Update doc regarding bwa_index

nextflow_schema.json

@@ -115,7 +115,7 @@
                 },
                 "bwa_index": {
                     "type": "string",
-                    "description": "Path to directory containing pre-made BWA indices (i.e. everything before the endings '.amb' '.ann' '.bwt'. Most likely the same path as --fasta). If not supplied will be made for you.",
+                    "description": "Path to directory containing pre-made BWA indices (i.e. everything before the path to the directory containing the '.amb' '.ann' '.bwt' files. Most likely the same directory of the file provided with --fasta). If not supplied will be made for you.",
                     "fa_icon": "fas fa-address-book",
                     "help_text": "If you want to use pre-existing `bwa index` indices, please supply the **directory** to the FASTA you also specified in `--fasta` nf-core/eager will automagically detect the index files by searching for the FASTA filename with the corresponding `bwa` index file suffixes.\n\nFor example:\n\n```bash\nnextflow run nf-core/eager \\\n-profile test,docker \\\n--input '*{R1,R2}*.fq.gz'\n--fasta 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta' \\\n--bwa_index 'results/reference_genome/bwa_index/BWAIndex/'\n```\n\n> `bwa index` does not give you an option to supply alternative suffixes/names for these indices. Thus, the file names generated by this command _must not_ be changed, otherwise nf-core/eager will not be able to find them."
                 },