diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 253f71c..10c3c23 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,7 @@ include:
       file: "wf-containers.yaml"
 
 variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
               --de_analysis --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
               --transcriptome_source reference-guided \
@@ -14,6 +14,7 @@ variables:
               CI_FLAVOUR: "new"
               PYTEST_CONTAINER_NAME: "wf-common"
               PYTEST_CONTAINER_CONFIG_KEY: "common_sha"
+              MEM_CFG: "echo 'process { withName:build_minimap_index { memory = '16.GB' };  withName:build_minimap_index_transcriptome { memory = '16.GB' } }' > ${CI_PROJECT_NAME}/data/mm2.config"
 
 macos-run:
   # Let's avoid those ARM64 runners for now
@@ -41,7 +42,6 @@ docker-run:
             - ${CI_PROJECT_NAME}/**/*.fna
             - ${CI_PROJECT_NAME}/**/*.fasta
             - ${CI_PROJECT_NAME}/**/*.mmi
-    
 
     # Define a 1D job matrix to inject a variable named MATRIX_NAME into
     #   the CI environment, we can use the value of MATRIX_NAME to determine
@@ -65,38 +65,38 @@ docker-run:
           when: never
         - if: $MATRIX_NAME == "isoforms"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
                   --ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
-                  -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                  -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "isoforms_bam"
           variables:
-            NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+            NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
             NF_WORKFLOW_OPTS: "--bam  ${CI_PROJECT_NAME}/data/ERR6053095_chr20.bam --transcriptome_source reference-guided \
                   --ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa --ref_annotation ${CI_PROJECT_NAME}/data/chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm \
-                  -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                  -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
             NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,check_annotation_strand,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "no_ref_annotation"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/wf-isoforms_test_data.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/ERR6053095_chr20.fastq --transcriptome_source reference-guided \
                   --ref_genome ${CI_PROJECT_NAME}/data/chr20/hg38_chr20.fa \
-                  -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                  -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: run_gffcompare,check_annotation_strand,preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "differential_expression"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
                   --de_analysis \
                   --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
                 --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/gencode.v22.annotation.chr20.gtf \
                 --direct_rna --minimap2_index_opts '-k 15'  --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "only_differential_expression"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
                   --transcriptome_source precomputed \
                   --de_analysis \
@@ -105,13 +105,13 @@ docker-run:
                 --direct_rna --minimap2_index_opts '-k 15' \
                 --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression/ref_transcriptome.fasta \
                 --sample_sheet test_data/sample_sheet.csv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,faidx,gz_faidx,merge_transcriptomes,merge_gff_bundles,assemble_transcripts,decompress_annotation,decompress_ref,
                 build_minimap_index,get_transcriptome,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "differential_expression_gff3"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq   ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
                   --transcriptome_source precomputed \
                   --de_analysis \
@@ -120,81 +120,81 @@ docker-run:
                 --direct_rna --minimap2_index_opts '-k 15' \
                 --ref_transcriptome  ${CI_PROJECT_NAME}/data/differential_expression/ref_transcriptome.fasta \
                 --sample_sheet test_data/sample_sheet.csv \
-                -c  ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c  ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "ncbi_gzip"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O  ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
-              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
-                  --fastq   ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O  ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
+              NF_WORKFLOW_OPTS:
+                  "--fastq   ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
                   --de_analysis \
                   --ref_genome  ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \
                 --ref_annotation  ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \
                 --direct_rna --minimap2_index_opts '-w 25' \
                --sample_sheet test_data/sample_sheet.csv \
-               -c  ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+               -c  ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome           
         - if: $MATRIX_NAME == "ncbi_no_gene_id"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O  ${CI_PROJECT_NAME}/data/demo.nextflow.config  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
-              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
-                --fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O  ${CI_PROJECT_NAME}/data/demo.nextflow.config  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
+              NF_WORKFLOW_OPTS:
+                "--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
                 --transcriptome_source precomputed --de_analysis \
                 --ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
                 --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
                 --direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
                 --sample_sheet test_data/sample_sheet.csv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome      
         - if: $MATRIX_NAME == "ensembl_with_versions"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
-              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
-                --fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
+              NF_WORKFLOW_OPTS:
+                "--fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
                 --de_analysis \
                 --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz \
                 --ref_annotation  ${CI_PROJECT_NAME}/data/differential_expression/Homo_sapiens.GRCh38.109.gtf.gz \
                 --direct_rna --ref_transcriptome  ${CI_PROJECT_NAME}/data/differential_expression/Homo_sapiens.GRCh38.cdna.all.fa.gz \
                 --sample_sheet test_data/sample_sheet.csv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "differential_expression_mouse"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_mouse.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz -C ${CI_PROJECT_NAME}/data/&&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
-              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
-                --fastq  ${CI_PROJECT_NAME}/data/differential_expression_mouse/differential_expression_fastq \
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_mouse.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_mouse.tar.gz -C ${CI_PROJECT_NAME}/data/&&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
+              NF_WORKFLOW_OPTS:
+                "--fastq  ${CI_PROJECT_NAME}/data/differential_expression_mouse/differential_expression_fastq \
                 --transcriptome_source precomputed --de_analysis \
                 --ref_genome  ${CI_PROJECT_NAME}/data/differential_expression_mouse/GRCm39.genome.fa.gz \
                 --ref_annotation  ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.annotation.gtf \
                 --direct_rna --ref_transcriptome  ${CI_PROJECT_NAME}/data/differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
                 --sample_sheet  ${CI_PROJECT_NAME}/data/differential_expression_mouse/sample_sheet.csv \
-                -c  ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c  ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,faidx,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam    
         - if: $MATRIX_NAME == "unstranded_annotation_error"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
                   --de_analysis \
                   --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa --transcriptome_source reference-guided \
                 --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression/unstranded_annotation.gtf \
                 --direct_rna --minimap2_index_opts '-k 15'  --sample_sheet ${CI_PROJECT_NAME}/data/differential_expression/sample_sheet.csv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: preprocess_reads,faidx,gz_faidx,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
               ASSERT_NEXTFLOW_FAILURE: "test_fail" # set to any non-zero length str to allow the nextflow CMD to fail
               ASSERT_NEXTFLOW_FAILURE_REXP: "In ref_annotation, transcript features must have a strand of either '+' or '-'"
         - if: $MATRIX_NAME == "igv"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf ${CI_PROJECT_NAME}/data/differential_expression.tar.gz -C ${CI_PROJECT_NAME}/data/  &&  wget -O ${CI_PROJECT_NAME}/data/demo.nextflow.config https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
               NF_WORKFLOW_OPTS: "--fastq  ${CI_PROJECT_NAME}/data/differential_expression/differential_expression_fastq \
                   --de_analysis \
                   --ref_genome ${CI_PROJECT_NAME}/data/differential_expression/hg38_chr20.fa \
@@ -203,22 +203,22 @@ docker-run:
                 --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression/ref_transcriptome.fasta \
                 --sample_sheet test_data/sample_sheet.csv \
                 --igv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,gz_faidx,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
         - if: $MATRIX_NAME == "igv_fai_gz"
           variables:
-              NF_BEFORE_SCRIPT: mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression_ncbi.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O  ${CI_PROJECT_NAME}/data/demo.nextflow.config  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config
-              NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
-                --fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
+              NF_BEFORE_SCRIPT: "mkdir -p ${CI_PROJECT_NAME}/data/ && wget -O ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/differential_expression_ncbi.tar.gz && tar -xzvf  ${CI_PROJECT_NAME}/data/differential_expression_ncbi.tar.gz -C  ${CI_PROJECT_NAME}/data/ &&  wget -O  ${CI_PROJECT_NAME}/data/demo.nextflow.config  https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/demo.nextflow.config; ${MEM_CFG}"
+              NF_WORKFLOW_OPTS:
+                "--fastq ${CI_PROJECT_NAME}/data/differential_expression_ncbi/differential_expression_fastq \
                 --transcriptome_source precomputed --de_analysis \
                 --ref_genome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.fna.gz \
                 --ref_annotation ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_genomic.gff.gz \
                 --direct_rna --ref_transcriptome ${CI_PROJECT_NAME}/data/differential_expression_ncbi/GCF_000001405.40_GRCh38.p14_rna.fna.gz \
                 --sample_sheet test_data/sample_sheet.csv \
                 --igv \
-                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config"
+                -c ${CI_PROJECT_NAME}/data/demo.nextflow.config -c ${CI_PROJECT_NAME}/data/mm2.config"
               NF_IGNORE_PROCESSES: >
                 preprocess_reads,merge_transcriptomes,assemble_transcripts,
                 build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome,faidx,gz_faidx 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cbb2e7c..cd2fe4c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,9 +4,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+### Changed
+- `split_bam` and `build_minimap_index_transcriptome` process memory allocation increased.
+
 ## [v1.6.1]
 ### Fixed
-- merge_gff_compare failing with empty GFF files.
+- `merge_gff_compare` failing with empty GFF files.
 
 ## [v1.6.0]
 ### Fixed
diff --git a/main.nf b/main.nf
index 8861eeb..5a8ec3e 100644
--- a/main.nf
+++ b/main.nf
@@ -193,12 +193,11 @@ process split_bam{
     Partition BAM file into loci or bundles with `params.bundle_min_reads` minimum size
     If no splitting required, just create single symbolic link to a single bundle.
 
-    Output tuples containing `sample_id` so bundles can be combined later in th pipeline.
     */
 
     label 'isoforms'
     cpus params.threads
-    memory "4 GB"
+    memory "15 GB"
 
     input:
         tuple val(sample_id), path(bam)
diff --git a/nextflow.config b/nextflow.config
index adac441..6154534 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -95,7 +95,7 @@ params {
       ]
     agent = null
     container_sha = "shad8671ea3a8ed52f2c0f40355e8eb5c6f00d2cbda"
-	common_sha= "shaabceef445fb63214073cbf5836fdd33c04be4ac7"
+	common_sha = "shaabceef445fb63214073cbf5836fdd33c04be4ac7"
     }
 }
 
diff --git a/subworkflows/differential_expression.nf b/subworkflows/differential_expression.nf
index 2e8db1b..29863b4 100644
--- a/subworkflows/differential_expression.nf
+++ b/subworkflows/differential_expression.nf
@@ -109,7 +109,7 @@ process build_minimap_index_transcriptome{
     */
     label "isoforms"
     cpus params.threads
-    memory "16 GB"
+    memory "31 GB"
     input:
         path reference
     output: