Skip to content

Commit

Permalink
Merge pull request #216 from woook/moka_onc_v1.4
Browse files Browse the repository at this point in the history
Moka onc v1.4
  • Loading branch information
andyb3 authored Jul 5, 2018
2 parents bd09523 + a4c3fc0 commit e412dfb
Show file tree
Hide file tree
Showing 2 changed files with 8 additions and 9 deletions.
10 changes: 4 additions & 6 deletions DNANexus_upload_agent.py
Original file line number Diff line number Diff line change
Expand Up @@ -37,21 +37,19 @@ def loop_through_runs(self):

# create a list of all the folders in the runfolders directory
if debug: # use test folder
all_runfolders = ['999999_NB551068_0024_AHHVCTAFXX_ALED_TEST']
all_runfolders = ['999999_NB551068_testWES','999999_M02353_testOnco']
else:
#all_runfolders = ['999999_NB551068_testWES','999999_M02353_testOnco']
all_runfolders = os.listdir(runfolders)
#all_runfolders = ['99999_M02353_0119_000000000-D2RWA']

#create instance of the class
upload=upload2Nexus()

# for each folder if it is not samplesheets pass the runfolder to the next class
for folder in all_runfolders:
if folder != "samplesheets":
if folder.endswith('.gz'):
pass
else:
upload.already_uploaded(folder, self.now)
# don't create a re-used instance of the class
upload2Nexus().already_uploaded(folder, self.now)

self.combine_log_files()

Expand Down
7 changes: 4 additions & 3 deletions automate_demultiplex_config.py
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
debug = False

# =====git release for the automate_demultiplexing repo=====
script_release = "v17.0"
script_release = "v18.0"

# =====location of input/output files=====
# path to run folders
Expand Down Expand Up @@ -58,7 +58,8 @@
# Current Mokapipe ID
mokapipe_pipeline_ID = "2209"
# Current MokaWES ID
mokawes_pipeline_ID = "2210"
mokawes_pipeline_ID = "2405"

# -- Moka WES test status--
# Test Status = NextSEQ sequencing
mokastat_nextsq_ID = "1202218804"
Expand All @@ -79,7 +80,7 @@
# path to the WES workflow in the app project
wes_path = "Workflows/MokaWES_v1.1"
# path to the oncology workflow in the app project
onco_path = "Workflows/Mokaonc_v1.3"
onco_path = "Workflows/Mokaonc_v1.4"
# path to paddy app
peddy_path = "Apps/peddy_v1.2"
# path to multiqc app
Expand Down

0 comments on commit e412dfb

Please sign in to comment.