Update qsub t include read_qc option. Update IRMA and Dais containers with no vulnerability conatiners,. update change log

Author: Amanda Sullivan

CHANGELOG.md

@@ -14,12 +14,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Now maintaining code on cdcgov.
 - [PR #10](https://github.com/CDCgov/MIRA-NF/pull/10) - reformat the outputs structure
 - [PR #11](https://github.com/CDCgov/MIRA-NF/pull/11) - changes the parquet_files flag to reformat_tables flag. This flag now reformats the report tables into parquet files and csv files.
+- [PR #12](https://github.com/CDCgov/MIRA-NF/pull/12) - Restructure so that the readqc subworkflow only runs when the flag `--read_qc` is set to true. Otherwise FastQC and MultiQC will not run.
+- [PR #12](https://github.com/CDCgov/MIRA-NF/pull/12) - creating and updating docker containers so that they contain no vulnerabilities.
 
 ### Parameters
 
 | Old parameter | New parameter                |
 | ------------- | ---------------------------- |
 | `--reformat_tables`| `--parquet_files` |
+|                    | `--read_qc` |
 
 ## v1.1.0 - 2024-09-19
 
@@ -32,7 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #21](https://github.com/CDCgov/MIRA-NF/commit/f9ea0bfb933adf5617920a8a046998e4f5ba304d) - add amended_consensus.fasta to email
 - [PR #22](https://github.com/CDCgov/MIRA-NF/commit/07f5320ecd2462f62c7b0846fe08fc3dafd94598) - add flag that skips the nf-samplesheet creation step. To use this flag you will have to provide a samplesheet that is described as amd platform format in the usage doc
 - [PR #23](https://github.com/CDCgov/MIRA-NF/commit/55c9092dfbbfd9ce639633e38fc49bbda28681af) - added in test profile configuration. Added logos.
-- [PR #24](https://github.com/CDCgov/MIRA-NF/commit/c2550c30b44de6cd8b5fe3e0b590a9099bb66a10) - Changed nasme of hpc profile to sge profile. Added slurm profile.
+- [PR #24](https://github.com/CDCgov/MIRA-NF/commit/c2550c30b44de6cd8b5fe3e0b590a9099bb66a10) - Changed name of hpc profile to sge profile. Added slurm profile.
 - [PR #26](https://github.com/CDCgov/MIRA-NF/commit/6baa9681d0c578093d4e32b1f39249104637b206) - Added the RSV Illumina and RSV ONT workflows.
 
 ### Parameters

MIRA_nextflow.sh

@@ -10,14 +10,14 @@
 #$ -V
 
 usage() {
-	echo -e "Usage in git cloned CLI: \n bash $0 -d <pth_to_mira-cli> -i <path_to_samplesheet.csv> -o <outdir> -r <run_id> -e <experiment_type> -f <nextflow_profiles> <optional: -p amplicon_library> <optional: -g custom_amplicon_library> <optional: -a reformat_tables> <optional: -c read_counts> <optional: -q processing_q> <optional: -m email_address> <optional: -b irma_config> <optional: -n > " 1>&2
+	echo -e "Usage in git cloned CLI: \n bash $0 -d <pth_to_mira-cli> -i <path_to_samplesheet.csv> -o <outdir> -r <run_id> -e <experiment_type> -f <nextflow_profiles> <optional: -p amplicon_library> <optional: -g custom_amplicon_library> <optional: -a reformat_tables> <optional: -c read_counts> <optional: -q processing_q> <optional: -m email_address> <optional: -b irma_config> <optional: -k read_qc> <optional: -n > " 1>&2
 	exit 1
 }
 
 # Experiment type options: Flu-ONT, SC2-Spike-Only-ONT, Flu_Illumina, SC2-Whole-Genome-ONT, SC2-Whole-Genome-Illumina
 # Primer Schema options: articv3, articv4, articv4.1, articv5.3.2, qiagen, swift, swift_211206
 
-while getopts 'd:i:o:r:e:p:g:f:a:c:q:m:b:na' OPTION; do
+while getopts 'd:i:o:r:e:p:g:f:a:c:q:m:b:k:na' OPTION; do
 	case "$OPTION" in
 	d) DIRNAME="$OPTARG" ;;
 	i) INPUT="$OPTARG" ;;
@@ -32,6 +32,7 @@ while getopts 'd:i:o:r:e:p:g:f:a:c:q:m:b:na' OPTION; do
 	q) PROCESSQ="$OPTARG" ;;
 	m) EMAIL="$OPTARG" ;;
 	b) OTHER_IRMA_CONFIG="$OPTARG" ;;
+	k) READS_QC="$OPTARG" ;;
 	*) usage ;;
 	esac
 done
@@ -78,6 +79,12 @@ else
 	OPTIONALARGS6="--email $EMAIL"
 fi
 
+if [[ -z "${READS_QC}" ]]; then
+	OPTIONALARGS7=""
+else
+	OPTIONALARGS7="--read_qc $READS_QC"
+fi
+
 # Archive previous run using the summary.xlsx file sent in email
 if [ -d "$1/dash-json/" ] && [ -n "${TAR}" ]; then
 	tar --remove-files -czf ${RUNPATH}/previous_run_$(date -d @$(stat -c %Y ${RUNPATH}/dash-json/) "+%Y%b%d-%H%M%S").tar.gz ${RUNPATH}/*html ${RUNPATH}/*fasta ${RUNPATH}/*txt ${RUNPATH}/*xlsx ${RUNPATH}/IRMA ${RUNPATH}/dash-json
@@ -97,4 +104,5 @@ nextflow run "$DIRNAME"/MIRA-NF/main.nf \
 	$OPTIONALARGS3 \
 	$OPTIONALARGS4 \
 	$OPTIONALARGS5 \
-	$OPTIONALARGS6
+	$OPTIONALARGS6 \
+	$OPTIONALARGS7

README.md

@@ -166,7 +166,7 @@ nextflow run ./main.nf \
    --read_qc false (optional)
 ```
 
-For in house testing (note that the read_qc parameter is not available when using the qsub - default set to false):
+For in house testing:
 
 ```bash
 qsub MIRA_nextflow.sh \
@@ -183,6 +183,7 @@ qsub MIRA_nextflow.sh \
    -c <SUBSAMPLED_READ_COUNTS> \ (optional)
    -b <OTHER_IRMA_CONFIG> (optional)
    -m <EMAIL_ADDRESS> \ (optional)
+   -k <READ_QC> \ (optional)
 
 ```
 

modules/local/daisribosome.nf

@@ -1,7 +1,7 @@
 process DAISRIBOSOME {
     label 'process_medium'
 
-    container 'cdcgov/dais-ribosome:v1.5.4'
+    container 'cdcgov/dais-ribosome:bookworm-test5'
     containerOptions '--bind ${launchDir}/tmp:/dais-ribosome/workdir --bind ${launchDir}/tmp:/dais-ribosome/lib/sswsort/workdir/'
 
     input:

modules/local/irma.nf

@@ -2,7 +2,7 @@ process IRMA {
     tag "${sample}"
     label 'process_high'
 
-    container 'cdcgov/irma:latest'
+    container 'cdcgov/irma:bookworm-test5'
 
     input:
     tuple val(sample), path(subsampled_fastq_files), val(irma_custom_0), val(irma_custom_1), val(module)