95 remove hardcoded nextflowconfig paths #97
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nextflow.config
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| save_trimmed_fail = false // Check if reads failed in the trimming process need to be saved (True/False, default: False) | ||
| save_merged = true // Check if merged reads need to be saved (True/False, default: True) | ||
| trim_tool = "fastp" // Select which trimming tool to use (fastp/trimmomatic/trimgalore) | ||
| adapter_fasta = null // location for adapator database (fasta file) |
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Corrected, changed to 'null'
| nanopore_summary_file = "/mnt/cidgoh-object-storage/hackathon/seqqc/isolate_wgs/nanopore/run_summary/sequencing_summary_FAT24492_18678559.txt" | ||
| // ID for nanopore summary file to be used by PycoQC | ||
| nanopore_summary_file_id = 'test' | ||
| nanopore_summary_file = null // Path to nanopore summary file to be used by PycoQC |
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This is correct, but need to update the nanopore_raw_reads_qc subworkflow to check for file. If file is not provided, empty channel [[],[]] should be passed
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Added logic evaluation to run PYCOQC only if summary file is available. Name is obtained directly from summary file instead of the nanopore_summary_file_id
Test: working with and without providing the path to the summary file
nextflow.config
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| // ID for nanopore summary file to be used by PycoQC | ||
| nanopore_summary_file_id = 'test' | ||
| nanopore_summary_file = null // Path to nanopore summary file to be used by PycoQC | ||
| nanopore_summary_file_id = 'test' // ID for nanopore summary file to be used by PycoQC |
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remove this parameter and update in the subworkflow to take file name as meta.id
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Fix: params.nanopore_summary_file is used to obtain an id tag
| classified_reads = true | ||
| // Boolean for whether to output unclassified reads as a fastq file | ||
| unclassified_reads = true | ||
| kraken2_db = null // Path to Kraken2 database used for querying reads during taxonomic classification |
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when specifying null for a path value, we need to test if it throws an error when the module/sub-workflow is skipped
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fix: improved logical evaluation of databases in taxonomy_qc, updated centrifuge pipeline
subworkflows/local/seqqc.nf
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| // Validate database paths | ||
| // | ||
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| if (!params.skip_kraken2) { |
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move these tests to specific subworkflows
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Fix: moved to taxonomy_qc, raw_reads_qc, or assembly_qc
--pointmutations in resfinder if a species is not specifiedPR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).