Nextflow Modules
Showing module(s) with keyword "download"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/irods/getfile | Process | 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 | Process | annotation download installation structural variants | Install the AnnotSV annotations |
| nf-core/aria2 | Process | download utility http(s) | CLI Download utility |
| nf-core/bakta/baktadbdownload | Process | bakta annotation fasta bacteria database download | Downloads BAKTA database from Zenodo |
| nf-core/bigslice/downloaddb | Process | 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 | Process | fasta blast download database | Downloads a BLAST database from NCBI |
| nf-core/caalm/downloadmodels | Process | 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/cache_download_ensemblvep_snpeff | Workflow | ensemblvep snpeff download annotation cache | downlad annotation cache for snpeff and ensemblvep |
| nf-core/catpack/download | Process | taxonomic classification classification database download | Downloads the required files for either Nr or GTDB for building into a CAT database |
| nf-core/checkv/downloaddatabase | Process | checkv checkm mag metagenome quality isolates virus completeness contamination download database | Construct the database necessary for checkv's quality assessment |
| nf-core/cleanifier/download | Process | download index metagenomics contamination removal microbiome | Download human reference index |
| nf-core/deeparg/downloaddata | Process | 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 | Process | 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 | Process | annotation cache download | Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. |
| nf-core/fastqdl | Process | download ena fastq sra | Download FASTQ files from SRA or ENA repositories. |
| nf-core/fastq_fetch_clean_hostile | Workflow | hostile decontamination human removal download host removal clean | Downloads required reference genomes for hostile and removes host reads from short-read FASTQ sequencing files |
| nf-core/fungtion/downloadmodels | Process | fungal effector protein prediction language model deep learning model download | Downloads the pretrained ESM-1b weights (esm1b_t33_650M_UR50S.pt) that fungtion uses for fungal effector prediction into a local models/ directory via `fungtion setup-models`. The downloaded directory is used as input to the FUNGTION_FUNGTION prediction module. |
| nf-core/fusionreport/download | Process | sort RNA-seq fusion_report download | Build DB for fusionreport |
| nf-core/genomad/download | Process | metagenomics genomad database download phage virus plasmid | Download geNomad databases and related files |
| nf-core/genomad/endtoend | Process | metagenomics genomad database download phage virus plasmid | Identify mobile genetic elements present in genomic assemblies |