Nextflow Modules
Showing module(s) with keyword "download"
| Module | Keywords | Description |
|---|---|---|
| cellgeni/irods/getfile | iRODS download checksum md5 | Downloads a file from iRODS to the local working directory and verifies its integrity by comparing the local MD5 checksum against the iRODS-recorded checksum. |
| nf-core/annotsv/installannotations | annotation download installation structural variants | Install the AnnotSV annotations |
| nf-core/aria2 | download utility http(s) | CLI Download utility |
| nf-core/bakta/baktadbdownload | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/bigslice/downloaddb | biosynthetic gene clusters genomics database download | Downloads and extracts the BiG-SLiCE HMM database (biosynthetic and sub Pfams) using the bundled `download_bigslice_hmmdb` script shipped with BiG-SLiCE. The resulting directory can be passed directly as the `hmmdb` input to the `BIGSLICE` module. |
| nf-core/blast/updateblastdb | fasta blast download database | Downloads a BLAST database from NCBI |
| nf-core/caalm/downloadmodels | cazyme model download huggingface deep learning | Downloads the CAALM model weights from HuggingFace Hub (lczong/CAALM) into a local models/ directory. The downloaded directory is used as input to the CAALM_CAALM annotation module for CAZyme prediction. |
| nf-core/catpack/download | taxonomic classification classification database download | Downloads the required files for either Nr or GTDB for building into a CAT database |
| nf-core/checkv/downloaddatabase | checkv checkm mag metagenome quality isolates virus completeness contamination download database | Construct the database necessary for checkv's quality assessment |
| nf-core/deeparg/downloaddata | download database deeparg antimicrobial resistance genes deep learning prediction | A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes |
| nf-core/deepbgc/download | database download BGC biosynthetic gene cluster deep learning neural network random forest genomes bacteria fungi | Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning. |
| nf-core/ensemblvep/download | annotation cache download | Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. |
| nf-core/fastqdl | download ena fastq sra | Download FASTQ files from SRA or ENA repositories. |
| nf-core/fusionreport/download | sort RNA-seq fusion_report download | Build DB for fusionreport |
| nf-core/genomad/download | metagenomics genomad database download phage virus plasmid | Download geNomad databases and related files |
| nf-core/genomad/endtoend | metagenomics genomad database download phage virus plasmid | Identify mobile genetic elements present in genomic assemblies |
| nf-core/getorganelle/config | assembly organelle mitochondria download database | Downloads databases needed for running getorganelle |
| nf-core/gget/gget |