diff --git a/CHANGELOG.md b/CHANGELOG.md
index 02c6831d..b7af38b8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 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).
 
-## v1.1.0 'Brass Pigeon' - [2025-05-08]
+## v1.1.0 'Brass Pigeon' - [2025-07-11]
 
 ### `Added`
 
diff --git a/conf/old.modules.config b/conf/old.modules.config
deleted file mode 100644
index 6c0c27b2..00000000
--- a/conf/old.modules.config
+++ /dev/null
@@ -1,597 +0,0 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
-----------------------------------------------------------------------------------------
-*/
-
-process {
-    // General catch-all
-    publishDir = [
-        path: { "${params.outdir}/${meta.id}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-    /*
-    ----------
-    Reads in
-    ONT
-    ----------
-    */
-    // nanoq: local module; QC
-    withName: NANOQ {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/nanoq" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // only local module
-    withName: COLLECT {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/collect" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // porechop: nf-core module
-    withName: PORECHOP {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/porechop" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // Genomescope / jellyfish: local modules
-    withName: COUNT {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/genomescope/jellyfish/count/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: DUMP {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/genomescope/jellyfish/dump/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: STATS {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/genomescope/jellyfish/stats/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: HISTO {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/genomescope/jellyfish/histo/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: GENOMESCOPE {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/genomescope/genomescope/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    /*
-    ----------
-    Reads in
-    HiFi
-    all nf-core
-    ----------
-    */
-    withName: LIMA {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/lima/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: TO_FASTQ {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/lima/fastq/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    /*
-    ----------
-    Reads in
-    Short reads
-    all nf-core
-    ----------
-    */
-    withName: TRIMGALORE {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/trimgalore" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: MERYL_COUNT {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/meryl/count/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: MERYL_UNIONSUM {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/reads/meryl/unionsum/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    /*
-    ----------
-    ASSEMBLY
-    ----------
-    */
-    // FLYE: nf-core
-    withName: FLYE {
-        ext.args = {
-            [
-                meta.genome_size ? "--genome-size ${meta.genome_size}" : '',
-                params.flye_args
-            ].join(" ").trim()
-        }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/flye/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // HIFIASM:
-    /* updated nf-core module */
-
-    withName: HIFIASM {
-        ext.args = { [ params.hifiasm_args ].join(" ").trim() }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/hifiasm/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: HIFIASM_ONT {
-        ext.args = { [ params.hifiasm_args, "--ont" ].join(" ").trim() }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/hifiasm_ont/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: GFA_2_FA {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/hifiasm/fasta" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: GFA_2_FA_HIFI {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/hifiasm/fasta" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: GFA_2_FA_ONT {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/hifiasm_ont/fasta" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*ASSEMBLE:.*RAGTAG_PATCH' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/ragtag/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_assembly_patch" }
-    }
-
-    /*
-    ----------
-    Polishing
-    ----------
-    */
-    // Medaka: local; nf-core module cant deal with gzipped input
-    withName: MEDAKA {
-        ext.args1 = { } // args mini_align
-        ext.args2 = { [params.medaka_model ? "--model ${params.medaka_model}" : ''].join(" ").trim() } // args medaka_inference
-        ext.args3 = {  } // args medaka sequence
-        ext.prefix = { "${meta.id}_medaka" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/polish/medaka" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // Pilon: nf-core
-    withName: PILON {
-        ext.prefix = { "${meta.id}_pilon" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/polish/pilon" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    /*
-    ----------
-    Scaffolding
-    ----------
-    */
-    // RagTag
-    withName: '.*SCAFFOLD:.*RAGTAG_SCAFFOLD' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/scaffold/ragtag/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_ragtag" }
-        ext.args   = [
-                "-C",
-                "-u",
-                "-r",
-                "-w"
-            ].join(" ").trim()
-    }
-
-    withName: LINKS {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/scaffold/links/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_links" }
-        ext.args = ["-t 40,200", "-d 500,2000,5000"].join(" ").trim()
-    }
-
-    // No nf-core module yet.
-    withName: LONGSTITCH {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/scaffold/longstitch/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_longstitch" }
-    }
-    /*
-    --------
-    Annotations
-    liftoff nf-core module
-    --------
-    gff file goes with fasta file
-    */
-
-    withName: '.*ASSEMBLE:.*LIFTOFF' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/assembly/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_assembly" }
-    }
-
-    withName: '.*PILON:.*LIFTOFF' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/polish/pilon/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_pilon" }
-    }
-
-    withName: '.*MEDAKA:.*LIFTOFF' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/polish/medaka" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_medaka" }
-    }
-
-    withName: '.*RAGTAG:.*LIFTOFF' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/scaffold/ragtag/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_ragtag" }
-    }
-
-    withName: '.*LONGSTITCH:.*LIFTOFF' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/scaffold/longstitch" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_longstitch" }
-    }
-
-    withName: '.*LINKS:.*LIFTOFF' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/scaffold/links" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_links" }
-    }
-
-    /*
-    ----------
-    QC
-    ----------
-    */
-
-    // BUSCO: nf-core
-    withName: '.*:ASSEMBLE:.*:BUSCO' {
-        ext.prefix = { "${meta.id}_assembly-${lineage}" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
-            mode: params.publish_dir_mode,
-            pattern: "*{-busco,_summary}*",
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*PILON:.*:BUSCO' {
-        ext.prefix = { "${meta.id}_pilon-${lineage}" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
-            mode: params.publish_dir_mode,
-            pattern: "*{-busco,_summary}*",
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*MEDAKA:.*:BUSCO' {
-        ext.prefix = { "${meta.id}_medaka-${lineage}" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
-            mode: params.publish_dir_mode,
-            pattern: "*{-busco,_summary}*",
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*LINKS:.*:BUSCO' {
-        ext.prefix = { "${meta.id}_links-${lineage}" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
-            mode: params.publish_dir_mode,
-            pattern: "*{-busco,_summary}*",
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*LONGSTITCH:.*:BUSCO' {
-        ext.prefix = { "${meta.id}_longstitch-${lineage}" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
-            mode: params.publish_dir_mode,
-            pattern: "*{-busco,_summary}*",
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // avoid catching ragtag from ont_on_hifi assembly
-    withName: '.*:SCAFFOLD:.*RAGTAG:.*:BUSCO' {
-        ext.prefix = { "${meta.id}_ragtag-${lineage}" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/BUSCO/" },
-            mode: params.publish_dir_mode,
-            pattern: "*{-busco,_summary}*",
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    // QUAST: Prefer to keep the local module since it can deal with the inputs I have
-    withName: '.*:ASSEMBLE:.*:QUAST' {
-        ext.prefix = { "${meta.id}_assembly" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/QUAST" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*PILON:.*:QUAST' {
-        ext.prefix = { "${meta.id}_pilon" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/QUAST" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*MEDAKA:.*:QUAST' {
-        ext.prefix = { "${meta.id}_medaka" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/QUAST" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*LINKS:.*:QUAST' {
-        ext.prefix = { "${meta.id}_links" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/QUAST/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*LONGSTITCH:.*:QUAST' {
-        ext.prefix = { "${meta.id}_longstitch" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/QUAST/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // avoid catching ragtag from ont_on_hifi assembly
-    withName: '.*:SCAFFOLD:.*RAGTAG:.*:QUAST' {
-        ext.prefix = { "${meta.id}_ragtag" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/QUAST/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    // MERQURY: nf-core
-    withName: '.*:ASSEMBLE:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_assembly" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/merqury/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*PILON:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_pilon" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/merqury/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*MEDAKA:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_medaka" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/merqury/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*LINKS:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_links" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/merqury/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    withName: '.*LONGSTITCH:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_longstitch" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/merqury/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // avoid catching ragtag from ont_on_hifi assembly
-    withName: '.*:SCAFFOLD:.*RAGTAG:.*:MERQURY' {
-        ext.prefix = { "${meta.id}_ragtag" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/merqury/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-    // Refence
-    withName: '.*MAP_TO_REF.*' {
-        ext.prefix = { "${meta.id}_to_reference" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/reference/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    // Assembly mappings
-    withName: '.*ASSEMBLE:.*MAP_TO_ASSEMBLY.*' {
-        ext.prefix = { "${meta.id}_assembly" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    withName: '.*MEDAKA:.*MAP_TO_ASSEMBLY.*' {
-        ext.prefix = { "${meta.id}_medaka" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    withName: '.*PILON:.*MAP_TO_ASSEMBLY.*' {
-        ext.prefix = { "${meta.id}_pilon" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    withName: '.*LONGSTITCH:.*MAP_TO_ASSEMBLY.*' {
-        ext.prefix = { "${meta.id}_longstitch" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    withName: '.*LINKS:.*MAP_TO_ASSEMBLY.*' {
-        ext.prefix = { "${meta.id}_links" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    withName: '.*RAGTAG:.*MAP_TO_ASSEMBLY.*' {
-        ext.prefix = { "${meta.id}_ragtag" }
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.args = {
-            (params.hifi && params.ont) ? (params.qc_reads == 'ONT' ? "-ax map-ont" : "-ax map-hifi") : (params.ont) ? "-ax map-ont" : "-ax map-hifi"
-        }
-    }
-    // Pilon mapping
-    withName: '.*PILON:MAP_SR.*' {
-        publishDir = [
-            path: { "${params.outdir}/${meta.id}/QC/alignments/shortreads/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-        ext.prefix = { "${meta.id}_shortreads" }
-        ext.args = { "-ax sr " }
-    }
-    /*
-    --------
-    Report
-    */
-    withName: REPORT {
-        publishDir = [
-            path: { "${params.outdir}/report/" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
diff --git a/conf/test.config b/conf/test.config
index b8875c0f..be3dc0e5 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -17,13 +17,7 @@ process {
         time: '1.h'
     ]
 }
-/*
-process {
-    withName: 'HIFIASM.*' {
-        memory = '15.GB'
-    }
-}
-*/
+
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
diff --git a/nextflow.config b/nextflow.config
index 17bb4d91..45e4f254 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -239,8 +239,7 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa
 
 
 // Load nf-core/genomeassembler custom profiles from different institutions.
-includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/genomeassembler.config" : "/dev/null"
-
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/genomeassembler.config" : "/dev/null"
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers