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extends: default | ||
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rules: | ||
line-length: | ||
max: 80 | ||
level: warning |
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--- | ||
#Input: runfolder_name | ||
# Input: runfolder_name | ||
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#Currently named runfolderpath and runfolder to harmonize with rnaseq config by Monika, but for specific runfolder delivery, technically, these could be "merged" to one. | ||
# Currently named runfolderpath and runfolder to harmonize with rnaseq config | ||
# by Monika, but for specific runfolder delivery, technically, these could be | ||
# "merged" to one. | ||
variables: | ||
runfolderpath: /proj/ngi2016001/incoming | ||
runfolder: "{runfolderpath}/{runfolder_name}" | ||
organised: "{runfolder}/Projects/" | ||
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#current path is /proj/ngi2016001/incoming/<RUNFOLDER>/Projects/<PROJECT>/<RUNFOLDER>/ | ||
#The following is based on that we are to keep the same directory structure as above. | ||
# current path is | ||
# /proj/ngi2016001/incoming/<RUNFOLDER>/Projects/<PROJECT>/<RUNFOLDER>/ The | ||
# following is based on that we are to keep the same directory structure as | ||
# above. | ||
files_to_organize: | ||
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#The fastq files | ||
# The fastq files | ||
- source: "{runfolder}/Unaligned/*" | ||
destination: "{organised}/{projectid}/{runfolder_name}/Sample_{samplename}/" | ||
options: | ||
required: True | ||
required: true | ||
link_type: softlink | ||
regex: (?P<projectid>[\w-]+)/Sample_(?P<samplename>[\w-]+)/(?P=samplename)_S(?P<samplenumber>\d+)_L(?P<lanes>\d+)_R(?P<read>\d)_001.fastq.gz | ||
regex: (?P<projectid>[\w-]+)/Sample_(?P<samplename>[\w-]+)/(?P=samplename)_S(?P<samplenumber>\d+)_L(?P<lanes>\d+)_R(?P<read>\d)_001.fastq.gz # yamllint disable-line | ||
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# The MultiQC files | ||
# The MultiQC files | ||
- source: "{runfolder}/seqreports/project/*" | ||
destination: "{organised}/{projectid}/<runfolder_name>/" | ||
options: | ||
required: True | ||
required: true | ||
link_type: softlink | ||
regexp: (?P<projectid>[\w-]+)/\w+_(?P=projectid)_multiqc_report[\w.-]+ | ||
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# what we are lacking, and what might need to be created outside the config is: | ||
# 1. checksums.md5 | ||
# 2. Encrypted samplesheet | ||
# As far as I know, these don't exist prior to organization. | ||
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#what we are lacking, and what might need to be created outside the config is: | ||
#1. checksums.md5 | ||
#2. Encrypted samplesheet | ||
#As far as I know, these don't exist prior to organization. | ||
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# #hypothethical undetermined, needs an input of lane(s) connected to project | ||
# #We will not include this at this point, as it requires additional input. Will maybe end up in its own config or something. | ||
# hypothethical undetermined, needs an input of lane(s) connected to project | ||
# We will not include this at this point, as it requires additional input. Will | ||
# maybe end up in its own config or something. | ||
# - source: <RUNFOLDER>/Unaligned/Undetermined/Undetermined_S0_L<lanes>_R<read>_001.fastq.gz | ||
# destination: <RUNFOLDER>/Unaligned/<PROJECT>/Undetermined/ | ||
# options: | ||
# required: False | ||
# symlink: True | ||
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-r prod | ||
mock==4.0.3 | ||
nose==1.3.7 | ||
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yamllint==1.32.0 |