[Do not merge!] Pseudo PR for first release #159
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Merging template updates
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.2.0. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Important! Template update for nf-core/tools v3.2.1
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@mashehu and @mahesh-panchal, Thanks for all the detailed feedback! I believe I have addressed all of your comments so far. |
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| cpus = { 4 } | ||
| memory = { 8.GB * Math.pow(3, task.attempt - 1) } |
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If you have a rough idea of what usually causes process failure with regard to resources, not that there is also https://www.nextflow.io/docs/latest/process.html#dynamic-task-resources-with-previous-execution-trace
| ext.args = { secrets.NCBI_API_KEY ? "--api-key ${secrets.NCBI_API_KEY}" : "" } | ||
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| // Settings to avoid API rate limits and not put too much stress on servers | ||
| maxForks = 1 // NCBI seems to be not allowing concurrent downloads with this command, althogh I cannot find any documentation about this |
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| maxForks = 1 // NCBI seems to be not allowing concurrent downloads with this command, althogh I cannot find any documentation about this | |
| maxForks = 1 // NCBI seems to be not allowing concurrent downloads with this command, although I cannot find any documentation about this |
| memory = { 1.GB * task.attempt } | ||
| time = { 12.h * task.attempt } | ||
| storeDir = { params.data_dir == "false" ? null : "${params.data_dir}/assembly_metadata" } | ||
| ext.args = { secrets.NCBI_API_KEY ? "--as-json-lines --api-key ${secrets.NCBI_API_KEY}" : "--as-json-lines" } |
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An alternate way to write this is:
| ext.args = { secrets.NCBI_API_KEY ? "--as-json-lines --api-key ${secrets.NCBI_API_KEY}" : "--as-json-lines" } | |
| ext.args = { [ | |
| secrets.NCBI_API_KEY ? "--api-key ${secrets.NCBI_API_KEY}": "", | |
| "--as-json-lines" | |
| ].minus("").join(" ") } |
This avoids repetition and makes it easier to add to later, particularly if extra conditions are introduced.
| The typical command for running the pipeline is as follows: | ||
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| ```bash | ||
| nextflow run nf-core/pathogensurveillance --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker | ||
| nextflow run nf-core/pathogensurveillance -profile <REPLACE WITH RUN TOOL> -resume --input <REPLACE WITH TSV/CSV> --outdir <REPLACE WITH OUTPUT PATH> |
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I find the term RUN TOOL confusing here. Perhaps use package manager.
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| # Dockerfile to create container with Cell Ranger v8.0.0 and bcl2fastq v2.20.0 | |||
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I don't see these tools in this file.
This looks like something that could be created with Seqera Containers instead. https://seqera.io/containers/
| versions = versions.mix(BAKTA_BAKTA.out.versions) | ||
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| // For references that have a gff already, combine the assembly with the gff the same way bakta outputs | ||
| MAKE_GFF_WITH_FASTA ( |
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Versions also missing here. Please check the other processes below too.
| } | ||
| messages = messages.mix(spades_warnings) | ||
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| FLYE_NANOPORE ( |
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Please add versions for both FLYEs
| messages = Channel.empty() | ||
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| // Parse input tables | ||
| SAMPLESHEET_CHECK ( sample_data_tsv, reference_data_tsv, params.max_samples ) |
| versions = versions.mix(FIND_ASSEMBLIES.out.versions) | ||
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| // Parse assembly metadata to TSVs to save time when multiple samples use the same data | ||
| PARSE_ASSEMBLIES ( |
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Please add versions, and for other processes below too.
| .map {[[id: it.getSimpleName()], it]} | ||
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| // For each group, assign references for variant calling if not user-defined | ||
| ASSIGN_MAPPING_REFERENCE ( |
Do not merge! This is a PR of
devcompared to theTEMPLATEbranch for whole-pipeline reviewing purposes. Changes should be made todevand this PR should not be merged! The actual release PR is at #136