Final samplesheet is not created when --skip_fastq_download is provided

[SchwarzMarek]

Description of the bug

The --skip_fastq_download flag implies that only the fastq files will not be downloaded. When using the --skip_fastq_download and --nf_core_pipeline rnaseq together, the fastq files are not downloaded (expected), but sample sheet is not created (unexpected).

Command used and terminal output

nextflow run nf-core/fetchngs -profile docker --nf_core_pipeline rnaseq --outdir test --input temp.txt --max_cpus 2 --max_memory 5.GB --skip_fastq_download

Relevant files

temp.txt

System information

N E X T F L O W ~ version 22.04.5
Launching https://github.com/nf-core/fetchngs [nostalgic_meitner] DSL2 - revision: b79cde2 [master]

[pinin4fjords]

• 1 following, encountered this today

[drpatelh]

This will be fixed in #124

A merged samplesheet will now also be generated if using --skip_fastq_download. The only difference will be that the original ftp download links will be populated in the fastq_1 and fastq_2 fields rather than the local paths relative to --outdir where fastq_1 and fastq_2 would have been downloaded if not using --skip_fastq_download. Note, that if the ftp download links don't exist as part of the ENA metadata then the fastq_1 and fastq_2 fields will be empty in the samplesheet but there is nothing we can do about that really.