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Commit b074f0dc authored by Amandine  PERRIN's avatar Amandine PERRIN
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add path to sequence formatted

parent c00044d0
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......@@ -31,7 +31,7 @@ def run_annotation_all(genomes, threads, force, annot_folder, prodigal_only=Fals
Parameters
----------
genomes : dict
{genome: [name, gpath_cut_gembase, size, nbcont, l90]}
{genome: [gembase_name, path_to_origfile, path_split_gembase, gsize, nbcont, L90]}
threads : int
max number of threads that can be used
force : bool
......@@ -126,7 +126,7 @@ def run_prokka(arguments):
Parameters
----------
arguments : tuple
(gpath, prok_folder, cores_annot, name, force, nbcont, q) with:
(gpath, prok_folder, cores_annot, name, force, nbcont, small, q) with:
* gpath: path and filename of genome to annotate
* prok_folder: path to folder where all prokka folders for all genomes are saved
......@@ -134,6 +134,7 @@ def run_prokka(arguments):
* name: output name of annotated genome
* force: True if force run (override existing files), False otherwise
* nbcont: number of contigs in the input genome, to check prokka results
* small: used for prodigal, if sequences to annotate are small. Not used here
* q : queue where logs are put
Returns
......
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