formatting change

dags/dag2_disk_usage.py

@@ -55,51 +55,51 @@ with dag:
   ## TASK
   check_orwell_disk = \
     SSHOperator(
-      task_id = 'check_orwell_disk',
-      dag = dag,
-      ssh_hook = orwell_ssh_hook,
+      task_id='check_orwell_disk',
+      dag=dag,
+      ssh_hook=orwell_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/orwell_disk_usage.sh ')
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/orwell_disk_usage.sh ')
   ## TASK
   check_eliot_disk = \
     SSHOperator(
-      task_id = 'check_eliot_disk',
-      dag = dag,
-      ssh_hook = eliot_ssh_hook,
+      task_id='check_eliot_disk',
+      dag=dag,
+      ssh_hook=eliot_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/git_repos/IGF-cron-scripts/eliot/eliot_disk_usage.sh ')
+      command='bash /home/igf/git_repos/IGF-cron-scripts/eliot/eliot_disk_usage.sh ')
   ## TASK
   check_woolf_disk = \
     SSHOperator(
-      task_id = 'check_woolf_disk',
-      dag = dag,
-      ssh_hook = woolf_ssh_hook,
+      task_id='check_woolf_disk',
+      dag=dag,
+      ssh_hook=woolf_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/git_repos/IGF-cron-scripts/woolf/woolf_disk_usage.sh ')
+      command='bash /home/igf/git_repos/IGF-cron-scripts/woolf/woolf_disk_usage.sh ')
   ## TASK
   check_igf_lims_disk = \
     SSHOperator(
-      task_id = 'check_igf_lims_disk',
-      dag = dag,
-      ssh_hook = igf_lims_ssh_hook,
+      task_id='check_igf_lims_disk',
+      dag=dag,
+      ssh_hook=igf_lims_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/github/IGF-cron-scripts/igf_lims/igf_lims_disk_usage.sh ')
+      command='bash /home/igf/github/IGF-cron-scripts/igf_lims/igf_lims_disk_usage.sh ')
   ## TASK
   merge_disk_usage = \
     SSHOperator(
-      task_id = 'merge_disk_usage',
-      dag = dag,
-      ssh_hook = eliot_ssh_hook,
+      task_id='merge_disk_usage',
+      dag=dag,
+      ssh_hook=eliot_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/git_repos/IGF-cron-scripts/eliot/merge_disk_usage.sh ')
+      command='bash /home/igf/git_repos/IGF-cron-scripts/eliot/merge_disk_usage.sh ')
   ## TASK
   internal_usage = \
     SSHOperator(
-      task_id = 'internal_usage',
-      dag = dag,
-      ssh_hook = eliot_ssh_hook,
+      task_id='internal_usage',
+      dag=dag,
+      ssh_hook=eliot_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/git_repos/IGF-cron-scripts/eliot/internal_usage.sh ')
+      command='bash /home/igf/git_repos/IGF-cron-scripts/eliot/internal_usage.sh ')
 
   ## PIPELINE
   merge_disk_usage << \

dags/dag4_lims_metadata.py

@@ -28,11 +28,11 @@ with dag:
   ## TASK
   submit_metadata_fetch_job = \
     BashOperator(
-      task_id = 'submit_metadata_fetch_job',
-      dag = dag,
+      task_id='submit_metadata_fetch_job',
+      dag=dag,
       xcom_push=True,
       queue='hpc_4G',
-      bash_command = 'bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/lims_metadata/fetch_lims_metadata_qsub.sh ')
+      bash_command='bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/lims_metadata/fetch_lims_metadata_qsub.sh ')
 
   ## PIPELINE
   submit_metadata_fetch_job

dags/dag5_primary_analysis_and_qc_processing.py

@@ -38,26 +38,26 @@ with dag:
   ## TASK
   update_exp_metadata = \
     BashOperator(
-      task_id = 'update_exp_metadata',
-      dag = dag,
+      task_id='update_exp_metadata',
+      dag=dag,
       queue='hpc_4G',
-      bash_command = 'bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/update_exp_metadata.sh ')
+      bash_command='bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/update_exp_metadata.sh ')
   ## TASK
   find_new_exp_for_analysis = \
     SSHOperator(
-      task_id = 'find_new_exp_for_analysis',
-      dag = dag,
-      ssh_hook = orwell_ssh_hook,
+      task_id='find_new_exp_for_analysis',
+      dag=dag,
+      ssh_hook=orwell_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/find_new_exp_for_analysis.sh ')
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/find_new_exp_for_analysis.sh ')
   ## TASK
   seed_analysis_pipeline = \
     SSHOperator(
-      task_id = 'seed_analysis_pipeline',
-      dag = dag,
+      task_id='seed_analysis_pipeline',
+      dag=dag,
       ssh_hook=hpc_hook,
       queue='hpc_4G',
-      command = 'bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/seed_analysis_pipeline.sh ')
+      command='bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/seed_analysis_pipeline.sh ')
 
   ## PIPELINE
   update_exp_metadata >> find_new_exp_for_analysis >> seed_analysis_pipeline

dags/dag6_seqrun_processing.py

@@ -39,51 +39,51 @@ with dag:
   ## TASK
   switch_off_project_barcode = \
     SSHOperator(
-      task_id = 'switch_off_project_barcode',
-      dag = dag,
-      ssh_hook = orwell_ssh_hook,
+      task_id='switch_off_project_barcode',
+      dag=dag,
+      ssh_hook=orwell_ssh_hook,
       queue='hpc_4G',
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/switch_off_project_barcode_check.sh ')
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/switch_off_project_barcode_check.sh ')
   ## TASK
   change_samplesheet_for_run = \
     SSHOperator(
-      task_id = 'change_samplesheet_for_run',
-      dag = dag,
+      task_id='change_samplesheet_for_run',
+      dag=dag,
       queue='hpc_4G',
-      ssh_hook = orwell_ssh_hook,
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/change_samplesheet_for_seqrun.sh ')
+      ssh_hook=orwell_ssh_hook,
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/change_samplesheet_for_seqrun.sh ')
   ## TASK
   restart_seqrun_processing = \
     SSHOperator(
-      task_id = 'restart_seqrun_processing',
-      dag = dag,
+      task_id='restart_seqrun_processing',
+      dag=dag,
       queue='hpc_4G',
-      ssh_hook = orwell_ssh_hook,
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/restart_seqrun_processing.sh ')
+      ssh_hook=orwell_ssh_hook,
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/restart_seqrun_processing.sh ')
   ## TASK
   register_project_metadata = \
     SSHOperator(
-      task_id = 'register_project_metadata',
-      dag = dag,
+      task_id='register_project_metadata',
+      dag=dag,
       queue='hpc_4G',
-      ssh_hook = orwell_ssh_hook,
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/register_metadata.sh ')
+      ssh_hook=orwell_ssh_hook,
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/register_metadata.sh ')
   ## TASK
   find_new_seqrun = \
     SSHOperator(
-      task_id = 'find_new_seqrun',
-      dag = dag,
+      task_id='find_new_seqrun',
+      dag=dag,
       queue='hpc_4G',
-      ssh_hook = orwell_ssh_hook,
-      command = 'bash /home/igf/igf_code/IGF-cron-scripts/orwell/find_new_seqrun.sh ')
+      ssh_hook=orwell_ssh_hook,
+      command='bash /home/igf/igf_code/IGF-cron-scripts/orwell/find_new_seqrun.sh ')
   ## TASK
   seed_demultiplexing_pipe = \
     SSHOperator(
-      task_id = 'seed_demultiplexing_pipe',
-      dag = dag,
+      task_id='seed_demultiplexing_pipe',
+      dag=dag,
       ssh_hook=hpc_hook,
       queue='hpc_4G',
-      command = 'bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/seed_demultiplexing_pipeline.sh ')
+      command='bash /rds/general/user/igf/home/git_repo/IGF-cron-scripts/hpc/seed_demultiplexing_pipeline.sh ')
 
   ## PIPELINE
   switch_off_project_barcode >> change_samplesheet_for_run >> restart_seqrun_processing

dags/dag8_copy_ongoing_seqrun.py

@@ -51,10 +51,6 @@ dag = \
     default_args=default_args,
     orientation='LR')
 
-'''
-## FUNCTIONS
-
-'''
 
 with dag:
   ## TASK