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Workflow v2

Merged Workflow v2
workflow_v2 into dev
2 unresolved threads
Merged Loraine Gueguen requested to merge workflow_v2 into dev
2 unresolved threads
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  • 696dea98
    Loraine Gueguen
    Merge branch 'dev' into workflow_v2 · 696dea98
    Loraine Gueguen authored 
    # Conflicts:
#	gga_init.py
#	speciesData.py
#	templates/gspecies_compose.yml.j2
#	workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v3.ga
gga_get_data.py
+ 9
− 9
@@ -122,14 +122,14 @@ class GetData(speciesData.SpeciesData):
# Where to store blast results?
# search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"]
# # These datasets will not be searched if missing in the input file
# These datasets will not be searched if missing in the input file
# Copy datasets in the organism src_data dir tree correct folder
for k, v in datasets_to_get.items():
if v: # If dataset is not present in input file, skip copy
if k in genome_datasets:
logging.info("Copying {0} ({1}) into {2}".format(k, v, organism_genome_dir))
genome_fname = "v%s.fasta" % self.genome_version
genome_fname = "{0}_v{1}.fasta".format(self.dataset_prefix, self.genome_version)
try:
shutil.copyfile(os.path.abspath(v), os.path.join(organism_genome_dir, genome_fname))
except Exception as exc:
@@ -137,19 +137,19 @@ class GetData(speciesData.SpeciesData):
elif k in annotation_datasets:
dataset_fname = ""
if k == "gff_path":
dataset_fname = "OGS%s.gff" % self.ogs_version
dataset_fname = "{0}_OGS{1}.gff".format(self.dataset_prefix, self.ogs_version)
elif k == "transcripts_path":
dataset_fname = "OGS%s_transcripts.fasta" % self.ogs_version
dataset_fname = "{0}_OGS{1}_transcripts.fasta".format(self.dataset_prefix, self.ogs_version)
elif k == "proteins_path":
dataset_fname = "OGS%s_proteins.fasta" % self.ogs_version
dataset_fname = "{0}_OGS{1}_proteins.fasta".format(self.dataset_prefix, self.ogs_version)
elif k == "orthofinder_path":
dataset_fname = "OGS%s_orthofinder.tsv" % self.ogs_version
dataset_fname = "{0}_OGS{1}_orthofinder.tsv".format(self.dataset_prefix, self.ogs_version)
elif k == "interpro_path":
dataset_fname = "OGS%s_interproscan.xml" % self.ogs_version
dataset_fname = "{0}_OGS{1}_interproscan.xml".format(self.dataset_prefix, self.ogs_version)
elif k == "blastp_path":
dataset_fname = "OGS%s_blastp.xml" % self.ogs_version
dataset_fname = "{0}_OGS{1}_blastp.xml".format(self.dataset_prefix, self.ogs_version)
elif k == "blastx_path":
dataset_fname = "OGS%s_blastx.xml" % self.ogs_version
dataset_fname = "{0}_OGS{1}_blastx.xml".format(self.dataset_prefix, self.ogs_version)
logging.info("Copying {0} ({1}) into {2}".format(k, v, organism_annotation_dir))
try:
shutil.copyfile(os.path.abspath(v), os.path.join(organism_annotation_dir, dataset_fname))