The genome_note_template.docx provided in the pipeline has inconsistent naming of some variables. For instance, the scaffold N50 is indicated with both SCAFF_N50 (in the text) and scaffold_N50 (in the table). The pipeline uses SCAFF_N50 as the variable, leaving the field in the table empty.
The contig N50 is indicated as contig_N50 in the table but the pipeline provides CONTIG_N50 so the table is still empty.
The title of the table 2 refers to a variable named species but SPECIES_GENUS is defined by the pipeline so it remains empty.
There are probably more examples like this.
Description of the bug
The
genome_note_template.docxprovided in the pipeline has inconsistent naming of some variables. For instance, the scaffold N50 is indicated with bothSCAFF_N50(in the text) andscaffold_N50(in the table). The pipeline usesSCAFF_N50as the variable, leaving the field in the table empty. The contig N50 is indicated ascontig_N50in the table but the pipeline providesCONTIG_N50so the table is still empty. The title of the table 2 refers to a variable namedspeciesbutSPECIES_GENUSis defined by the pipeline so it remains empty. There are probably more examples like this.Something to pass on to Karen ?
Command used and terminal output
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Relevant files
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System information
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