new module: FASTQDL #7506
new module: FASTQDL #7506
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See here for the tools linting issue |
Co-authored-by: Simon Pearce <[email protected]>
One for the March hackathon! |
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| mkdir ${prefix} | ||
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I think this needs to be a bit more specific:
| echo "" | gzip > ${accession}.fastq.gz | |
| echo "" | gzip > ${accession}_1.fastq.gz | |
| echo "" | gzip > ${accession}_2.fastq.gz | |
| touch ${prefix}-run-info.tsv |
| tuple val(meta), val(accession) | ||
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| output: | ||
| tuple val(meta), path("test"), emit: db |
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| tuple val(meta), path("test"), emit: db | |
| tuple val(meta), path("*.fastq.gz"), emit: fastq | |
| tuple val(meta), path("*-run-info.tsv"), emit: runinfo | |
| tuple val(meta), path("*-run-mergers.tsv"), emit: runmergers, optional: true |
I would update this to emit each file that we expect (might be a bit complicated now but I think this will makle handling everything in the pipeline easier).
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After changing this here we also need to adjust the meta.yml :)
| $args \\ | ||
| --accession $accession \\ | ||
| --cpus $task.cpus \\ | ||
| --outdir ${prefix} |
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| --outdir ${prefix} | |
| --outdir . |
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
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| mkdir ${prefix} |
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| mkdir ${prefix} |
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| fastq-dl \\ | ||
| $args \\ |
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| $args \\ | |
| $args \\ | |
| -- prefix ${prefix} \\ |
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The run you used belongs to Experiment ERX4876079
BioSample: SAMEA7787147
Study / Project: PRJEB37886
But I downloading a whole project or Sample will definetly be too many files :D
Maybe we can also test to use the Experiment Accession and then put a comment in the module that this is only tested for Runs & Experiments
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(E|D|S)RR[0-9]{6,}: Run accession E = Ena, S = NCBI, D= DDBJ |
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The run you used belongs to Experiment ERX4876079
BioSample: SAMEA7787147
Study / Project: PRJEB37886
But I downloading a whole project or Sample will definetly be too many files :D
Maybe we can also test to use the Experiment Accession and then put a comment in the module that this is only tested for Runs & Experiments
PR checklist
Closes #7505 by adding new module: FASTQDL
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda