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Arcadia-Science / metagenomics

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
MIT License
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Reconfigure workflow into separate illumina and nanopore workflows #25

Closed elizabethmcd closed 1 year ago

elizabethmcd commented 1 year ago

This PR starts working towards integrating long reads by making separate illumina and nanopore workflows by requiring a ---platform parameter. Inspired by the nf-core/viralrecon workflow: https://github.com/nf-core/viralrecon. Currently the test configuration include the illumina platform by default but when the long read tools are ready I will create separate test configs for short and long reads respectively. This PR also fixes parameter usage for fastp which I figured out wasn't specified correctly before.

The pipeline works with nextflow run main.nf -profile test,docker --outdir test Summary:

[b1/b061a1] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:INPUT_CHECK:SAMPLESHEET_CHECK (sampleshe... [100%] 1 of 1 ✔
[d1/05d31f] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:FASTP (vir_1_T1)                            [100%] 2 of 2 ✔
[5f/4e5e58] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:METASPADES (vir_1_T1)                       [100%] 2 of 2 ✔
[32/c10061] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:MAPPING_DEPTH:BOWTIE2_ASSEMBLY_BUILD (SP... [100%] 2 of 2 ✔
[a6/84a594] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:MAPPING_DEPTH:BOWTIE2_ASSEMBLY_ALIGN (SP... [100%] 2 of 2 ✔
[52/6559f0] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:MAPPING_DEPTH:METABAT2_JGISUMMARIZEBAMCO... [100%] 2 of 2 ✔
[b0/a16ef0] process > ARCADIASCIENCE_METAGENOMICS:ILLUMINA:CUSTOM_DUMPSOFTWAREVERSIONS (1)             [100%] 1 of 1 ✔
Completed at: 19-Jan-2023 17:06:28
Duration    : 2m 49s
CPU hours   : 0.1
Succeeded   : 12