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antunderwood / SKA fasta experimentation
Last active April 23, 2019 19:28
SKA fasta experimentation
Description
@antunderwood
antunderwood / .nextflow.log
Created November 12, 2018 06:58
Nov-11 22:34:33.780 [main] DEBUG nextflow.Session - >>> barrier register (process: overall_quality)
Nov-11 22:34:33.780 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > overall_quality -- maxForks: 2
Nov-11 22:34:33.807 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Nov-11 22:34:33.807 [main] DEBUG nextflow.Session - Session await
Nov-11 22:34:33.865 [Actor Thread 2] TRACE n.cloud.aws.batch.AwsBatchExecutor - [AWS BATCH] Launching process > determine_min_read_length (ERR230474) -- work folder: s3://anthony
-torok-2014/workdir/83/48ad905eb66ddc94a7228e8b3ffd73
Nov-11 22:34:33.880 [Actor Thread 7] TRACE n.cloud.aws.batch.AwsBatchExecutor - [AWS BATCH] Launching process > qc_pre_trimming (ERR230474) -- work folder: s3://anthony-torok-201
4/workdir/f7/aa9a19a5f813325e13559bf273a135
Nov-11 22:34:33.893 [Actor Thread 4] TRACE n.cloud.aws.batch.AwsBatchExecutor - [AWS BATCH] Launching process > determine_min_read_length (ERR156451) -- work folder: s3://anthony
-torok-2014/workdir/
@antunderwood
antunderwood / Alpine_Linux_Brew.md
Last active December 30, 2021 14:38

Start alpine docker image

docker run -it alpine /bin/sh

Install dependencies

apk update
apk add bash build-base curl file git gzip libc6-compat ncurses ruby ruby-dbm ruby-etc ruby-irb ruby-json sudo
@antunderwood
antunderwood / nextflow.config
Created August 31, 2018 20:20
nextflow.config for flowcraft inspect-compatible pipeline
trace {
enabled = true
file = "pipeline_stats.txt"
fields = "task_id,\
hash,\
process,\
tag,\
status,\
exit,\
start,\
@antunderwood
antunderwood / .nextflow.log t2.micro -c 3
Created September 22, 2017 16:18
Sep-22 16:12:34.401 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow run aunderwo/nextflow_ariba -with-docker --get_database card --input_dir s3://nextflow-data/ariba-fastqs --output_dir s3://nextflow-data/ariba-output --fastq_pattern *.{R1,R2}.fastq.gz -with-trace -with-timeline
Sep-22 16:12:34.732 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.25.7
Sep-22 16:12:35.236 [main] INFO nextflow.cli.CmdRun - Pulling aunderwo/nextflow_ariba ...
Sep-22 16:12:35.241 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/nextflow.config
Sep-22 16:12:37.350 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/ariba.nf
Sep-22 16:12:38.000 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba
Sep-22 16:12:38.130 [main] DEBUG nextflow.scm.AssetManager - Pulling a
@antunderwood
antunderwood / .nextflow.log m4.large -c 3
Created September 22, 2017 15:33
Sep-22 15:27:05.913 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow run aunderwo/nextflow_ariba -with-docker --get_database card --input_dir s3://nextflow-data/ariba-fastqs --output_dir s3://nextflow-data/ariba-output --fastq_pattern *.{R1,R2}.fastq.gz -with-trace -with-timeline
Sep-22 15:27:06.113 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.25.7
Sep-22 15:27:06.556 [main] INFO nextflow.cli.CmdRun - Pulling aunderwo/nextflow_ariba ...
Sep-22 15:27:06.557 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/nextflow.config
Sep-22 15:27:08.058 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/ariba.nf
Sep-22 15:27:08.274 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba
Sep-22 15:27:08.418 [main] DEBUG nextflow.scm.AssetManager - Pulling a
@antunderwood
antunderwood / .nextflow.log m4.large -c 2
Last active September 22, 2017 15:31
Sep-22 14:58:25.188 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow run aunderwo/nextflow_ariba -with-docker --get_database card --input_dir s3://nextflow-data/ariba-fastqs --output_dir s3://nextflow-data/ariba-output --fastq_pattern *.{R1,R2}.fastq.gz -with-trace -with-timeline
Sep-22 14:58:25.374 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.25.7
Sep-22 14:58:25.866 [main] INFO nextflow.cli.CmdRun - Pulling aunderwo/nextflow_ariba ...
Sep-22 14:58:25.867 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/nextflow.config
Sep-22 14:58:27.474 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/ariba.nf
Sep-22 14:58:27.692 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba
Sep-22 14:58:27.819 [main] DEBUG nextflow.scm.AssetManager - Pulling a
@antunderwood
antunderwood / .nextflow.log m4.xlarge -c 2
Last active September 22, 2017 15:32
Sep-22 14:44:26.803 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow run aunderwo/nextflow_ariba -with-docker --get_database card --input_dir s3://nextflow-data/ariba-fastqs --output_dir s3://nextflow-data/ariba-output --fastq_pattern *.{R1,R2}.fastq.gz -with-trace -with-timeline
Sep-22 14:44:26.935 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 0.25.7
Sep-22 14:44:27.225 [main] INFO nextflow.cli.CmdRun - Pulling aunderwo/nextflow_ariba ...
Sep-22 14:44:27.225 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/nextflow.config
Sep-22 14:44:28.300 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba/contents/ariba.nf
Sep-22 14:44:28.514 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/aunderwo/nextflow_ariba
Sep-22 14:44:28.653 [main] DEBUG nextflow.scm.AssetManager - Pulling a
@antunderwood
antunderwood / person.rb
Created January 20, 2011 11:05
class Person < ActiveRecord::Base
..........
named_scope :not_a_member_of_group_with_name, lambda{|group_name| {
:conditions => ["people.id NOT IN
(SELECT distinct people.id
FROM people
LEFT OUTER JOIN memberships ON people.id = memberships.member_id
LEFT OUTER JOIN groups ON groups.id = memberships.group_id
LEFT OUTER JOIN groups AS parent_groups ON groups.parent_group_id = parent_groups.id
@antunderwood
antunderwood / edit.html.erb
Created December 10, 2010 00:14
<%- content_for :page_title do -%>
<h2><%= form_description %></h2>
<%- end -%>
<%= form_for @event do |f| %>
<%- if @staff # company event-%>
<div class="inline"><%= f.label :name %><%= f.text_field :name, :class => "field large" %></div>
<div class="inline"><%= f.label :start_at, "Start date: " %><%= f.datetime_select :start_at, {:order => [:day, :month, :year, :hour, :minute], :datetime_separator => "<label class='small_label'>Time: </label>", :time_separator => "",:default => @start_at}, {:class => "event_date_select select"} %></div>
<div class="inline"><%= f.label :end_at, "End date" %><%= f.datetime_select :end_at, {:order => [:day, :month, :year, :hour, :minute], :datetime_separator => "<label class='small_label'>Time: </label>",:time_separator => "",:default => @end_at}, {:class => "event_date_select select"} %></div>
<div class="inline"><%= f.label :all_day %><div class="checkbox_wrapper"><%= f.check_box :all_day, :class => "checkbox" %></div></div>