fetchngs

File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files.

Constraint · matches ^\S+\.(csv|tsv|txt)$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Feeds into

• ampliseq — fetchngs writes an ampliseq samplesheet (sample, fastq_1, fastq_2, run) with --nf-core-pipeline ampliseq. Its run column is empty, so ampliseq treats every sample as one sequencing run and learns one DADA2 error model for all of them; data from several sequencing runs needs run filled per sequencing run: an inline handoff whose set templates it from a column that identifies the run, or your own samplesheet. ampliseq assumes Illumina reads unless told otherwise: for PacBio or Ion Torrent runs (the instrument_platform column) set --pacbio or --iontorrent in the stage's params.
• atacseq — fetchngs writes an atacseq samplesheet (every run as replicate 1 of its sample) with --nf-core-pipeline atacseq. Runs whose ENA instrument_platform is not a short-read platform (the ones nf-core/mag accepts as short reads: ILLUMINA, BGISEQ, DNBSEQ, ELEMENT, ULTIMA, ION_TORRENT, LS454, …) are refused: atacseq analyses short reads, and long-read, capillary or colour-space runs would be processed as if they were.
• mag — fetchngs writes a mag samplesheet whose read columns predate mag's short_reads_1/short_reads_2; the columns are renamed, each sample gets its own group, and each run keeps its own run id. fetchngs labels every run's reads ILLUMINA short reads; the short-read platform is taken from the run's ENA instrument_platform instead, so a long-read run (OXFORD_NANOPORE, PACBIO_SMRT) is refused rather than analysed as short reads. Different samples are not pooled for binning or assembly; use an inline handoff to supply study-specific pooling groups.
• metatdenovo — fetchngs writes a metatdenovo samplesheet (sample, fastq_1, fastq_2) with --nf-core-pipeline metatdenovo. Runs whose ENA instrument_platform is not a short-read platform (the ones nf-core/mag accepts as short reads: ILLUMINA, BGISEQ, DNBSEQ, ELEMENT, ULTIMA, ION_TORRENT, LS454, …) are refused: metatdenovo analyses short reads, and long-read, capillary or colour-space runs would be processed as if they were.
• rnaseq — fetchngs downloads the FastQ files and, with --nf-core-pipeline rnaseq, writes samplesheet/samplesheet.csv for rnaseq (absolute FastQ paths; strandedness from --nf-core-rnaseq-strandedness, default auto). Runs whose ENA instrument_platform is not a short-read platform (the ones nf-core/mag accepts as short reads: ILLUMINA, BGISEQ, DNBSEQ, ELEMENT, ULTIMA, ION_TORRENT, LS454, …) are refused: rnaseq analyses short reads, and long-read, capillary or colour-space runs would be processed as if they were.
• sarek — fetchngs writes a sarek samplesheet (patient = the ENA sample accession) with --nf-core-pipeline sarek; it has no lane, so each run's accession becomes its lane — sarek needs patient, sample and lane to be unique together; sarek reads paired-end FastQ only, so every row needs a fastq_2. No status or sex column is written: sarek treats every sample as normal tissue (status 0, sex NA) and runs germline analyses only; a tumour/normal design needs its own sarek samplesheet (a handoff's set gives every row the same value). Runs whose ENA instrument_platform is not a short-read platform (the ones nf-core/mag accepts as short reads: ILLUMINA, BGISEQ, DNBSEQ, ELEMENT, ULTIMA, ION_TORRENT, LS454, …) are refused: sarek analyses short reads, and long-read, capillary or colour-space runs would be processed as if they were.
• taxprofiler — fetchngs writes a taxprofiler samplesheet with --nf-core-pipeline taxprofiler; run_accession and instrument_platform come from the ENA metadata. The profiling databases (--databases) are the stage's own.
• viralrecon — fetchngs writes a viralrecon samplesheet (sample, fastq_1, fastq_2) with --nf-core-pipeline viralrecon. Runs whose ENA instrument_platform is not a short-read platform (the ones nf-core/mag accepts as short reads: ILLUMINA, BGISEQ, DNBSEQ, ELEMENT, ULTIMA, ION_TORRENT, LS454, …) are refused: viralrecon analyses short reads, and long-read, capillary or colour-space runs would be processed as if they were. Pass --platform illumina: viralrecon's nanopore mode does not read this samplesheet.