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genomic-medicine-sweden / meta-val

nf-core/taxprofiler post-processing; verification of classification results; consensus maps
MIT License
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Prepare and structure input #3

Closed LilyAnderssonLee closed 10 months ago

LilyAnderssonLee commented 11 months ago

Description of feature

The expected input CSV file includes metadata, input reads for classifiers, and classification outputs.

sample run_accession instrument_platform reads_type fastq_1 fastq_2 kraken2_report kraken2_classifiedout centrifuge_out centrifuge_result diamond
sample1 sample1 ILLUMINA short bowtie2/align/sample1.unmapped_1.fastq.gz bowtie2/align/sample1.unmapped_2.fastq.gz kraken2/k2_pluspf/sample1.kraken2.kraken2.report.txt kraken2/k2_pluspf/sample1.kraken2.kraken2.classifiedreads.txt centrifuge/p_compressed+h+v/sample1.centrifuge.txt centrifuge/p_compressed+h+v/sample1.centrifuge.results.txt diamond/diamond/sample1.diamond.tsv
sample2 sample2 ILLUMINA short bowtie2/align/sample2.unmapped_1.fastq.gz bowtie2/align/sample2.unmapped_2.fastq.gz kraken2/k2_pluspf/sample2.kraken2.kraken2.report.txt kraken2/k2_pluspf/sample2.kraken2.kraken2.classifiedreads.txt centrifuge/p_compressed+h+v/sample2.centrifuge.txt centrifuge/p_compressed+h+v/sample2.centrifuge.results.txt diamond/diamond/sample2.diamond.tsv
sample3 sample3 OXFORD_NANOPORE long samtools/bam2fq/sample3.unmapped.fq.gz kraken2/k2_pluspf/sample3.kraken2.kraken2.report.txt kraken2/k2_pluspf/sample3.kraken2.kraken2.classifiedreads.txt centrifuge/p_compressed+h+v/sample3.centrifuge.txt centrifuge/p_compressed+h+v/sample3.centrifuge.results.txt diamond/diamond/sample3.diamond.tsv