Fix multiqc report gen by removing filter paths; update to MultiQC v1…

….22.1

assets/multiqc_config.yaml

@@ -20,20 +20,14 @@ module_order:
  name: 'Samtools (Minimap2)'
  anchor: 'samtools_minimap2'
  info: 'This section of the report shows Samtools counts/statistics after mapping with Minimap2.'
- path_filters:
- - './samtools/*'
  - mosdepth:
  name: 'Mosdepth (Minimap2)'
  anchor: 'mosdepth_minimap2'
  info: 'This section of the report shows Mosdepth calculated depth statistics after mapping with Minimap2'
- path_filters:
- - './mosdepth/*'
  - bcftools:
  name: 'Bcftools Stats'
  anchor: 'bcftools'
  info: 'This section of the report shows Bcftools calculated statistics after variant calling using Clair3/Medaka and filter frameshift'
- path_filters:
- - './bcftools/*'
 
 extra_fn_clean_exts:
  - type: remove

modules/local/multiqc.nf

@@ -1,11 +1,11 @@
 process MULTIQC {
  label 'process_low'
 
- conda "bioconda::multiqc=1.21"
+ conda "bioconda::multiqc=1.22.1"
  if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
- container 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0'
+ container 'https://depot.galaxyproject.org/singularity/multiqc:1.22.1--pyhdfd78af_0'
  } else {
- container 'quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0'
+ container 'quay.io/biocontainers/multiqc:1.22.1--pyhdfd78af_0'
  }
 
  input:

tests/run-nanopore-test.sh

@@ -0,0 +1,138 @@
+#!/bin/bash
+
+set -euo pipefail
+
+error_handler() {
+ echo -e "\n\033[1;31mError on line $1\033[0m"
+ # Perform any cleanup or logging here
+}
+
+cleanup() {
+ echo "Cleaning up before exiting..."
+ # Cleanup commands go here
+}
+
+handle_interrupt() {
+ echo -e "\n\033[1;31mERROR:\033[1m Script interrupted...\033[0m"
+ cleanup
+ exit 1
+}
+
+# Trap ERR signal to handle errors
+trap 'error_handler $LINENO' ERR
+
+# Trap EXIT signal to perform cleanup
+trap cleanup EXIT
+
+# Trap SIGINT and SIGTERM to handle interruptions
+trap handle_interrupt SIGINT SIGTERM
+
+
+error() {
+ echo -e "$(date -Is) \033[1;31mERROR: \033[0m\033[1m$1\033[0m"
+}
+
+info() {
+ echo -e "$(date -Is) \033[1;32mINFO: \033[0m\033[1m$1\033[0m"
+}
+
+
+WORKFLOW_PATH="CFIA-NCFAD/nf-flu"
+CPU=$(nproc)
+MEMORY="8 GB"
+
+print_help() {
+ echo "Usage: $0 [-w WORKFLOW_PATH] [-m MEMORY] [-c CPU]"
+ echo
+ echo "Options:"
+ echo " -w WORKFLOW_PATH Path to the Nextflow workflow (default: ${WORKFLOW_PATH})"
+ echo " -m MEMORY Memory allocation for the Nextflow run (default: ${MEMORY})"
+ echo " -c CPU CPU allocation for the Nextflow run (default: ${CPU})"
+ echo " -h Display this help message"
+}
+
+while getopts "w:m:c:h" opt; do
+ case $opt in
+ w) WORKFLOW_PATH=$OPTARG ;;
+ m) MEMORY=$OPTARG ;;
+ c) CPU=$OPTARG ;;
+ h) print_help; exit 0 ;;
+ \?) error "Invalid option: -$OPTARG" >&2; print_help; exit 1 ;;
+ :) error "Option -$OPTARG requires an argument." >&2; print_help; exit 1 ;;
+ esac
+done
+
+info "Starting nf-flu Nanopore test execution script with ${CPU} CPU cores and ${MEMORY} memory..."
+
+FASTA_ZST_URL="https://api.figshare.com/v2/file/download/41415330"
+CSV_ZST_URL="https://api.figshare.com/v2/file/download/41415333"
+
+download_file() {
+ local url=$1
+ local output=$2
+
+ if [ ! -f "$output" ]; then
+ info "Downloading $output from $url..."
+ curl --silent -SLk "$url" -o "$output"
+ info "Downloaded $output."
+ else
+ info "$output already exists. Skipping download."
+ fi
+}
+
+create_samplesheet() {
+ local samplesheet=$1
+ echo "sample,reads" | tee "$samplesheet"
+ echo "ERR6359501-10k,$(realpath reads/ERR6359501-10k.fastq.gz)" | tee -a "$samplesheet"
+ echo "ERR6359501,$(realpath reads/run1)" | tee -a "$samplesheet"
+ echo "ERR6359501,$(realpath reads/run2)" | tee -a "$samplesheet"
+ echo "SRR24826962,$(realpath reads/SRR24826962.fastq.gz)" | tee -a "$samplesheet"
+ echo "ntc-bc15,$(realpath reads/ntc-bc15.fastq.gz)" | tee -a "$samplesheet"
+ echo "ntc-bc31,$(realpath reads/ntc-bc31.fastq.gz)" | tee -a "$samplesheet"
+ echo "ntc-bc47,$(realpath reads/ntc-bc47.fastq.gz)" | tee -a "$samplesheet"
+}
+
+FASTA_ZST_FILE="influenza.fna.zst"
+CSV_ZST_FILE="influenza.csv.zst"
+
+# Create directories
+mkdir -p reads/{run1,run2}
+
+# Download test data files
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/SRR24826962.sampled.fastq.gz" "reads/SRR24826962.fastq.gz"
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ERR6359501-10k.fastq.gz" "reads/ERR6359501-10k.fastq.gz"
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run1-s11-ERR6359501.fastq.gz" "reads/run1/s11-ERR6359501.fastq.gz"
+if [ ! -f "reads/run1/s1-ERR6359501.fastq" ]; then
+ download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run1-s1-ERR6359501.fastq.gz" "reads/run1/s1-ERR6359501.fastq.gz"
+ gunzip reads/run1/s1-ERR6359501.fastq.gz
+else
+ info "'reads/run1/s1-ERR6359501.fastq' already exists!"
+fi
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run2-s22-ERR6359501.fastq.gz" "reads/run2/s22-ERR6359501.fastq.gz"
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/run2-s2-ERR6359501.fastq.gz" "reads/run2/s2-ERR6359501.fastq.gz"
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ntc-bc15.fastq.gz" "reads/ntc-bc15.fastq.gz"
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ntc-bc31.fastq.gz" "reads/ntc-bc31.fastq.gz"
+download_file "https://github.com/CFIA-NCFAD/nf-test-datasets/raw/nf-flu/nanopore/fastq/ntc-bc47.fastq.gz" "reads/ntc-bc47.fastq.gz"
+
+info "Creating samplesheet.csv"
+create_samplesheet "samplesheet.csv"
+
+info "Download FASTA and CSV files"
+download_file "$FASTA_ZST_URL" "$FASTA_ZST_FILE"
+download_file "$CSV_ZST_URL" "$CSV_ZST_FILE"
+
+if [ -d "$WORKFLOW_PATH" ]; then
+ info "Running Nextflow pipeline from local path: $WORKFLOW_PATH"
+else
+ info "Pulling Nextflow pipeline from remote: $WORKFLOW_PATH"
+ nextflow pull "$WORKFLOW_PATH"
+fi
+
+nextflow run "$WORKFLOW_PATH" \
+ -profile test_nanopore,docker \
+ -resume \
+ --platform nanopore \
+ --input samplesheet.csv \
+ --ncbi_influenza_fasta $FASTA_ZST_FILE \
+ --ncbi_influenza_metadata $CSV_ZST_FILE \
+ --max_cpus $CPU --max_memory "$MEMORY"