-                    "format": "path",
-                    "fa_icon": "fas fa-file",
-                    "pattern": "^\\S+\\.intervals?(\\_list)?$",
-                    "description": "Path to the interval list of the non control mitochondral region in shifted fasta.",
-                    "help_text": "Path to the interval list of the non control mitochondral regions in shifted fasta for Mutect2"
-                },
                 "known_dbsnp": {
                     "type": "string",
                     "format": "path",
@@ -211,7 +195,7 @@
                     "description": "Path to sentieon machine learning model file.",
                     "hidden": true
                 },
-                "mt_fasta_shift": {
+                "mt_fasta": {
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/plain",
@@ -219,38 +203,6 @@
                     "description": "Path to mitochondrial FASTA genome file.",
                     "fa_icon": "far fa-file-code"
                 },
-                "mt_fai_shift": {
-                    "type": "string",
-                    "format": "file-path",
-                    "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.fn?a(sta)?\\.fai?$",
-                    "description": "Path to mitochondrial FASTA genome index file.",
-                    "fa_icon": "far fa-file-code"
-                },
-                "mt_bwa_index_shift": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory for pre-built bwa index for shifted mitochondrial fasta (used for alignment with sentioen)",
-                    "help_text": "If none provided, will be generated automatically from the FASTA reference.",
-                    "fa_icon": "fas fa-folder-open",
-                    "hidden": true
-                },
-                "mt_bwamem2_index_shift": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory for pre-built bwamem2 index for shifted mitochondrial fasta.",
-                    "help_text": "If none provided, will be generated automatically from the FASTA reference.",
-                    "fa_icon": "fas fa-folder-open",
-                    "hidden": true
-                },
-                "mt_backchain_shift": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Chain file describing the alignment between the mitochondrial shifted fasta and typical mitochondrial fasta",
-                    "help_text": "For more information, check https://genome.ucsc.edu/goldenPath/help/chain.html",
-                    "fa_icon": "fas fa-folder-open",
-                    "hidden": true
-                },
                 "reduced_penetrance": {
                     "type": "string",
                     "format": "path",
@@ -280,14 +232,6 @@
                     "description": "Genome dictionary file",
                     "hidden": true
                 },
-                "mt_sequence_dictionary_shift": {
-                    "type": "string",
-                    "format": "path",
-                    "fa_icon": "fas fa-chart-bar",
-                    "pattern": "^\\S+\\.dict$",
-                    "description": "Shifted mitochondrial genome dictionary file",
-                    "hidden": true
-                },
                 "vep_filters": {
                     "type": "string",
                     "format": "path",
diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
index 0138cbaa..0ac46211 100644
--- a/subworkflows/local/prepare_references.nf
+++ b/subworkflows/local/prepare_references.nf
@@ -10,9 +10,12 @@ include { GATK4_BEDTOINTERVALLIST as GATK_BILT               } from '../../modul
 include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD          } from '../../modules/nf-core/gatk4/createsequencedictionary/main'
 include { GATK4_CREATESEQUENCEDICTIONARY as GATK_SD_SHIFT_MT } from '../../modules/nf-core/gatk4/createsequencedictionary/main'
 include { GATK4_INTERVALLISTTOOLS as GATK_ILT                } from '../../modules/nf-core/gatk4/intervallisttools/main'
+include { GATK4_SHIFTFASTA as GATK_SHIFTFASTA                } from '../../modules/nf-core/gatk4/shiftfasta/main'
 include { GET_CHROM_SIZES                                    } from '../../modules/local/get_chrom_sizes'
+include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT              } from '../../modules/nf-core/samtools/faidx/main'
 include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME            } from '../../modules/nf-core/samtools/faidx/main'
-include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_SHIFT_MT          } from '../../modules/nf-core/samtools/faidx/main'
+include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT                } from '../../modules/nf-core/samtools/faidx/main'
+include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT_SHIFT          } from '../../modules/nf-core/samtools/faidx/main'
 include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME      } from '../../modules/local/sentieon/bwamemindex'
 include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_SHIFT_MT    } from '../../modules/local/sentieon/bwamemindex'
 include { TABIX_BGZIPTABIX as TABIX_PBT                      } from '../../modules/nf-core/tabix/bgziptabix/main'
@@ -24,7 +27,8 @@ include { UNTAR as UNTAR_VEP_CACHE                           } from '../../modul
 workflow PREPARE_REFERENCES {
     take:
         ch_fasta           // channel: [mandatory] [ val(meta), path(fasta) ]
-        ch_fasta_mt        // channel: [mandatory for dedicated mt analysis] [ val(meta), path(fasta) ]
+        ch_genome_fai      // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_fasta_mt        // channel: [optional for dedicated mt analysis] [ val(meta), path(fasta) ]
         ch_gnomad_af_tab   // channel: [optional; used in for snv annotation] [ val(meta), path(tab) ]
         ch_known_dbsnp     // channel: [optional; used only by sentieon] [ val(meta), path(vcf) ]
         ch_target_bed      // channel: [mandatory for WES] [ path(bed) ]
@@ -40,15 +44,21 @@ workflow PREPARE_REFERENCES {
         // Genome indices
         BWA_INDEX_GENOME(ch_fasta).index.set{ch_bwa}
         BWAMEM2_INDEX_GENOME(ch_fasta)
-        BWAMEM2_INDEX_SHIFT_MT(ch_fasta_mt)
         SENTIEON_BWAINDEX_GENOME(ch_fasta).index.set{ch_sentieonbwa}
-        SENTIEON_BWAINDEX_SHIFT_MT(ch_fasta_mt)
-        SAMTOOLS_FAIDX_GENOME(ch_fasta)
-        SAMTOOLS_FAIDX_SHIFT_MT(ch_fasta_mt)
+        SAMTOOLS_FAIDX_GENOME(ch_fasta, [[],[]])
         GATK_SD(ch_fasta)
-        GATK_SD_SHIFT_MT(ch_fasta_mt)
         GET_CHROM_SIZES( SAMTOOLS_FAIDX_GENOME.out.fai )
 
+        // MT indices
+        BWAMEM2_INDEX_SHIFT_MT(ch_fasta_mt)
+        SENTIEON_BWAINDEX_SHIFT_MT(ch_fasta_mt)
+        ch_fai = Channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect()
+        SAMTOOLS_EXTRACT_MT(ch_fasta, ch_fai)
+        ch_mt_fasta = Channel.empty().mix(ch_genome_fai, SAMTOOLS_FAIDX_GENOME.out.fai).collect()
+        GATK_SD_SHIFT_MT(SAMTOOLS_EXTRACT_MT.out.fa)
+        SAMTOOLS_FAIDX_MT_SHIFT(SAMTOOLS_EXTRACT_MT.out.fa, [[],[]])
+        GATK_SHIFTFASTA(SAMTOOLS_EXTRACT_MT.out.fa,SAMTOOLS_FAIDX_MT_SHIFT.out.fai, GATK_SD_SHIFT_MT.out.dict)
+
         // Vcf, tab and bed indices
         TABIX_DBSNP(ch_known_dbsnp)
         TABIX_GNOMAD_AF(ch_gnomad_af_tab)
@@ -75,7 +85,7 @@ workflow PREPARE_REFERENCES {
         ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_GENOME.out.versions)
         ch_versions = ch_versions.mix(SENTIEON_BWAINDEX_SHIFT_MT.out.versions)
         ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_GENOME.out.versions)
-        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_SHIFT_MT.out.versions)
+        ch_versions = ch_versions.mix(SAMTOOLS_FAIDX_MT_SHIFT.out.versions)
         ch_versions = ch_versions.mix(GATK_SD.out.versions)
         ch_versions = ch_versions.mix(GATK_SD_SHIFT_MT.out.versions)
         ch_versions = ch_versions.mix(GET_CHROM_SIZES.out.versions)
@@ -94,8 +104,8 @@ workflow PREPARE_REFERENCES {
         bwamem2_index          = BWAMEM2_INDEX_GENOME.out.index.collect()                         // channel: [ val(meta), path(index) ]
         bwamem2_index_mt_shift = BWAMEM2_INDEX_SHIFT_MT.out.index.collect()                       // channel: [ val(meta), path(index) ]
         chrom_sizes            = GET_CHROM_SIZES.out.sizes.collect()                              // channel: [ path(sizes) ]
-        fai                    = SAMTOOLS_FAIDX_GENOME.out.fai.collect()                          // channel: [ val(meta), path(fai) ]
-        fai_mt_shift           = SAMTOOLS_FAIDX_SHIFT_MT.out.fai.collect()                        // channel: [ val(meta), path(fai) ]
+        fai                    = ch_fai                                                           // channel: [ val(meta), path(fai) ]
+        fai_mt_shift           = SAMTOOLS_FAIDX_MT_SHIFT.out.fai.collect()                        // channel: [ val(meta), path(fai) ]
         gnomad_af_idx          = TABIX_GNOMAD_AF.out.tbi.collect()                                // channel: [ val(meta), path(fasta) ]
         known_dbsnp_tbi        = TABIX_DBSNP.out.tbi.collect()                                    // channel: [ val(meta), path(fasta) ]
         sequence_dict          = GATK_SD.out.dict.collect()                                       // channel: [ path(dict) ]
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index 8555e1f4..61aa8a29 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -30,14 +30,7 @@ def checkPathParamList = [
     params.known_indels,
     params.known_mills,
     params.ml_model,
-    params.mt_backchain_shift,
-    params.mt_bwa_index_shift,
-    params.mt_bwamem2_index_shift,
-    params.mt_fasta_shift,
-    params.mt_fai_shift,
-    params.mt_intervals,
-    params.mt_intervals_shift,
-    params.mt_sequence_dictionary_shift,
+    params.mt_fasta,
     params.multiqc_config,
     params.reduced_penetrance,
     params.score_config_snv,
@@ -82,8 +75,7 @@ if (!params.skip_sv_annotation) {
 }
 
 if (!params.skip_mt_analysis) {
-    mandatoryParams += ["genome", "mt_backchain_shift", "mito_name", "mt_fasta_shift", "mt_intervals",
-    "mt_intervals_shift", "vcfanno_resources", "vcfanno_toml", "vep_cache_version", "vep_cache"]
+    mandatoryParams += ["genome", "mito_name", "vcfanno_resources", "vcfanno_toml", "vep_cache_version", "vep_cache"]
 }
 
 if (params.analysis_type.equals("wes")) {
@@ -190,6 +182,8 @@ workflow RAREDISEASE {
                                                                            : Channel.value([])
     ch_call_interval            = params.call_interval                     ? Channel.fromPath(params.call_interval).collect()
                                                                            : Channel.value([])
+    ch_genome_fai               = params.fai                               ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : Channel.value([])
     ch_gnomad_af_tab            = params.gnomad_af                         ? Channel.fromPath(params.gnomad_af).map{ it -> [[id:it[0].simpleName], it] }.collect()
                                                                            : Channel.value([[],[]])
     ch_intervals_wgs            = params.intervals_wgs                     ? Channel.fromPath(params.intervals_wgs).collect()
@@ -200,14 +194,8 @@ workflow RAREDISEASE {
                                                                            : Channel.value([[],[]])
     ch_ml_model                 = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).collect()
                                                                            : Channel.value([])
-    ch_mt_backchain_shift       = params.mt_backchain_shift                ? Channel.fromPath(params.mt_backchain_shift).map{ it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.value([])
-    ch_mt_fasta_shift           = params.mt_fasta_shift                    ? Channel.fromPath(params.mt_fasta_shift).map { it -> [[id:it[0].simpleName], it] }.collect()
+    ch_mt_fasta                 = params.mt_fasta                          ? Channel.fromPath(params.mt_fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
                                                                            : Channel.empty()
-    ch_mt_intervals             = params.mt_intervals                      ? Channel.fromPath(params.mt_intervals).collect()
-                                                                           : Channel.value([])
-    ch_mt_intervals_shift       = params.mt_intervals_shift                ? Channel.fromPath(params.mt_intervals_shift).collect()
-                                                                           : Channel.value([])
     ch_reduced_penetrance       = params.reduced_penetrance                ? Channel.fromPath(params.reduced_penetrance).collect()
                                                                            : Channel.value([])
     ch_score_config_snv         = params.score_config_snv                  ? Channel.fromPath(params.score_config_snv).collect()
@@ -239,7 +227,8 @@ workflow RAREDISEASE {
     // Prepare references and indices.
     PREPARE_REFERENCES (
         ch_genome_fasta,
-        ch_mt_fasta_shift,
+        ch_genome_fai,
+        ch_mt_fasta,
         ch_gnomad_af_tab,
         ch_known_dbsnp,
         ch_target_bed_unprocessed,
@@ -258,10 +247,17 @@ workflow RAREDISEASE {
     ch_bwamem2_index_mt_shift       = params.mt_bwamem2_index_shift        ? Channel.fromPath(params.mt_bwamem2_index_shift).map {it -> [[id:it[0].simpleName], it]}.collect()
                                                                            : ch_references.bwamem2_index_mt_shift
     ch_chrom_sizes                  = ch_references.chrom_sizes
-    ch_genome_fai                   = params.fai                           ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.fai
+    ch_mt_backchain_shift       = params.mt_backchain_shift                ? Channel.fromPath(params.mt_backchain_shift).map{ it -> [[id:it[0].simpleName], it] }.collect()
+                                                                           : Channel.value([])
+    ch_mt_fasta_shift           = params.mt_fasta_shift                    ? Channel.fromPath(params.mt_fasta_shift).map { it -> [[id:it[0].simpleName], it] }.collect()
+                                                                           : Channel.empty()
+    ch_mt_intervals             = params.mt_intervals                      ? Channel.fromPath(params.mt_intervals).collect()
+                                                                           : Channel.value([])
+    ch_mt_intervals_shift       = params.mt_intervals_shift                ? Channel.fromPath(params.mt_intervals_shift).collect()
+                                                                           : Channel.value([])
     ch_mt_shift_fai                 = params.mt_fai_shift                  ? Channel.fromPath(params.mt_fai_shift).map {it -> [[id:it[0].simpleName], it]}.collect()
                                                                            : ch_references.fai_mt_shift
+    ch_genome_fai                   = ch_references.fai
     ch_gnomad_af_idx                = params.gnomad_af_idx                 ? Channel.fromPath(params.gnomad_af_idx).collect()
                                                                            : ch_references.gnomad_af_idx
     ch_gnomad_af                    = params.gnomad_af                     ? ch_gnomad_af_tab.join(ch_gnomad_af_idx).map {meta, tab, idx -> [tab,idx]}.collect()

From 49dd613f6c2861a839ab9f0c51ad9cd7a838bfce Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 26 May 2023 10:36:38 +0200
Subject: [PATCH 2/8] update configs

---
 conf/modules/align_and_call_MT.config       |  14 +-
 conf/modules/analyse_MT.config              |   2 +-
 conf/modules/convert_mt_bam_to_fastq.config |   3 -
 conf/modules/merge_annotate_MT.config       |   3 -
 conf/test.config                            |   4 -
 conf/test_one_sample.config                 |   4 -
 subworkflows/local/analyse_MT.nf            |  62 ++++----
 subworkflows/local/prepare_references.nf    |  40 ++---
 workflows/raredisease.nf                    | 157 ++++++++++----------
 9 files changed, 131 insertions(+), 158 deletions(-)

diff --git a/conf/modules/align_and_call_MT.config b/conf/modules/align_and_call_MT.config
index c4915c11..32e9ed0c 100644
--- a/conf/modules/align_and_call_MT.config
+++ b/conf/modules/align_and_call_MT.config
@@ -16,18 +16,15 @@
 //
 
 process {
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:.*' {
-        ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") }
-    }
 
     withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:BWAMEM2_MEM_MT' {
-        ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
     }
 
     withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
-        ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
         ext.prefix = { "${meta.id}.sorted" }
     }
 
@@ -69,18 +66,15 @@ process {
 //
 
 process {
-    withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:.*' {
-        ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") }
-    }
 
     withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:BWAMEM2_MEM_MT' {
-        ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2" }
         ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
     }
 
     withName: '.*ANALYSE_MT:ALIGN_AND_CALL_MT_SHIFT:SENTIEON_BWAMEM_MT' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group}" }
-        ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon" }
         ext.prefix = { "${meta.id}.sorted" }
     }
 
diff --git a/conf/modules/analyse_MT.config b/conf/modules/analyse_MT.config
index 85568e3e..4ee1b693 100644
--- a/conf/modules/analyse_MT.config
+++ b/conf/modules/analyse_MT.config
@@ -17,6 +17,7 @@
 
 process {
     withName: '.*ANALYSE_MT:.*' {
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") }
         publishDir = [
             enabled: false
         ]
@@ -25,7 +26,6 @@ process {
 
 process {
     withName: '.*ANALYSE_MT:PICARD_LIFTOVERVCF' {
-        ext.when = { params.mt_fasta_shift && params.mt_intervals_shift && !(params.analysis_type == "wes") }
         ext.prefix = { "${meta.id}_liftover" }
     }
 }
diff --git a/conf/modules/convert_mt_bam_to_fastq.config b/conf/modules/convert_mt_bam_to_fastq.config
index 5cba99b5..9a683b6e 100644
--- a/conf/modules/convert_mt_bam_to_fastq.config
+++ b/conf/modules/convert_mt_bam_to_fastq.config
@@ -16,9 +16,6 @@
 //
 
 process {
-    withName: '.*ANALYSE_MT:CONVERT_MT_BAM_TO_FASTQ:.*' {
-        ext.when = { params.mt_fasta_shift && !(params.analysis_type == "wes") }
-    }
 
     withName: '.*ANALYSE_MT:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT' {
         beforeScript = {"mkdir ./tmp"}
diff --git a/conf/modules/merge_annotate_MT.config b/conf/modules/merge_annotate_MT.config
index d62cf73c..a1b41a90 100644
--- a/conf/modules/merge_annotate_MT.config
+++ b/conf/modules/merge_annotate_MT.config
@@ -16,9 +16,6 @@
 //
 
 process {
-    withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:.*' {
-        ext.when = { params.mt_fasta_shift && params.mt_intervals && !(params.analysis_type == "wes") }
-    }
 
     withName: '.*ANALYSE_MT:MERGE_ANNOTATE_MT:GATK4_MERGEVCFS_LIFT_UNLIFT_MT' {
         ext.prefix = { "${meta.id}_merged" }
diff --git a/conf/test.config b/conf/test.config
index 805f84d6..c3ed9011 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -34,10 +34,6 @@ params {
     intervals_y          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
     known_dbsnp          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
     ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
-    mt_fasta_shift       = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.fa"
-    mt_intervals         = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt.intervals"
-    mt_intervals_shift   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.intervals"
-    mt_backchain_shift   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.back_chain"
     reduced_penetrance   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
     score_config_snv     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
     score_config_sv      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
diff --git a/conf/test_one_sample.config b/conf/test_one_sample.config
index e4f73a33..85efab52 100644
--- a/conf/test_one_sample.config
+++ b/conf/test_one_sample.config
@@ -34,10 +34,6 @@ params {
     intervals_y          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
     known_dbsnp          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
     ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
-    mt_fasta_shift       = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.fa"
-    mt_intervals         = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt.intervals"
-    mt_intervals_shift   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.intervals"
-    mt_backchain_shift   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mt_shift8000.back_chain"
     reduced_penetrance   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
     score_config_snv     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
     score_config_sv      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
diff --git a/subworkflows/local/analyse_MT.nf b/subworkflows/local/analyse_MT.nf
index 60db58ec..1dbe2911 100644
--- a/subworkflows/local/analyse_MT.nf
+++ b/subworkflows/local/analyse_MT.nf
@@ -9,35 +9,35 @@ include { MERGE_ANNOTATE_MT                            } from './mitochondria/me
 
 workflow ANALYSE_MT {
     take:
-        ch_bam                    // channel: [mandatory] [ val(meta), file(bam), file(bai) ]
-        ch_cadd_header            // channel: [mandatory] [ path(txt) ]
-        ch_cadd_resources         // channel: [mandatory] [ path(annotation) ]
-        ch_genome_bwa_index       // channel: [mandatory] [ path(index) ]
-        ch_genome_bwamem2_index   // channel: [mandatory] [ path(index) ]
-        ch_genome_fasta           // channel: [mandatory] [ val(meta), path(fasta) ]
-        ch_genome_fai             // channel: [mandatory] [ path(fai) ]
-        ch_genome_dict            // channel: [mandatory] [ val(meta), path(dict) ]
-        ch_mt_intervals           // channel: [mandatory] [ path(interval_list) ]
-        ch_shift_mt_bwa_index     // channel: [mandatory] [ path(index) ]
-        ch_shift_mt_bwamem2_index // channel: [mandatory] [ path(index) ]
-        ch_shift_mt_fasta         // channel: [mandatory] [ path(fasta) ]
-        ch_shift_mt_dict          // channel: [mandatory] [ path(dict) ]
-        ch_shift_mt_fai           // channel: [mandatory] [ path(fai) ]
-        ch_shift_mt_intervals     // channel: [mandatory] [ path(interval_list) ]
-        ch_shift_mt_backchain     // channel: [mandatory] [ path(back_chain) ]
-        ch_vcfanno_resources      // channel: [mandatory] [ path(resources) ]
-        ch_vcfanno_toml           // channel: [mandatory] [ path(toml) ]
-        val_vep_genome            // string:  [mandatory] GRCh37 or GRCh38
-        val_vep_cache_version     // string:  [mandatory] 107
-        ch_vep_cache              // channel: [mandatory] [ path(cache) ]
-        ch_case_info              // channel: [mandatory] [ val(case_info) ]
+        ch_bam_bai               // channel: [mandatory] [ val(meta), file(bam), file(bai) ]
+        ch_cadd_header           // channel: [mandatory] [ path(txt) ]
+        ch_cadd_resources        // channel: [mandatory] [ path(annotation) ]
+        ch_genome_bwa_index      // channel: [mandatory] [ val(meta), path(index) ]
+        ch_genome_bwamem2_index  // channel: [mandatory] [ val(meta), path(index) ]
+        ch_genome_fasta          // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_genome_fai            // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_genome_dict           // channel: [mandatory] [ val(meta), path(dict) ]
+        ch_mt_intervals          // channel: [mandatory] [ path(interval_list) ]
+        ch_mtshift_bwaindex      // channel: [mandatory] [ val(meta), path(index) ]
+        ch_mtshift_bwamem2index  // channel: [mandatory] [ val(meta), path(index) ]
+        ch_mtshift_fasta         // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_mtshift_dict          // channel: [mandatory] [ val(meta), path(dict) ]
+        ch_mtshift_fai           // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_mtshift_intervals     // channel: [mandatory] [ path(interval_list) ]
+        ch_mtshift_backchain     // channel: [mandatory] [ val(meta), path(back_chain) ]
+        ch_vcfanno_resources     // channel: [mandatory] [ path(resources) ]
+        ch_vcfanno_toml          // channel: [mandatory] [ path(toml) ]
+        val_vep_genome           // string:  [mandatory] GRCh37 or GRCh38
+        val_vep_cache_version    // string:  [mandatory] 107
+        ch_vep_cache             // channel: [mandatory] [ path(cache) ]
+        ch_case_info             // channel: [mandatory] [ val(case_info) ]
 
     main:
         ch_versions = Channel.empty()
 
         // PREPARING READS FOR MT ALIGNMENT
         CONVERT_MT_BAM_TO_FASTQ (
-            ch_bam,
+            ch_bam_bai,
             ch_genome_fasta,
             ch_genome_fai,
             ch_genome_dict
@@ -58,20 +58,20 @@ workflow ANALYSE_MT {
         ALIGN_AND_CALL_MT_SHIFT (
             CONVERT_MT_BAM_TO_FASTQ.out.fastq,
             CONVERT_MT_BAM_TO_FASTQ.out.bam,
-            ch_shift_mt_bwa_index,
-            ch_shift_mt_bwamem2_index,
-            ch_shift_mt_fasta,
-            ch_shift_mt_dict,
-            ch_shift_mt_fai,
-            ch_shift_mt_intervals
+            ch_mtshift_bwaindex,
+            ch_mtshift_bwamem2index,
+            ch_mtshift_fasta,
+            ch_mtshift_dict,
+            ch_mtshift_fai,
+            ch_mtshift_intervals
         )
 
         // LIFTOVER VCF FROM REFERENCE MT TO SHIFTED MT
         PICARD_LIFTOVERVCF (
             ALIGN_AND_CALL_MT_SHIFT.out.vcf,
             ch_genome_dict,
-            ch_shift_mt_backchain,
-            ch_genome_fasta
+            ch_genome_fasta,
+            ch_mtshift_backchain,
         )
 
         // MT MERGE AND ANNOTATE VARIANTS
diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
index d59baba5..f9a8fb47 100644
--- a/subworkflows/local/prepare_references.nf
+++ b/subworkflows/local/prepare_references.nf
@@ -101,28 +101,28 @@ workflow PREPARE_REFERENCES {
         ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions)
 
     emit:
-        genome_bwa_index       = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect()            // channel: [ val(meta), path(index) ]
-        genome_bwamem2_index   = BWAMEM2_INDEX_GENOME.out.index.collect()                         // channel: [ val(meta), path(index) ]
-        genome_chrom_sizes     = GET_CHROM_SIZES.out.sizes.collect()                              // channel: [ path(sizes) ]
-        genome_fai             = ch_fai                                                           // channel: [ val(meta), path(fai) ]
-        genome_dict            = GATK_SD.out.dict.collect()                                       // channel: [ path(dict) ]
+        genome_bwa_index      = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect()              // channel: [ val(meta), path(index) ]
+        genome_bwamem2_index  = BWAMEM2_INDEX_GENOME.out.index.collect()                           // channel: [ val(meta), path(index) ]
+        genome_chrom_sizes    = GET_CHROM_SIZES.out.sizes.collect()                                // channel: [ path(sizes) ]
+        genome_fai            = ch_fai                                                             // channel: [ val(meta), path(fai) ]
+        genome_dict           = GATK_SD.out.dict.collect()                                         // channel: [ path(dict) ]
 
-        mt_intervals           = GATK_SHIFTFASTA.out.intervals.collect()
-        mtshift_intervals      = GATK_SHIFTFASTA.out.shift_intervals.collect()
-        mtshift_backchain      = GATK_SHIFTFASTA.out.shift_back_chain.collect()
-        mtshift_fai            = GATK_SHIFTFASTA.out.shift_fai.collect()                          // channel: [ val(meta), path(fai) ]
-        mtshift_fasta          = GATK_SHIFTFASTA.out.shift_fa.collect()                          // channel: [ val(meta), path(fai) ]
-        mtshift_dict           = GATK_SHIFTFASTA.out.dict.collect()                               // channel: [ path(dict) ]
-        mtshift_bwa_index      = SENTIEON_BWAINDEX_MT_SHIFT.out.index.collect()                   // channel: [ val(meta), path(index) ]
-        mtshift_bwamem2_index  = BWAMEM2_INDEX_MT_SHIFT.out.index.collect()                       // channel: [ val(meta), path(index) ]
+        mt_intervals          = GATK_SHIFTFASTA.out.intervals.map{ meta, it -> it}.collect()       // channel: [ path(intervals) ]
+        mtshift_intervals     = GATK_SHIFTFASTA.out.shift_intervals.map{ meta, it -> it}.collect() // channel: [ path(intervals) ]
+        mtshift_backchain     = GATK_SHIFTFASTA.out.shift_back_chain.collect()
+        mtshift_fai           = GATK_SHIFTFASTA.out.shift_fai.collect()                            // channel: [ val(meta), path(fai) ]
+        mtshift_fasta         = GATK_SHIFTFASTA.out.shift_fa.collect()                             // channel: [ val(meta), path(fai) ]
+        mtshift_dict          = GATK_SHIFTFASTA.out.dict.collect()                                 // channel: [ path(dict) ]
+        mtshift_bwa_index     = SENTIEON_BWAINDEX_MT_SHIFT.out.index.collect()                     // channel: [ val(meta), path(index) ]
+        mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect()                         // channel: [ val(meta), path(index) ]
 
-        gnomad_af_idx          = TABIX_GNOMAD_AF.out.tbi.collect()                                // channel: [ val(meta), path(fasta) ]
-        known_dbsnp_tbi        = TABIX_DBSNP.out.tbi.collect()                                    // channel: [ val(meta), path(fasta) ]
-        target_bed             = Channel.empty().mix(ch_tbi, ch_bgzip_tbi).collect()              // channel: [ val(meta), path(bed), path(tbi) ]
-        bait_intervals         = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect()   // channel: [ path(intervals) ]
-        target_intervals       = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect() // channel: [ path(interval_list) ]
-        vep_resources          = UNTAR_VEP_CACHE.out.untar.map{meta, files -> [files]}.collect()  // channel: [ path(cache) ]
-        versions               = ch_versions                                                      // channel: [ path(versions.yml) ]
+        gnomad_af_idx         = TABIX_GNOMAD_AF.out.tbi.collect()                                  // channel: [ val(meta), path(fasta) ]
+        known_dbsnp_tbi       = TABIX_DBSNP.out.tbi.collect()                                      // channel: [ val(meta), path(fasta) ]
+        target_bed            = Channel.empty().mix(ch_tbi, ch_bgzip_tbi).collect()                // channel: [ val(meta), path(bed), path(tbi) ]
+        bait_intervals        = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect()     // channel: [ path(intervals) ]
+        target_intervals      = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect()   // channel: [ path(interval_list) ]
+        vep_resources         = UNTAR_VEP_CACHE.out.untar.map{meta, files -> [files]}.collect()    // channel: [ path(cache) ]
+        versions              = ch_versions                                                        // channel: [ path(versions.yml) ]
 
 }
 
diff --git a/workflows/raredisease.nf b/workflows/raredisease.nf
index 45e8491b..1e1b70e5 100644
--- a/workflows/raredisease.nf
+++ b/workflows/raredisease.nf
@@ -173,49 +173,92 @@ workflow RAREDISEASE {
     CHECK_INPUT (ch_input)
     ch_versions = ch_versions.mix(CHECK_INPUT.out.versions)
 
-    // Initialize all file channels including unprocessed vcf, bed and tab files
-    ch_cadd_header              = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect()
+    // Initialize file channels for PREPARE_REFERENCES subworkflow
     ch_genome_fasta             = Channel.fromPath(params.fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
-    ch_variant_consequences     = Channel.fromPath("$projectDir/assets/variant_consequences_v1.txt", checkIfExists: true).collect()
+    ch_genome_fai               = params.fai            ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                        : Channel.empty()
+    ch_gnomad_af_tab            = params.gnomad_af      ? Channel.fromPath(params.gnomad_af).map{ it -> [[id:it[0].simpleName], it] }.collect()
+                                                        : Channel.value([[],[]])
+    ch_dbsnp                    = params.known_dbsnp    ? Channel.fromPath(params.known_dbsnp).map{ it -> [[id:it[0].simpleName], it] }.collect()
+                                                        : Channel.value([[],[]])
+    ch_mt_fasta                 = params.mt_fasta       ? Channel.fromPath(params.mt_fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
+                                                        : Channel.empty()
+    ch_target_bed_unprocessed   = params.target_bed     ? Channel.fromPath(params.target_bed).map{ it -> [[id:it[0].simpleName], it] }.collect()
+                                                        : Channel.value([[],[]])
+    ch_vep_cache_unprocessed    = params.vep_cache      ? Channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()
+                                                        : Channel.value([[],[]])
+
+    // Prepare references and indices.
+    PREPARE_REFERENCES (
+        ch_genome_fasta,
+        ch_genome_fai,
+        ch_mt_fasta,
+        ch_gnomad_af_tab,
+        ch_dbsnp,
+        ch_target_bed_unprocessed,
+        ch_vep_cache_unprocessed
+    )
+    .set { ch_references }
 
+
+    // Gather built indices or get them from the params
+    ch_bait_intervals           = ch_references.bait_intervals
+    ch_cadd_header              = Channel.fromPath("$projectDir/assets/cadd_to_vcf_header_-1.0-.txt", checkIfExists: true).collect()
     ch_cadd_resources           = params.cadd_resources                    ? Channel.fromPath(params.cadd_resources).collect()
                                                                            : Channel.value([])
     ch_call_interval            = params.call_interval                     ? Channel.fromPath(params.call_interval).collect()
                                                                            : Channel.value([])
-    ch_genome_fai               = params.fai                               ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : Channel.value([])
-    ch_gnomad_af_tab            = params.gnomad_af                         ? Channel.fromPath(params.gnomad_af).map{ it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.value([[],[]])
+    ch_dbsnp_tbi                = params.known_dbsnp_tbi                   ? Channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : ch_references.known_dbsnp_tbi.ifEmpty([[],[]])
+    ch_genome_bwaindex          = params.bwa                               ? Channel.fromPath(params.bwa).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : ch_references.genome_bwa_index
+    ch_genome_bwamem2index      = params.bwamem2                           ? Channel.fromPath(params.bwamem2).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : ch_references.genome_bwamem2_index
+    ch_genome_chrsizes          = ch_references.genome_chrom_sizes
+    ch_genome_fai               = ch_references.genome_fai
+    ch_genome_dictionary        = params.sequence_dictionary               ? Channel.fromPath(params.sequence_dictionary).map {it -> [[id:it[0].simpleName], it]}.collect()
+                                                                           : ch_references.genome_dict
+    ch_gnomad_afidx             = params.gnomad_af_idx                     ? Channel.fromPath(params.gnomad_af_idx).collect()
+                                                                           : ch_references.gnomad_af_idx
+    ch_gnomad_af                = params.gnomad_af                         ? ch_gnomad_af_tab.join(ch_gnomad_afidx).map {meta, tab, idx -> [tab,idx]}.collect()
+                                                                           : Channel.empty()
     ch_intervals_wgs            = params.intervals_wgs                     ? Channel.fromPath(params.intervals_wgs).collect()
                                                                            : Channel.empty()
     ch_intervals_y              = params.intervals_y                       ? Channel.fromPath(params.intervals_y).collect()
                                                                            : Channel.empty()
-    ch_known_dbsnp              = params.known_dbsnp                       ? Channel.fromPath(params.known_dbsnp).map{ it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.value([[],[]])
     ch_ml_model                 = params.variant_caller.equals("sentieon") ? Channel.fromPath(params.ml_model).collect()
                                                                            : Channel.value([])
-    ch_mt_fasta                 = params.mt_fasta                          ? Channel.fromPath(params.mt_fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.empty()
+    ch_mt_intervals             = ch_references.mt_intervals
+    ch_mtshift_backchain        = ch_references.mtshift_backchain
+    ch_mtshift_bwaindex         = ch_references.mtshift_bwa_index
+    ch_mtshift_bwamem2index     = ch_references.mtshift_bwamem2_index
+    ch_mtshift_dictionary       = ch_references.mtshift_dict
+    ch_mtshift_fai              = ch_references.mtshift_fai
+    ch_mtshift_fasta            = ch_references.mtshift_fasta
+    ch_mtshift_intervals        = ch_references.mtshift_intervals
     ch_reduced_penetrance       = params.reduced_penetrance                ? Channel.fromPath(params.reduced_penetrance).collect()
                                                                            : Channel.value([])
     ch_score_config_snv         = params.score_config_snv                  ? Channel.fromPath(params.score_config_snv).collect()
                                                                            : Channel.value([])
     ch_score_config_sv          = params.score_config_sv                   ? Channel.fromPath(params.score_config_sv).collect()
                                                                            : Channel.value([])
-    ch_target_bed_unprocessed   = params.target_bed                        ? Channel.fromPath(params.target_bed).map{ it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.value([[],[]])
+    ch_target_bed               = ch_references.target_bed
+    ch_target_intervals         = ch_references.target_intervals
     ch_variant_catalog          = params.variant_catalog                   ? Channel.fromPath(params.variant_catalog).map { it -> [[id:it[0].simpleName],it]}.collect()
                                                                            : Channel.value([[],[]])
+    ch_variant_consequences     = Channel.fromPath("$projectDir/assets/variant_consequences_v1.txt", checkIfExists: true).collect()
     ch_vcfanno_resources        = params.vcfanno_resources                 ? Channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect()
                                                                            : Channel.value([])
     ch_vcfanno_lua              = params.vcfanno_lua                       ? Channel.fromPath(params.vcfanno_lua).collect()
                                                                            : Channel.value([])
     ch_vcfanno_toml             = params.vcfanno_toml                      ? Channel.fromPath(params.vcfanno_toml).collect()
                                                                            : Channel.value([])
-    ch_vep_cache_unprocessed    = params.vep_cache                         ? Channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()
-                                                                           : Channel.value([[],[]])
+    ch_vep_cache                = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") )  ? ch_references.vep_resources
+                                                                           : ( params.vep_cache    ? Channel.fromPath(params.vep_cache).collect() : Channel.value([]) )
     ch_vep_filters              = params.vep_filters                       ? Channel.fromPath(params.vep_filters).collect()
                                                                            : Channel.value([])
+    ch_versions                 = ch_versions.mix(ch_references.versions)
+
 
     // Generate pedigree file
     ch_pedfile = CHECK_INPUT.out.samples.toList().map { makePed(it) }
@@ -224,56 +267,6 @@ workflow RAREDISEASE {
     FASTQC (CHECK_INPUT.out.reads)
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
-    // Prepare references and indices.
-    PREPARE_REFERENCES (
-        ch_genome_fasta,
-        ch_genome_fai,
-        ch_mt_fasta,
-        ch_gnomad_af_tab,
-        ch_known_dbsnp,
-        ch_target_bed_unprocessed,
-        ch_vep_cache_unprocessed
-    )
-    .set { ch_references }
-
-    // Gather built indices or get them from the params
-    ch_bait_intervals               = ch_references.bait_intervals
-    ch_bwa_index                    = params.bwa                           ? Channel.fromPath(params.bwa).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.bwa_index
-    ch_bwa_index_mt_shift           = params.mt_bwa_index_shift            ? Channel.fromPath(params.mt_bwa_index_shift).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.bwa_index_mt_shift
-    ch_bwamem2_index                = params.bwamem2                       ? Channel.fromPath(params.bwamem2).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.bwamem2_index
-    ch_bwamem2_index_mt_shift       = params.mt_bwamem2_index_shift        ? Channel.fromPath(params.mt_bwamem2_index_shift).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.bwamem2_index_mt_shift
-    ch_chrom_sizes                  = ch_references.chrom_sizes
-    ch_mt_backchain_shift       = params.mt_backchain_shift                ? Channel.fromPath(params.mt_backchain_shift).map{ it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.value([])
-    ch_mt_fasta_shift           = params.mt_fasta_shift                    ? Channel.fromPath(params.mt_fasta_shift).map { it -> [[id:it[0].simpleName], it] }.collect()
-                                                                           : Channel.empty()
-    ch_mt_intervals             = params.mt_intervals                      ? Channel.fromPath(params.mt_intervals).collect()
-                                                                           : Channel.value([])
-    ch_mt_intervals_shift       = params.mt_intervals_shift                ? Channel.fromPath(params.mt_intervals_shift).collect()
-                                                                           : Channel.value([])
-    ch_mt_shift_fai                 = params.mt_fai_shift                  ? Channel.fromPath(params.mt_fai_shift).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.fai_mt_shift
-    ch_genome_fai                   = ch_references.fai
-    ch_gnomad_af_idx                = params.gnomad_af_idx                 ? Channel.fromPath(params.gnomad_af_idx).collect()
-                                                                           : ch_references.gnomad_af_idx
-    ch_gnomad_af                    = params.gnomad_af                     ? ch_gnomad_af_tab.join(ch_gnomad_af_idx).map {meta, tab, idx -> [tab,idx]}.collect()
-                                                                           : Channel.empty()
-    ch_known_dbsnp_tbi              = params.known_dbsnp_tbi               ? Channel.fromPath(params.known_dbsnp_tbi).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.known_dbsnp_tbi.ifEmpty([[],[]])
-    ch_genome_dictionary          = params.sequence_dictionary           ? Channel.fromPath(params.sequence_dictionary).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.sequence_dict
-    ch_sequence_dictionary_mt_shift = params.mt_sequence_dictionary_shift  ? Channel.fromPath(params.mt_sequence_dictionary_shift).map {it -> [[id:it[0].simpleName], it]}.collect()
-                                                                           : ch_references.sequence_dict_mt_shift
-    ch_target_bed                   = ch_references.target_bed
-    ch_target_intervals             = ch_references.target_intervals
-    ch_vep_cache                    = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") )  ? ch_references.vep_resources
-                                                                           : ( params.vep_cache    ? Channel.fromPath(params.vep_cache).collect() : Channel.value([]) )
-    ch_versions                     = ch_versions.mix(ch_references.versions)
-
     // CREATE CHROMOSOME BED AND INTERVALS
     SCATTER_GENOME (
         ch_genome_dictionary,
@@ -289,10 +282,10 @@ workflow RAREDISEASE {
         CHECK_INPUT.out.reads,
         ch_genome_fasta,
         ch_genome_fai,
-        ch_bwa_index,
-        ch_bwamem2_index,
-        ch_known_dbsnp,
-        ch_known_dbsnp_tbi,
+        ch_genome_bwaindex,
+        ch_genome_bwamem2index,
+        ch_dbsnp,
+        ch_dbsnp_tbi,
         params.platform
     )
     .set { ch_mapped }
@@ -307,7 +300,7 @@ workflow RAREDISEASE {
         ch_genome_fai,
         ch_bait_intervals,
         ch_target_intervals,
-        ch_chrom_sizes,
+        ch_genome_chrsizes,
         ch_intervals_wgs,
         ch_intervals_y
     )
@@ -349,8 +342,8 @@ workflow RAREDISEASE {
         ch_mapped.bam_bai,
         ch_genome_fasta,
         ch_genome_fai,
-        ch_known_dbsnp,
-        ch_known_dbsnp_tbi,
+        ch_dbsnp,
+        ch_dbsnp_tbi,
         ch_call_interval,
         ch_ml_model,
         CHECK_INPUT.out.case_info
@@ -361,7 +354,7 @@ workflow RAREDISEASE {
         ch_mapped.marked_bam,
         ch_mapped.marked_bai,
         ch_mapped.bam_bai,
-        ch_bwa_index,
+        ch_genome_bwaindex,
         ch_genome_fasta,
         ch_genome_fai,
         CHECK_INPUT.out.case_info,
@@ -431,19 +424,19 @@ workflow RAREDISEASE {
             ch_mapped.bam_bai,
             ch_cadd_header,
             ch_cadd_resources,
-            ch_bwa_index,
-            ch_bwamem2_index,
+            ch_genome_bwaindex,
+            ch_genome_bwamem2index,
             ch_genome_fasta,
             ch_genome_fai,
             ch_genome_dictionary,
             ch_mt_intervals,
-            ch_bwa_index_mt_shift,
-            ch_bwamem2_index_mt_shift,
-            ch_mt_fasta_shift,
-            ch_sequence_dictionary_mt_shift,
-            ch_mt_shift_fai,
-            ch_mt_intervals_shift,
-            ch_mt_backchain_shift,
+            ch_mtshift_bwaindex,
+            ch_mtshift_bwamem2index,
+            ch_mtshift_fasta,
+            ch_mtshift_dictionary,
+            ch_mtshift_fai,
+            ch_mtshift_intervals,
+            ch_mtshift_backchain,
             ch_vcfanno_resources,
             ch_vcfanno_toml,
             params.genome,

From fd79ab76593604549ba4cf7e754d079b7dbbfdf7 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 26 May 2023 10:49:42 +0200
Subject: [PATCH 3/8] update input channel definitions

---
 .../local/mitochondria/align_and_call_MT.nf   | 22 +++++++++----------
 .../mitochondria/convert_mt_bam_to_fastq.nf   | 10 ++++-----
 .../local/mitochondria/merge_annotate_MT.nf   |  4 ++--
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/subworkflows/local/mitochondria/align_and_call_MT.nf b/subworkflows/local/mitochondria/align_and_call_MT.nf
index 3d992322..7121168c 100644
--- a/subworkflows/local/mitochondria/align_and_call_MT.nf
+++ b/subworkflows/local/mitochondria/align_and_call_MT.nf
@@ -16,21 +16,21 @@ include { TABIX_TABIX as TABIX_TABIX_MT                                     } fr
 
 workflow ALIGN_AND_CALL_MT {
     take:
-        ch_fastq         // channel: [mandatory] [ val(meta), [ path(reads) ] ]
-        ch_ubam          // channel: [mandatory] [ val(meta), path(bam) ]
-        ch_index_bwa     // channel: [mandatory for sentieon] [ val(meta), path(index) ]
-        ch_index_bwamem2 // channel: [mandatory for bwamem2] [ val(meta), path(index) ]
-        ch_fasta         // channel: [mandatory] [ val(meta), path(fasta) ]
-        ch_dict          // channel: [mandatory] [ val(meta), path(dict) ]
-        ch_fai           // channel: [mandatory] [ val(meta), path(fai) ]
-        ch_intervals_mt  // channel: [mandatory] [ path(interval_list) ]
+        ch_fastq        // channel: [mandatory] [ val(meta), [ path(reads) ] ]
+        ch_ubam         // channel: [mandatory] [ val(meta), path(bam) ]
+        ch_bwaindex     // channel: [mandatory for sentieon] [ val(meta), path(index) ]
+        ch_bwamem2index // channel: [mandatory for bwamem2] [ val(meta), path(index) ]
+        ch_fasta        // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_dict         // channel: [mandatory] [ val(meta), path(dict) ]
+        ch_fai          // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_intervals    // channel: [mandatory] [ path(interval_list) ]
 
     main:
         ch_versions = Channel.empty()
 
-        BWAMEM2_MEM_MT (ch_fastq , ch_index_bwamem2, true)
+        BWAMEM2_MEM_MT (ch_fastq , ch_bwamem2index, true)
 
-        SENTIEON_BWAMEM_MT ( ch_fastq, ch_fasta, ch_fai, ch_index_bwa )
+        SENTIEON_BWAMEM_MT ( ch_fastq, ch_fasta, ch_fai, ch_bwaindex )
 
         ch_mt_bam      = Channel.empty().mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam)
         ch_fastq_ubam  = ch_mt_bam.join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)
@@ -45,7 +45,7 @@ workflow ALIGN_AND_CALL_MT {
 
         SAMTOOLS_INDEX_MT(SAMTOOLS_SORT_MT.out.bam)
         ch_sort_index_bam        = SAMTOOLS_SORT_MT.out.bam.join(SAMTOOLS_INDEX_MT.out.bai, failOnMismatch:true, failOnDuplicate:true)
-        ch_sort_index_bam_int_mt = ch_sort_index_bam.combine(ch_intervals_mt)
+        ch_sort_index_bam_int_mt = ch_sort_index_bam.combine(ch_intervals)
 
         GATK4_MUTECT2_MT (ch_sort_index_bam_int_mt, ch_fasta, ch_fai, ch_dict, [], [], [],[])
 
diff --git a/subworkflows/local/mitochondria/convert_mt_bam_to_fastq.nf b/subworkflows/local/mitochondria/convert_mt_bam_to_fastq.nf
index 2df4406f..156f71bb 100644
--- a/subworkflows/local/mitochondria/convert_mt_bam_to_fastq.nf
+++ b/subworkflows/local/mitochondria/convert_mt_bam_to_fastq.nf
@@ -8,16 +8,16 @@ include { GATK4_SAMTOFASTQ as GATK4_SAMTOFASTQ_MT } from '../../../modules/nf-co
 
 workflow CONVERT_MT_BAM_TO_FASTQ {
     take:
-        ch_bam               // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
-        ch_genome_fasta_meta // channel: [mandatory] [ val(meta), path(fasta) ]
-        ch_genome_fai        // channel: [mandatory] [ val(meta), path(fai) ]
-        ch_genome_dict       // channel: [mandatory] [ val(meta), path(dict) ]
+        ch_bam_bai      // channel: [mandatory] [ val(meta), path(bam), path(bai) ]
+        ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
+        ch_genome_fai   // channel: [mandatory] [ val(meta), path(fai) ]
+        ch_genome_dict  // channel: [mandatory] [ val(meta), path(dict) ]
 
     main:
         ch_versions = Channel.empty()
 
         // Outputs bam containing only MT
-        GATK4_PRINTREADS_MT ( ch_bam, ch_genome_fasta_meta, ch_genome_fai, ch_genome_dict )
+        GATK4_PRINTREADS_MT ( ch_bam_bai, ch_genome_fasta, ch_genome_fai, ch_genome_dict )
 
         // Removes alignment information
         GATK4_REVERTSAM_MT ( GATK4_PRINTREADS_MT.out.bam )
diff --git a/subworkflows/local/mitochondria/merge_annotate_MT.nf b/subworkflows/local/mitochondria/merge_annotate_MT.nf
index 8d4f3da0..46e334f0 100644
--- a/subworkflows/local/mitochondria/merge_annotate_MT.nf
+++ b/subworkflows/local/mitochondria/merge_annotate_MT.nf
@@ -23,9 +23,9 @@ workflow MERGE_ANNOTATE_MT {
         ch_vcf2                // channel: [mandatory] [ val(meta), path(vcf) ]
         ch_cadd_header         // channel: [mandatory] [ path(txt) ]
         ch_cadd_resources      // channel: [mandatory] [ path(annotation) ]
-        ch_genome_fasta        // channel: [mandatory] [ path(fasta) ]
+        ch_genome_fasta        // channel: [mandatory] [ val(meta), path(fasta) ]
         ch_genome_dict         // channel: [mandatory] [ val(meta), path(dict) ]
-        ch_genome_fai          // channel: [mandatory] [ path(fai) ]
+        ch_genome_fai          // channel: [mandatory] [ val(meta), path(fai) ]
         ch_vcfanno_resources   // channel: [mandatory] [ path(resources) ]
         ch_vcfanno_toml        // channel: [mandatory] [ path(toml) ]
         val_vep_genome         // string:  [mandatory] GRCh37 or GRCh38

From 743c35bb24f801cd2573235e1784401403bf40f4 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 26 May 2023 10:56:08 +0200
Subject: [PATCH 4/8] update docs

---
 CHANGELOG.md  |  7 +++++++
 docs/usage.md | 22 ++++++++--------------
 2 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23a719c8..cf89d03d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.0.0 - []
+
+### `Added`
+
+- GATK's ShiftFasta to generate all the files required for mitochondrial variant calling
+- Feature to calculate CADD scores for indels
+
 ## v1.0.0 - [2023-03-31]
 
 Initial release of nf-core/raredisease, created with the [nf-core](https://nf-co.re/) template.
diff --git a/docs/usage.md b/docs/usage.md
index 482ed179..5dd5761a 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -219,20 +219,14 @@ The mandatory and optional parameters for each category are tabulated below.
 
 ##### 8. Mitochondrial analysis
 
-| Mandatory                      | Optional |
-| ------------------------------ | -------- |
-| genome                         |          |
-| mt_backchain_shift<sup>1</sup> |          |
-| mito_name                      |          |
-| mt_fasta_shift                 |          |
-| mt_intervals                   |          |
-| mt_intervals_shift             |          |
-| vcfanno_resources              |          |
-| vcfanno_toml                   |          |
-| vep_cache_version              |          |
-| vep_cache                      |          |
-
-<sup>1</sup>Can be generated by GATK's [ShiftFasta](https://gatk.broadinstitute.org/hc/en-us/articles/9570501436827-ShiftFasta-BETA-). Sample file [here](https://github.com/nf-core/test-datasets/blob/raredisease/reference/mt_shift8000.back_chain).
+| Mandatory         | Optional |
+| ----------------- | -------- |
+| genome            |          |
+| mito_name         |          |
+| vcfanno_resources |          |
+| vcfanno_toml      |          |
+| vep_cache_version |          |
+| vep_cache         |          |
 
 #### Run the pipeline
 

From f0f866d0d8d10f29e92b947fb85996cd55520dc3 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 26 May 2023 10:58:53 +0200
Subject: [PATCH 5/8] update changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf89d03d..55291bfa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- GATK's ShiftFasta to generate all the files required for mitochondrial variant calling
+- GATK's ShiftFasta to generate all the files required for mitochondrial analysis
 - Feature to calculate CADD scores for indels
 
 ## v1.0.0 - [2023-03-31]

From c0a869e9b629935d9cc492864053ac0f210301ab Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 26 May 2023 11:27:13 +0200
Subject: [PATCH 6/8] fix lint

---
 modules.json | 278 +++++++++++++--------------------------------------
 1 file changed, 70 insertions(+), 208 deletions(-)

diff --git a/modules.json b/modules.json
index 0622ed2e..5b778895 100644
--- a/modules.json
+++ b/modules.json
@@ -8,488 +8,350 @@
                     "bcftools/annotate": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/concat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/merge": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/norm": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/reheader": {
                         "branch": "master",
                         "git_sha": "0435e4eebc94e53721c194b2d5d06f455a79e407",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/roh": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwa/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "bwamem2/mem": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cadd": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "deepvariant": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "expansionhunter": {
                         "branch": "master",
                         "git_sha": "0260e5d22372eae434816d6970dedf3f5adc0053",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/bedtointervallist": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/filtermutectcalls": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/intervallisttools": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/mergebamalignment": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/printreads": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/revertsam": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/samtofastq": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/selectvariants": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/shiftfasta": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/splitintervals": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "gatk4/variantfiltration": {
                         "branch": "master",
                         "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "genmod/annotate": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "genmod/compound": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "genmod/models": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "genmod/score": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "glnexus": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "haplocheck": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "haplogrep2/classify": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "manta/germline": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "mosdepth": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "peddy": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/addorreplacereadgroups": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",
                         "git_sha": "0ce3ab0ac301f160225b22254fa238478b4389f2",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/collectmultiplemetrics": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/collectwgsmetrics": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/liftovervcf": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/renamesampleinvcf": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "picard/sortvcf": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "qualimap/bamqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "rhocall/annotate": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "bf8ff98531167f8245ba5c44ce7d781503ddf936",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "smncopynumbercaller": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "stranger": {
                         "branch": "master",
                         "git_sha": "0260e5d22372eae434816d6970dedf3f5adc0053",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "svdb/merge": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "svdb/query": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
                         "git_sha": "01b3b2509d76625b6d6cd613b349fb4777712a15",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tiddit/cov": {
                         "branch": "master",
                         "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "tiddit/sv": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "ucsc/wigtobigwig": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     },
                     "vcfanno": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": [
-                            "modules"
-                        ]
+                        "installed_by": ["modules"]
                     }
                 }
             }
         }
     }
-}
\ No newline at end of file
+}

From 4b6b9eac055a2d37250e12c477e8996cea4aa099 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Sat, 27 May 2023 23:06:31 +0200
Subject: [PATCH 7/8] update conf

---
 conf/modules/prepare_references.config        | 16 +++---
 .../local/mitochondria/align_and_call_MT.nf   | 10 ++--
 subworkflows/local/prepare_references.nf      | 51 +++++++++++--------
 3 files changed, 44 insertions(+), 33 deletions(-)

diff --git a/conf/modules/prepare_references.config b/conf/modules/prepare_references.config
index af73549a..a825250c 100644
--- a/conf/modules/prepare_references.config
+++ b/conf/modules/prepare_references.config
@@ -29,16 +29,16 @@ process {
         ext.when = {!params.bwamem2 && params.aligner == "bwamem2"}
     }
 
-    withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_SHIFT_MT' {
-        ext.when = {!params.mt_bwamem2_index_shift && params.mt_fasta_shift && !(params.analysis_type == "wes") && params.aligner == "bwamem2"}
+    withName: '.*PREPARE_REFERENCES:BWAMEM2_INDEX_MT_SHIFT' {
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "bwamem2"}
     }
 
     withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_GENOME' {
         ext.when = {!params.bwa && params.aligner == "sentieon"}
     }
 
-    withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_SHIFT_MT' {
-        ext.when = {!params.mt_bwa_index_shift && params.mt_fasta_shift && !(params.analysis_type == "wes") && params.aligner == "sentieon"}
+    withName: '.*PREPARE_REFERENCES:SENTIEON_BWAINDEX_MT_SHIFT' {
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes") && params.aligner == "sentieon"}
     }
 
     withName: '.*PREPARE_REFERENCES:BWA_INDEX_GENOME' {
@@ -54,8 +54,8 @@ process {
         ext.when = {!params.mt_fasta && !params.skip_mt_analysis}
     }
 
-    withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_SHIFT_MT' {
-        ext.when = {!params.mt_fai_shift && params.mt_fasta_shift && !(params.analysis_type == "wes")}
+    withName: '.*PREPARE_REFERENCES:SAMTOOLS_FAIDX_MT_SHIFT' {
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes")}
     }
 
     withName: '.*PREPARE_REFERENCES:GATK_SD' {
@@ -66,8 +66,8 @@ process {
         ext.args = { "--interval-file-name ${meta.id}_mt" }
     }
 
-    withName: '.*PREPARE_REFERENCES:GATK_SD_SHIFT_MT' {
-        ext.when = {!params.mt_sequence_dictionary_shift && params.mt_fasta_shift && !(params.analysis_type == "wes")}
+    withName: '.*PREPARE_REFERENCES:GATK_SD_MT_SHIFT' {
+        ext.when = { !params.skip_mt_analysis && !(params.analysis_type == "wes")}
     }
 
     withName: '.*PREPARE_REFERENCES:GET_CHROM_SIZES' {
diff --git a/subworkflows/local/mitochondria/align_and_call_MT.nf b/subworkflows/local/mitochondria/align_and_call_MT.nf
index 7121168c..dc629d84 100644
--- a/subworkflows/local/mitochondria/align_and_call_MT.nf
+++ b/subworkflows/local/mitochondria/align_and_call_MT.nf
@@ -28,14 +28,16 @@ workflow ALIGN_AND_CALL_MT {
     main:
         ch_versions = Channel.empty()
 
-        BWAMEM2_MEM_MT (ch_fastq , ch_bwamem2index, true)
+        BWAMEM2_MEM_MT (ch_fastq, ch_bwamem2index, true)
 
         SENTIEON_BWAMEM_MT ( ch_fastq, ch_fasta, ch_fai, ch_bwaindex )
 
-        ch_mt_bam      = Channel.empty().mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam)
-        ch_fastq_ubam  = ch_mt_bam.join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)
+        Channel.empty()
+            .mix(BWAMEM2_MEM_MT.out.bam, SENTIEON_BWAMEM_MT.out.bam)
+            .join(ch_ubam, failOnMismatch:true, failOnDuplicate:true)
+            .set {ch_bam_ubam}
 
-        GATK4_MERGEBAMALIGNMENT_MT (ch_fastq_ubam, ch_fasta, ch_dict)
+        GATK4_MERGEBAMALIGNMENT_MT (ch_bam_ubam, ch_fasta, ch_dict)
 
         PICARD_ADDORREPLACEREADGROUPS_MT (GATK4_MERGEBAMALIGNMENT_MT.out.bam)
 
diff --git a/subworkflows/local/prepare_references.nf b/subworkflows/local/prepare_references.nf
index f9a8fb47..54160fdc 100644
--- a/subworkflows/local/prepare_references.nf
+++ b/subworkflows/local/prepare_references.nf
@@ -57,11 +57,20 @@ workflow PREPARE_REFERENCES {
         GATK_SHIFTFASTA(ch_mt_fasta_in, SAMTOOLS_FAIDX_MT_SHIFT.out.fai, GATK_SD_MT_SHIFT.out.dict)
         BWAMEM2_INDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa)
         SENTIEON_BWAINDEX_MT_SHIFT(GATK_SHIFTFASTA.out.shift_fa)
+        GATK_SHIFTFASTA.out.intervals
+            .multiMap{ meta, files ->
+                    shift_intervals:
+                        ind = files.findIndexValues {it.toString().endsWith("shifted.intervals")}
+                        files[ind]
+                    intervals:
+                        ind = files.findIndexValues {!(it.toString().endsWith("shifted.intervals"))}
+                        files[ind]
+            }
+            .set {ch_shiftfasta_mtintervals}
 
         // Vcf, tab and bed indices
         TABIX_DBSNP(ch_known_dbsnp)
                 ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions)
-
         TABIX_GNOMAD_AF(ch_gnomad_af_tab)
         TABIX_PT(ch_target_bed).tbi.set { ch_tbi }
         TABIX_PBT(ch_target_bed).gz_tbi.set { ch_bgzip_tbi }
@@ -101,28 +110,28 @@ workflow PREPARE_REFERENCES {
         ch_versions = ch_versions.mix(UNTAR_VEP_CACHE.out.versions)
 
     emit:
-        genome_bwa_index      = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect()              // channel: [ val(meta), path(index) ]
-        genome_bwamem2_index  = BWAMEM2_INDEX_GENOME.out.index.collect()                           // channel: [ val(meta), path(index) ]
-        genome_chrom_sizes    = GET_CHROM_SIZES.out.sizes.collect()                                // channel: [ path(sizes) ]
-        genome_fai            = ch_fai                                                             // channel: [ val(meta), path(fai) ]
-        genome_dict           = GATK_SD.out.dict.collect()                                         // channel: [ path(dict) ]
+        genome_bwa_index      = Channel.empty().mix(ch_bwa, ch_sentieonbwa).collect()            // channel: [ val(meta), path(index) ]
+        genome_bwamem2_index  = BWAMEM2_INDEX_GENOME.out.index.collect()                         // channel: [ val(meta), path(index) ]
+        genome_chrom_sizes    = GET_CHROM_SIZES.out.sizes.collect()                              // channel: [ path(sizes) ]
+        genome_fai            = ch_fai                                                           // channel: [ val(meta), path(fai) ]
+        genome_dict           = GATK_SD.out.dict.collect()                                       // channel: [ path(dict) ]
 
-        mt_intervals          = GATK_SHIFTFASTA.out.intervals.map{ meta, it -> it}.collect()       // channel: [ path(intervals) ]
-        mtshift_intervals     = GATK_SHIFTFASTA.out.shift_intervals.map{ meta, it -> it}.collect() // channel: [ path(intervals) ]
-        mtshift_backchain     = GATK_SHIFTFASTA.out.shift_back_chain.collect()
-        mtshift_fai           = GATK_SHIFTFASTA.out.shift_fai.collect()                            // channel: [ val(meta), path(fai) ]
-        mtshift_fasta         = GATK_SHIFTFASTA.out.shift_fa.collect()                             // channel: [ val(meta), path(fai) ]
-        mtshift_dict          = GATK_SHIFTFASTA.out.dict.collect()                                 // channel: [ path(dict) ]
-        mtshift_bwa_index     = SENTIEON_BWAINDEX_MT_SHIFT.out.index.collect()                     // channel: [ val(meta), path(index) ]
-        mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect()                         // channel: [ val(meta), path(index) ]
+        mt_intervals          = ch_shiftfasta_mtintervals.intervals.collect()                    // channel: [ path(intervals) ]
+        mtshift_intervals     = ch_shiftfasta_mtintervals.shift_intervals.collect()              // channel: [ path(intervals) ]
+        mtshift_backchain     = GATK_SHIFTFASTA.out.shift_back_chain.collect()                   // channel: [ val(meta), path(backchain) ]
+        mtshift_fai           = GATK_SHIFTFASTA.out.shift_fai.collect()                          // channel: [ val(meta), path(fai) ]
+        mtshift_fasta         = GATK_SHIFTFASTA.out.shift_fa.collect()                           // channel: [ val(meta), path(fai) ]
+        mtshift_dict          = GATK_SHIFTFASTA.out.dict.collect()                               // channel: [ path(dict) ]
+        mtshift_bwa_index     = SENTIEON_BWAINDEX_MT_SHIFT.out.index.collect()                   // channel: [ val(meta), path(index) ]
+        mtshift_bwamem2_index = BWAMEM2_INDEX_MT_SHIFT.out.index.collect()                       // channel: [ val(meta), path(index) ]
 
-        gnomad_af_idx         = TABIX_GNOMAD_AF.out.tbi.collect()                                  // channel: [ val(meta), path(fasta) ]
-        known_dbsnp_tbi       = TABIX_DBSNP.out.tbi.collect()                                      // channel: [ val(meta), path(fasta) ]
-        target_bed            = Channel.empty().mix(ch_tbi, ch_bgzip_tbi).collect()                // channel: [ val(meta), path(bed), path(tbi) ]
-        bait_intervals        = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect()     // channel: [ path(intervals) ]
-        target_intervals      = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect()   // channel: [ path(interval_list) ]
-        vep_resources         = UNTAR_VEP_CACHE.out.untar.map{meta, files -> [files]}.collect()    // channel: [ path(cache) ]
-        versions              = ch_versions                                                        // channel: [ path(versions.yml) ]
+        gnomad_af_idx         = TABIX_GNOMAD_AF.out.tbi.collect()                                // channel: [ val(meta), path(fasta) ]
+        known_dbsnp_tbi       = TABIX_DBSNP.out.tbi.collect()                                    // channel: [ val(meta), path(fasta) ]
+        target_bed            = Channel.empty().mix(ch_tbi, ch_bgzip_tbi).collect()              // channel: [ val(meta), path(bed), path(tbi) ]
+        bait_intervals        = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect()   // channel: [ path(intervals) ]
+        target_intervals      = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect() // channel: [ path(interval_list) ]
+        vep_resources         = UNTAR_VEP_CACHE.out.untar.map{meta, files -> [files]}.collect()  // channel: [ path(cache) ]
+        versions              = ch_versions                                                      // channel: [ path(versions.yml) ]
 
 }
 

From 48af7d5167ac0ab8b632a59df50673e9cf167c1a Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 29 May 2023 10:39:51 +0200
Subject: [PATCH 8/8] update faidx

---
 modules.json                           | 2 +-
 modules/nf-core/samtools/faidx/main.nf | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules.json b/modules.json
index 5b778895..a061424c 100644
--- a/modules.json
+++ b/modules.json
@@ -267,7 +267,7 @@
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "bf8ff98531167f8245ba5c44ce7d781503ddf936",
+                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index c1e8ef3a..59ed3088 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -35,8 +35,12 @@ process SAMTOOLS_FAIDX {
     """
 
     stub:
+    def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll()
+    def fastacmd = match[0] ? "touch ${match[0][1]}" : ''
     """
+    ${fastacmd}
     touch ${fasta}.fai
+
     cat <<-END_VERSIONS > versions.yml
 
     "${task.process}":