diff --git a/episodes/03-channels.md b/episodes/03-channels.md index ed38f17a..17477bf4 100644 --- a/episodes/03-channels.md +++ b/episodes/03-channels.md @@ -550,56 +550,6 @@ Launching `channels.nf` [stupefied_lumiere] - revision: a3741edde2 :::::::::::::::::::::::::::::::::::::::::::::::::: -### The **fromSRA** Channel factory - -Another useful factory method is `fromSRA`. The `fromSRA` method makes it possible to query the [NCBI SRA](https://www.ncbi.nlm.nih.gov/sra) archive and returns a queue channel emitting the FASTQ files matching the specified selection criteria. - -The queries can be project IDs or accession numbers supported by the [NCBI ESearch API](https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch). - -If you want to use this functionality, you will need an [NCBI API KEY](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/), and to set the environment variable `NCBI_API_KEY` to its value. - -```groovy -sra_ch =Channel.fromSRA('SRP043510') -sra_ch.view() -``` - -This will print a tuple for every fastq file associated with that SRA project accession. - -```output -[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz] -[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz] -[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz] -[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz] -[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz] -[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz] -(remaining omitted) -``` - -Multiple accession IDs can be specified using a list object: - -```groovy -ids = ['ERR908507', 'ERR908506', 'ERR908505'] -sra_ch = Channel.fromSRA(ids) -sra_ch.view() -``` - -```output -[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]] -[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]] -[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]] -``` - -::::::::::::::::::::::::::::::::::::::::: callout - -## Read pairs from SRA - -Read pairs are implicitly managed, and are returned as a list of files. - - -:::::::::::::::::::::::::::::::::::::::::::::::::: - - - :::::::::::::::::::::::::::::::::::::::: keypoints - Channels must be used to import data into Nextflow. diff --git a/episodes/data/environment.yml b/episodes/data/environment.yml index 4ef8ef47..679a457a 100644 --- a/episodes/data/environment.yml +++ b/episodes/data/environment.yml @@ -3,8 +3,9 @@ channels: - conda-forge - bioconda dependencies: - - nextflow=20.10.0 + - nextflow - salmon=1.5 - fastqc=0.11 - - multiqc=1.10 + - multiqc - nf-core + - graphviz