Minimal pathogen fastq ENA upload workflow

This needs a CSV file with the format:

Sample Name	tax_id	scientific_name	sample_alias	sample_title	isolation_source	collection date	geographic location (country and/or sea)	host health state	host scientific name	isolate
DS135_SP	256318	metagenome	DS135_SP	DS135_SP	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
DS137_SP	256318	metagenome	DS137_SP	DS137_SP	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
DS138_SP	256318	metagenome	DS138_SP	DS138_SP	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
DS148_SP	256318	metagenome	DS148_SP	DS148_SP	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
H010066N9_NL	256318	metagenome	H010066N9_NL	H010066N9_NL	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
H010174N9_NL	256318	metagenome	H010174N9_NL	H010174N9_NL	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
H010175N9_NL	256318	metagenome	H010175N9_NL	H010175N9_NL	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
H010177N9_NL	256318	metagenome	H010177N9_NL	H010177N9_NL	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens
H010180N9_NL	256318	metagenome	H010180N9_NL	H010180N9_NL	Nasel or sputum	2,020	United Kingdom	diseased	Homo sapiens

Your ena account and password in the ena.netrc file in this format:

default login Webin-XXXXX password YOURENAPASSWORD

Your ena password in the ena.txt file.

Test with the following command.

nextflow run minimal_pathogen_fq_ENA_upload/main.nf \
        --fastqs submit_fqs \
        --sample_meta sample_meta.csv \
        --netrc ena.netrc \
        --webpasswd ena.txt \
        --webuser Webin-XXXXX \
        --studyName PRJEB62780 \
        --ENA test \
        -profile conda \
        -with-trace -resume

Then run live with the following command:

nextflow run minimal_pathogen_fq_ENA_upload/main.nf \
        --fastqs submit_fqs \
        --sample_meta sample_meta.csv \
        --netrc ena.netrc \
        --webpasswd ena.txt \
        --webuser Webin-XXXXX \
        --studyName PRJEB62780 \
        --ENA live \
        -profile conda \
        -with-trace -resume