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output name Data Format Data Concept relationship
assembly edam:format_1929 (FASTA) http://edamontology.org/data_0925 "Sequence assembly" derived from $(inputs.{forward,reverse,interleaved,single}_reads)
assembly_log iana:text/plain http://edamontology.org/data_3181 "Sequence assembly report" describes $(outputs.assembly)
samtools_index edam:format_2572 (BAM) + index alignment of reads to assembled contigs http://edamontology.org/data_1383 is multiple sequence alignment, need a data concept for the result of http://edamontology.org/operation_0523 "Mapping assembly" derives from both $(inputs.{forward,reverse,interleaved,single}_reads) & $(outputs.assembly)
coverage_tab iana:text/tab-separated-values "contig by bam depth matrix", and evidence report and quality metric derives from $(outputs.samtools_index)
trimmed_sequences gz-compressed edam:format_1929 (FASTA) Contigs over a certain minimal length Need an EDAM concept for the result of http://edamontology.org/operation_3192 "Sequence trimming" . Similar to http://edamontology.org/operation_3218 "Sequencing quality control" except for assembled contigs, not raw sequences as controlled by "min_contig_length"; derived from $(outputs.assembly)
logfile ??? "coverage from coverage.tab" derives from $(outputs.coveraget_tab)
input name (for reference)
forward_reads edam:format_1930 (FASTQ) paired with reverse_reads
reverse_reads edam:format_1930 (FASTQ) paired with forward_reads
interleaved_reads edam:format_1930 (FASTQ)
single_reads edam:format_1930 (FASTQ)
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