Created
May 23, 2019 12:42
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Mapping CWL outputs to concepts in EDAM etc. from https://github.com/EBI-Metagenomics/CWL-assembly/blob/5a63f965d5809dab3a8f79b5e08361c30ede7900/cwl/megahit_pipeline.cwl
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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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