diff --git a/nextflow_schema.json b/nextflow_schema.json index b13ded35..e6423c36 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -38,17 +38,17 @@ "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" }, + "do_compression": { + "type": "boolean", + "fa_icon": "fas fa-file-archive", + "description": "Compress output files." + }, "do_stats": { "type": "boolean", "default": true, "hidden": true, - "fa_icon": "fas fa-file-csv" - }, - "do_compression": { - "type": "boolean", - "default": false, - "hidden": false, - "fa_icon": "fas fa-file-csv" + "fa_icon": "fas fa-file-csv", + "description": "Perform statistics evaluation." } } }, @@ -78,26 +78,22 @@ "alignment_n_secondary": { "type": "integer", "default": 10, - "description": "Number of secondary mappings to retain in 'map' filter mode.", - "fa_icon": "fab fa-draft2digital" + "description": "Number of secondary mappings to retain in 'map' filter mode." }, "alignment_segment_length": { "type": "integer", "default": 10000, - "description": "Segment length for mapping.", - "fa_icon": "fab fa-draft2digital" + "description": "Segment length for mapping." }, "alignment_block_length": { "type": "integer", "default": 30000, - "description": "Minimum block length filter for mapping.", - "fa_icon": "fab fa-draft2digital" + "description": "Minimum block length filter for mapping." }, "alignment_mash_kmer": { "type": "integer", "default": 16, - "description": "Kmer size for mashmap.", - "fa_icon": "fab fa-draft2digital" + "description": "Kmer size for mashmap." }, "alignment_merge_segments": { "type": "boolean", @@ -125,14 +121,12 @@ "seqwish_min_match_length": { "type": "integer", "default": 19, - "description": "Ignore exact matches below this length.", - "fa_icon": "fab fa-draft2digital" + "description": "Ignore exact matches below this length." }, "seqwish_transclose_batch": { "type": "integer", "default": 1000000, - "description": "Number of bp to use for transitive closure batch.", - "fa_icon": "fab fa-draft2digital" + "description": "Number of bp to use for transitive closure batch." } }, "fa_icon": "fas fa-dna" @@ -146,26 +140,22 @@ "smoothxg_max_block_weight": { "type": "integer", "default": 10000, - "description": "Maximum seed sequence in block.", - "fa_icon": "fab fa-draft2digital" + "description": "Maximum seed sequence in block." }, "smoothxg_max_path_jump": { "type": "integer", "default": 5000, - "description": "Maximum path jump to include in block.", - "fa_icon": "fab fa-draft2digital" + "description": "Maximum path jump to include in block." }, "smoothxg_max_edge_jump": { "type": "integer", "default": 5000, - "description": "Maximum edge jump before breaking.", - "fa_icon": "fab fa-draft2digital" + "description": "Maximum edge jump before breaking." }, "smoothxg_max_poa_length": { "type": "integer", "default": 10000, - "description": "Maximum sequence length to put into POA.", - "fa_icon": "fab fa-draft2digital" + "description": "Maximum sequence length to put into POA." }, "smoothxg_consensus_spec": { "type": "string",