diff --git a/modules.json b/modules.json index 926c7ad..8cf7b1a 100644 --- a/modules.json +++ b/modules.json @@ -8,47 +8,65 @@ "assemblyscan": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gfastats": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "last/dotplot": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "last/lastal": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "last/lastdb": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "last/mafswap": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "last/split": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "last/train": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -57,20 +75,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 80fc55d..b2dcd60 100644 --- a/nextflow.config +++ b/nextflow.config @@ -64,8 +64,8 @@ params { m2m = false // Alignment options - lastal_args = 'C2' - lastal_extr_args = 'D1e9' + lastal_args = '-C2 -D1e9' + lastal_extr_args = '' last_split_mismap = '1e-05' lastal_params = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 4f69241..f99486b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -369,13 +369,12 @@ "properties": { "lastal_args": { "type": "string", - "default": "C2", - "description": "this defaults to -C2 and is applied to both the calls to last-train and lastal, like in the LAST cookbook and the last-genome-alignments tutorial." + "default": "-C2 -D1e9", + "description": "this defaults to -C2 -D1e9)and is applied to both the calls to last-train and lastal, like in the LAST cookbook and the last-genome-alignments tutorial." }, "lastal_extr_args": { "type": "string", - "default": "D1e9", - "description": "(default: -D1e9) is only passed to lastal and can be used for arguments that are not recognised by last-train." + "description": "(default: ' ' is only passed to lastal and can be used for arguments that are not recognised by last-train." }, "last_split_mismap": { "type": "string",