#reproducibility

2020-07-21

Kevin Rue-Albrecht (10:08:41): > @Kevin Rue-Albrecht has joined the channel

Kevin Rue-Albrecht (10:08:41): > set the channel description: Solutions for reproducible workflows and environments

Charlie George (10:12:30): > @Charlie George has joined the channel

2020-07-31

Erick Cuevas (12:03:32): > @Erick Cuevas has joined the channel

Lambda Moses (12:05:18): > @Lambda Moses has joined the channel

Daniela Cassol (12:05:27): > @Daniela Cassol has joined the channel

Charlotte Soneson (12:15:55): > @Charlotte Soneson has joined the channel

Paula Beati (12:19:46): > @Paula Beati has joined the channel

Qian Liu (12:21:05): > @Qian Liu has joined the channel

Qiang Hu (12:21:44): > @Qiang Hu has joined the channel

Zuzanna Nowicka (12:54:22): > @Zuzanna Nowicka has joined the channel

Vivek Das (12:58:53): > @Vivek Das has joined the channel

Charlie George (13:00:14): > Thanks for joining the discussion

Charlie George (13:01:09): > @Sara Keeblewould you mind mentioning why airflow is your chosen choice, what does it do well and have you used others that didn’t come up to scratch?

Sara Keeble (13:01:15): > @Sara Keeble has joined the channel

Charlie George (13:08:26): > Here is the link to the google doc feel free to add your thoughts, the more the merrier and there is no such thins as a ‘stupid opinion’ thankshttps://docs.google.com/document/d/1ok2H9HVoa8c-m-VcwdQM0ccOuMTmESKCzaaWHb6trwE/edit#

Sara Keeble (13:23:13): > Hi@Charlie George, I actually wasn’t the one who chose airflow for our team, so I can’t offer much in the way of comparisons. However, I’ve been happy with the performance relative to Luigi, which is what we were using before airflow. The main pipeline we’ve developed in airflow is complex and has to be run frequently, so the most important features for us are the ability to 1) handle tasks with many dependency relationships, and 2) little hands-on management time. The previous iteration of the pipeline in Luigi required a lot of babysitting and manual restarting. Of course, some of the burden of managing babysitting time falls on writing good idempotent tasks. The final thing that’s important for us is integration with Jenkins, which is what we use for automated regression testing. Overall, I think it works really well for production-level code.

Nathan Sheffield (16:10:34): > @Nathan Sheffield has joined the channel

Lori Shepherd (16:11:53): > @Lori Shepherd has joined the channel

2020-08-05

shr19818 (13:47:37): > @shr19818 has joined the channel

Charlotte Soneson (17:08:32): > https://www.biorxiv.org/content/10.1101/2020.08.04.236208v1

2020-08-06

Laurent Gatto (13:01:34): > @Laurent Gatto has joined the channel

2020-09-25

Anna Liza Kretzschmar (22:55:48): > @Anna Liza Kretzschmar has joined the channel

2020-10-11

Kozo Nishida (21:42:38): > @Kozo Nishida has joined the channel

2020-10-14

Nathan Sheffield (08:35:09): > hey all, I posted a preprint last week describing PEP, which helps with standardizing the descriptions of samples that you would then put into a workflow. check it out if interested:https://www.biorxiv.org/content/10.1101/2020.10.08.331322v1.full

Kevin Rue-Albrecht (18:02:38): > that sounds awesome! on my list to read, thanks!

Kevin Rue-Albrecht (18:03:27): > i gotta say, my first reaction was “what’s that gotta do with PEP8”:wink:

2020-10-23

Rebecca Howard (08:18:25): > @Rebecca Howard has joined the channel

2020-10-30

Nathan Sheffield (15:28:15): > yeah, seems like the space of acronyms is getting kind of crowded these days. I hoped it was a distant enough concept that it wouldn’t confuse too many people…

2020-11-02

Johannes Rainer (10:02:17): > @Johannes Rainer has joined the channel

2020-11-11

Joshua Shapiro (09:09:27): > @Joshua Shapiro has joined the channel

2020-11-12

Philippe Boileau (15:09:04): > @Philippe Boileau has joined the channel

2020-11-30

Roy Storey (04:56:03): > @Roy Storey has joined the channel

2020-12-02

Konstantinos Geles (Constantinos Yeles) (05:43:53): > @Konstantinos Geles (Constantinos Yeles) has joined the channel

2020-12-12

Huipeng Li (00:38:50): > @Huipeng Li has joined the channel

2020-12-14

Nick Owen (13:21:32): > @Nick Owen has joined the channel

2020-12-17

Manojkumar Selvaraju (11:10:08): > @Manojkumar Selvaraju has joined the channel

2021-01-01

Bernd (14:06:18): > @Bernd has joined the channel

2021-01-22

Annajiat Alim Rasel (15:45:15): > @Annajiat Alim Rasel has joined the channel

2021-02-02

Sanchit Saini (17:16:59): > @Sanchit Saini has joined the channel

2021-02-12

Janani Ravi (15:53:06): > @Janani Ravi has joined the channel

2021-03-12

Julia Romanowska (14:51:49): > @Julia Romanowska has joined the channel

2021-03-20

watanabe_st (01:58:17): > @watanabe_st has joined the channel

2021-04-12

Naohisa Goto (00:28:47): > @Naohisa Goto has joined the channel

2021-04-28

Mahmoud Ahmed (08:06:30): > @Mahmoud Ahmed has joined the channel

2021-05-01

Arjun Krishnan (21:43:57): > @Arjun Krishnan has joined the channel

2021-05-11

Megha Lal (16:45:31): > @Megha Lal has joined the channel

2021-05-28

Izaskun Mallona (10:16:03): > @Izaskun Mallona has joined the channel

2021-06-05

KP (17:22:07): > @KP has joined the channel

2021-07-19

Leo Lahti (17:02:18): > @Leo Lahti has joined the channel

2021-07-23

Batool Almarzouq (15:53:56): > @Batool Almarzouq has joined the channel

2021-07-30

Tom Sinden (04:19:35): > @Tom Sinden has joined the channel

2021-09-25

Haichao Wang (07:20:42): > @Haichao Wang has joined the channel

2021-11-08

Paula Nieto García (03:29:17): > @Paula Nieto García has joined the channel

2021-11-24

Helge Hecht (13:16:26): > @Helge Hecht has joined the channel

2022-01-28

Megha Lal (11:14:21): > @Megha Lal has left the channel

2022-05-03

Ray Su (06:56:23): > @Ray Su has joined the channel

2022-07-04

Andrew J. Rech (19:46:00): > @Andrew J. Rech has joined the channel

2022-07-22

Gary Sieling (14:49:04): > @Gary Sieling has joined the channel

2022-07-28

Krithika Bhuvanesh (13:53:01): > @Krithika Bhuvanesh has joined the channel

Mervin Fansler (17:20:41): > @Mervin Fansler has joined the channel

2022-08-11

Rene Welch (17:15:58): > @Rene Welch has joined the channel

2022-08-15

Michael Kaufman (13:15:25): > @Michael Kaufman has joined the channel

2022-09-04

Gurpreet Kaur (15:02:03): > @Gurpreet Kaur has joined the channel

2022-09-27

Jennifer Holmes (16:17:22): > @Jennifer Holmes has joined the channel

2022-12-13

Lea Seep (08:58:13): > @Lea Seep has joined the channel

2022-12-23

Pierre Gestraud (08:42:16): > @Pierre Gestraud has joined the channel

2023-01-21

Hien (16:04:17): > @Hien has joined the channel

2023-02-28

Krithika Bhuvanesh (16:54:14): > @Krithika Bhuvanesh has joined the channel

2023-03-16

Roger Giné Bertomeu (04:21:25): > @Roger Giné Bertomeu has joined the channel

2023-05-03

Rebecca Butler (16:17:02): > @Rebecca Butler has joined the channel

2023-05-11

Krithika Bhuvanesh (16:29:48): > @Krithika Bhuvanesh has left the channel

2023-05-25

Jacob Krol (17:14:03): > @Jacob Krol has joined the channel

2023-07-13

Brian Schilder (07:02:50): > @Brian Schilder has joined the channel

2023-07-28

Konstantinos Daniilidis (13:47:55): > @Konstantinos Daniilidis has joined the channel

Benjamin Yang (15:58:33): > @Benjamin Yang has joined the channel

2023-08-03

Jill Lundell (10:51:54): > @Jill Lundell has joined the channel

Ritika Giri (15:59:16): > @Ritika Giri has joined the channel

Abiud Cantu (17:16:34): > @Abiud Cantu has joined the channel

2023-08-07

Jiaji George Chen (11:22:18): > @Jiaji George Chen has joined the channel

2023-08-20

Jacques SERIZAY (10:39:23): > @Jacques SERIZAY has joined the channel

2023-09-15

Leo Lahti (04:56:19): > @Leo Lahti has joined the channel

2024-03-21

Francesc Català-Moll (02:20:46): > @Francesc Català-Moll has joined the channel

2024-03-22

Stevie Pederson (02:13:27): > @Stevie Pederson has joined the channel

2024-03-27

abhich (05:46:31): > @abhich has joined the channel

2024-05-14

Lori Shepherd (10:47:29): > archived the channel