Closed georgiesamaha closed 1 month ago
Closes #18
main.nf
concat_fastqs
run_pigz
parse_required_pycoqc_segments
modules/concat_fq.nf
modules/run_pigz.nf
pigz
modules/run_nanoplot.nf
sequencing_summary.fileName
nextflow.config
multiqc_config
pycoqc_header_file
${projectDir}
${baseDir}
pbspro
Closes #18
main.nf
: Updated the module inclusion forconcat_fastqs
to use therun_pigz
module and removed theparse_required_pycoqc_segments
module.modules/concat_fq.nf
: Removed theconcat_fastqs
process.modules/run_pigz.nf
: Added a newconcat_fastqs
process that usespigz
for concatenating FASTQ files.modules/run_nanoplot.nf
: Corrected the variable reference forsequencing_summary.fileName
.nextflow.config
: Updated paths formultiqc_config
andpycoqc_header_file
to use${projectDir}
instead of${baseDir}
. Added configuration for theconcat_fastqs
process to usepbspro
executor with specific resource allocations.